Journal articles on the topic 'Oligos'
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1
Kabanov, Alexander V., Sergei V. Vinogradov, Alexander V. Ovcharenko, Alexander V. Krivonos, Nikolai S. Melik-Nubarov, Vsevolod I. Kiselev, and Eugenii S. Severin. "Antisense oligonucleotides modified at 5'-end by fatty radicals effectively inhibit reproduction of influenza virus." Collection of Czechoslovak Chemical Communications 55, no. 2 (1990): 587–89. http://dx.doi.org/10.1135/cccc19900587.
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To enhance penetration of oligonucleotides ("oligos") into cells it was suggested that they should be chemically modified by fatty radicals at 5'-end. Two modified by undecanol at 5'-end phosphate group oligos, namely, oligo complementary to the protein binding sites, located at the influenza virus polymerases encoding RNA, and oligo complementary to the polyadenylation signal of the polymerase 3 encoding RNA were synthesized using DNA-synthetisator. These modified oligos effectively suppressed the influenza A/PR8/34 virus reproduction and inhibited the synthesis of virus-specific proteins in MDCK cells. The non-modified antisense oligos and modified nonsense oligos did not affect the virus development under the same conditions.
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Coleman, Christina, Danielle Levine, Raj Kishore, Gangjian Qin, Tina Thorne, Erin Lambers, Sharath P. Sasi, Mina Yaar, Barbara A. Gilchrest, and David A. Goukassian. "Inhibition of Melanoma Angiogenesis by Telomere Homolog Oligonucleotides." Journal of Oncology 2010 (2010): 1–14. http://dx.doi.org/10.1155/2010/928628.
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Telomere homolog oligonucleotides (T-oligos) activate an innate telomere-based program that leads to multiple anticancer effects. T-oligos act at telomeres to initiate signaling through the Werner protein and ATM kinase. We wanted to determine if T-oligos have antiangiogenic effects. We found that T-oligo-treated human melanoma (MM-AN) cells had decreased expression of vascular endothelial growth factor (VEGF), VEGF receptor 2, angiopoeitin-1 and -2 and decreased VEGF secretion. T-oligos activated the transcription factor E2F1 and inhibited the activity of the angiogenic transcription factor, HIF-1α. T-oligos inhibited EC tubulogenesis and total tumor microvascular density matrix invasion by MM-AN cells and ECs in vitro. In melanoma SCID xenografts, two systemic T-oligo injections decreased by 60% (P<.004) total tumor microvascular density and the functional vessels density by 80% (P<.002). These findings suggest that restriction of tumor angiogenesis is among the host's innate telomere-based anticancer responses and provide further evidence that T-oligos may offer a powerful new approach for melanoma treatment.
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Slodzinski, M. K., M. Juhaszova, and M. P. Blaustein. "Antisense inhibition of Na+/Ca2+ exchange in primary cultured arterial myocytes." American Journal of Physiology-Cell Physiology 269, no. 5 (November 1, 1995): C1340—C1345. http://dx.doi.org/10.1152/ajpcell.1995.269.5.c1340.
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The effects of chimeric phosphorothioated antisense oligodeoxynucleotides (AS-oligos) targeted against the Na+/Ca2+ exchanger (NCX) were tested in primary cultured rat mesenteric artery myocytes. In parallel cultures, myocytes proliferated and were morphologically normal in the presence of scrambled nonsense (NS-) or AS-oligos or no oligos (controls). NCX function was examined with digital imaging, using fura 2 to estimate the cytosolic free Ca2+ concentration ([Ca2+]cyt). Resting [Ca2+]cyt was higher (145 +/- 4 nM; P < 0.05) in AS-oligo-treated cells than in controls (125 +/- 5 nM) or NS-oligo-treated cells (131 +/- 4 nM). Lowering external Na+, to promote Ca2+ entry via NCX, increased [Ca2+]cyt transiently in controls and NS-oligo-treated cells but not in AS-oligo-treated cells. Raising the cytosolic free Na+ concentration with ouabain augmented the low-Na(+)-induced rise in [Ca2+]cyt in controls and NS-oligo-treated cells, but AS-oligo-treated cells still did not respond. Nevertheless, serotonin (5-HT) increased [Ca2+]cyt in all three groups. Thus AS-oligos selectively blocked NCX activity but not the 5-HT response. To determine the effect of NCX knockdown on the modulation of stored Ca2+, the 5-HT response was tested immediately after removal of external Ca2+. Ouabain augmented the 5-HT-induced rise in [Ca2+]cyt in control and NS-oligo-treated cells but not AS-oligo-treated cells. This indicates that the NCX can modulate intracellular Ca2+ stores. We conclude that AS-oligos are useful for investigating the physiological role of NCX in vascular smooth muscle.
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Liu, Shaolin, Nicholas A. Tinker, and Diane E. Mather. "Exact word matches in rice pseudomolecules." Genome 49, no. 8 (August 1, 2006): 1047–51. http://dx.doi.org/10.1139/g06-055.
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Using pseudomolecules of assembled genomic sequence, we computed the frequencies of 6 to 24 bp oligonucleotide (oligo) "words" across the genome of rice (Oryza sativa L. subsp. japonica). All oligos of 10 or fewer basepairs were repeated at least 12 times in the genome. The percentage of unique (non-repeated) oligos ranged from 0.1% for 12 bp oligos to 76.0% for 24 bp oligos. For three 200 kb regions, we annotated each nucleotide position with the genome-wide frequency of the 18 bp oligo starting at that position. These frequencies formed landscapes consisting of high- and low-frequency zones. Low-frequency zones contained occasional high-frequency spikes; these may represent footprints of RIM2 transposon activity. BLASTn searches of high-frequency non-SSR (simple sequence repeat) 18 bp oligos returned few sequences from species other than rice. These results demonstrate that, in rice, words are not randomly used between different regions within the same genome, and indicate that words that are frequently repeated within the rice genome tend to be unique to rice.Key words: oligonucleotide, sequence repetition, word match frequency, rice.
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Varliero, Gilda, Jared Wray, Cédric Malandain, and Gary Barker. "PhyloPrimer: a taxon-specific oligonucleotide design platform." PeerJ 9 (April 29, 2021): e11120. http://dx.doi.org/10.7717/peerj.11120.
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Many environmental and biomedical biomonitoring and detection studies aim to explore the presence of specific organisms or gene functionalities in microbiome samples. In such cases, when the study hypotheses can be answered with the exploration of a small number of genes, a targeted PCR-approach is appropriate. However, due to the complexity of environmental microbial communities, the design of specific primers is challenging and can lead to non-specific results. We designed PhyloPrimer, the first user-friendly platform to semi-automate the design of taxon-specific oligos (i.e., PCR primers) for a gene of interest. The main strength of PhyloPrimer is the ability to retrieve and align GenBank gene sequences matching the user’s input, and to explore their relationships through an online dynamic tree. PhyloPrimer then designs oligos specific to the gene sequences selected from the tree and uses the tree non-selected sequences to look for and maximize oligo differences between targeted and non-targeted sequences, therefore increasing oligo taxon-specificity (positive/negative consensus approach). Designed oligos are then checked for the presence of secondary structure with the nearest-neighbor (NN) calculation and the presence of off-target matches with in silico PCR tests, also processing oligos with degenerate bases. Whilst the main function of PhyloPrimer is the design of taxon-specific oligos (down to the species level), the software can also be used for designing oligos to target a gene without any taxonomic specificity, for designing oligos from preselected sequences and for checking predesigned oligos. We validated the pipeline on four commercially available microbial mock communities using PhyloPrimer to design genus- and species-specific primers for the detection of Streptococcus species in the mock communities. The software performed well on these mock microbial communities and can be found at https://www.cerealsdb.uk.net/cerealgenomics/phyloprimer.
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Medina-Cucurella, Angélica V., Paul J. Steiner, Matthew S. Faber, Jesús Beltrán, Alexandra N. Borelli, Monica B. Kirby, Sean R. Cutler, and Timothy A. Whitehead. "User-defined single pot mutagenesis using unamplified oligo pools." Protein Engineering, Design and Selection 32, no. 1 (January 2019): 41–45. http://dx.doi.org/10.1093/protein/gzz013.
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Abstract User-defined mutagenic libraries are fundamental for applied protein engineering workflows. Here we show that unamplified oligo pools can be used to prepare site saturation mutagenesis libraries from plasmid DNA with near-complete coverage of desired mutations and few off-target mutations. We find that oligo pools yield higher quality libraries when compared to individually synthesized degenerate oligos. We also show that multiple libraries can be multiplexed into a single oligo pool, making preparation of multiple libraries less expensive and more convenient. We provide software for automatic oligo pool design that can generate mutagenic oligos for saturating or focused libraries.
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Kulkarni, R. N., D. M. Smith, M. A. Ghatei, P. M. Jones, and S. R. Bloom. "Investigation of the effects of antisense oligodeoxynucleotides to islet amyloid polypeptide mRNA on insulin release, content and expression." Journal of Endocrinology 151, no. 3 (December 1996): 341–48. http://dx.doi.org/10.1677/joe.0.1510341.
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Abstract We have investigated the effects of antisense oligodeoxynucleotides (oligos) to islet amyloid polypeptide (IAPP) mRNA on the expression and secretion of IAPP and insulin, in the clonal β-cell line HIT-T15. Phosphorothioate-modified oligos were cytotoxic compared with phosphodiester (D)-oligos. Of the nine oligos tested using a lipofection reagent, 03, a 30-mer D-oligo complementary to a sequence downstream of the IAPP initiation codon, showed a significant dose-dependent suppression of IAPP mRNA, with a 42% decrease at 7·5 μm, compared with a scrambled (MS03) control oligo (n=3, P<0·01). A subsequent 89% suppression of IAPP release was observed in the 4-h period following antisense treatment (1·78 ± 0·13 (MS03) vs 0·19 ± 0·14 (03) pmol/106 cells per 240 min, n=7, P<0·01). A significant increase in insulin mRNA (100 ± 10% (MS03) vs 124 ± 8% (03), n=3, P<0·05) and insulin content (13·0 ± 0·9 (MS03) vs 17·4 ± 1·4 (03) pmol/106 cells, n=7, P=0·028) was observed following treatment with 03 at 7·5 μm. 08, a 20-mer D-oligo directed to a region of IAPP mRNA further downstream than 03, also showed a decrease in IAPP mRNA and peptide release and an increase in insulin content. No significant changes were observed in the expression and release of the unrelated β-cell peptide, neuropeptide Y. We thus show a suppression of synthesis and release of IAPP in HIT-T15 cells using antisense oligos. The associated increase in insulin mRNA and content in these cells after treatment with IAPP antisense oligos is in accord with an inhibitor action of IAPP on insulin availability. Journal of Endocrinology (1996) 151, 341–348
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SHARPE, CLAIRE C., MARK E. C. DOCKRELL, RIZALDY SCOTT, MAZHAR I. NOOR, LEX M. COWSERT, BRETT P. MONIA, and BRUCE M. HENDRY. "Evidence of a Role for Ki-RAS in the Stimulated Proliferation of Renal Fibroblasts." Journal of the American Society of Nephrology 10, no. 6 (June 1999): 1186–92. http://dx.doi.org/10.1681/asn.v1061186.
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Abstract. Progressive renal fibrosis is driven by a range of cytokines that act via membrane receptors and intracellular signaling cascades to evoke gene transcription events and related responses. The Ras family of GTPases has been implicated in many of these signaling cascades in model systems such as 3T3 fibroblasts. However, the role of the specific Ras isoforms Ki, Ha, and N in the stimulation of renal fibroblasts has not been defined. In this study, Ras has been inhibited in primate renal fibroblasts (vero cells) using specific phosphorothioate oligodeoxynucleotides (oligos) targeting the three isoforms. Lipofectin transfection with 200 to 400 nM Ki-Ras oligo inhibited the epidermal growth factor- and fibroblast growth factor-stimulated proliferation of vero cells by 25 to 35% with a lesser effect on serum-stimulated growth. Oligos against Ha-Ras and N-Ras were inactive with respect to control oligo. Total cellular Ras protein (estimated by Western blotting) was reduced by 60 to 90% 24 h after transfection with Ki-Ras oligo. N-Ras, Ha-Ras, and control oligos were inactive. Total Ras synthesis over 4 h measured using [35S]-cys/met pulse chase was reduced by approximately 70% by Ki-Ras oligo and not altered by other oligos. The fractional prenylation of Ras was quantified from the discrete bands on polyacrylamide gel electrophoresis and was increased by the Ki-Ras oligo alone. These data demonstrate that these renal fibroblasts predominantly express the Ki isoform of Ras and that this GTPase plays a role in the stimulated proliferation of these cells. Ras GTPases may be a target for the inhibition of processes leading to renal fibrosis.
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GUÉNOCHE, A. "SUPERSEQUENCES OF MASKS FOR OLIGO-CHIPS." Journal of Bioinformatics and Computational Biology 02, no. 03 (September 2004): 459–69. http://dx.doi.org/10.1142/s0219720004000685.
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On a very small surface, a chip, several thousands of oligonucleotides, can be synthesized using a mask technology. Given a set of oligos, the problems tackled here are: • What is the minimum number of masks necessary to synthesize one copy of each oligo? • How long will be the series of masks if each oligo is synthesized twice, such that the two copies are realized with two completely different series of masks? We establish that, for 20,000 oligos of 20 bases a single copy can be synthesized with around 67 masks and for two copies with less than the double.
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Rahmann, Sven. "Fast Large Scale Oligonucleotide Selection Using the Longest Common Factor Approach." Journal of Bioinformatics and Computational Biology 01, no. 02 (July 2003): 343–61. http://dx.doi.org/10.1142/s0219720003000125.
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We present a fast method that selects oligonucleotide probes (such as DNA 25-mers) for microarray experiments on a truly large scale. For example, reliable oligos for human genes can be found within four days, a speedup of one to two orders of magnitude compared to previous approaches. This speed is attained by using the longest common substring as a specificity measure for candidate oligos. We present a space- and time-efficient algorithm, based on a suffix array with additional information, to compute matching statistics (lengths of longest matches) between all candidate oligos and all remaining sequences. With the matching statistics available, we show how to incorporate constraints such as oligo length, melting temperature, and self-complementarity into the selection process at a postprocessing stage. As a result, we can now design custom oligos for any sequenced genome, just as the technology for on-site chip synthesis is becoming increasingly mature.
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Slodzinski, Martin K., and Mordecai P. Blaustein. "Physiological effects of Na+/Ca2+exchanger knockdown by antisense oligodeoxynucleotides in arterial myocytes." American Journal of Physiology-Cell Physiology 275, no. 1 (July 1, 1998): C251—C259. http://dx.doi.org/10.1152/ajpcell.1998.275.1.c251.
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Antisense oligodeoxynucleotides (AS-oligos) targeted to the Na+/Ca2+exchanger (NCX) inhibit NCX-mediated Ca2+ influx in mesenteric artery (MA) myocytes [ Am. J. Physiol.269 ( Cell Physiol. 38): C1340–C1345, 1995]. Here, we show AS-oligo knockdown of NCX-mediated Ca2+ efflux. In initial experiments, the cytosolic free Ca2+ concentration ([Ca2+]cyt) was raised, and sarcoplasmic reticulum (SR) Ca2+ sequestration was blocked with caffeine and cyclopiazonic acid; the extracellular Na+-dependent (NCX) component of Ca2+ efflux was then selectively inhibited in AS-oligo-treated cells but not in controls (no oligos or nonsense oligos). In contrast, the La3+-sensitive (plasmalemma Ca2+ pump) component of Ca2+ efflux was unaffected in AS-oligo-treated cells. Knockdown of NCX activity was reversed by incubating AS-oligo-treated cells in normal media for 5 days. Transient [Ca2+]cytelevations evoked by serotonin (5-HT) at 15-min intervals in AS-oligo-treated cells were indistinguishable from those in controls. When cells were stimulated every 3 min, however, the peak amplitudes of the second and third responses were larger, and [Ca2+]cytreturned to baseline more slowly, in AS-oligo-treated cells than in controls. Peak 5-HT-evoked responses in the controls, but not AS-oligo-treated cells, were augmented more than twofold in Na+-free media. This implies that NCX is involved in Na+ gradient modulation of SR Ca2+ stores and cell responsiveness. The repetitive stimulation data suggest that the NCX may be important during tonic activation of arterial myocytes.
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Yang, Linlin, and Ivan J. Dmochowski. "Conditionally Activated (“Caged”) Oligonucleotides." Molecules 26, no. 5 (March 9, 2021): 1481. http://dx.doi.org/10.3390/molecules26051481.
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Conditionally activated (“caged”) oligonucleotides provide useful spatiotemporal control for studying dynamic biological processes, e.g., regulating in vivo gene expression or probing specific oligonucleotide targets. This review summarizes recent advances in caging strategies, which involve different stimuli in the activation step. Oligo cyclization is a particularly attractive caging strategy, which simplifies the probe design and affords oligo stabilization. Our laboratory developed an efficient synthesis for circular caged oligos, and a circular caged antisense DNA oligo was successfully applied in gene regulation. A second technology is Transcriptome In Vivo Analysis (TIVA), where caged oligos enable mRNA isolation from single cells in living tissue. We highlight our development of TIVA probes with improved caging stability. Finally, we illustrate the first protease-activated oligo probe, which was designed for caspase-3. This expands the toolkit for investigating the transcriptome under a specific physiologic condition (e.g., apoptosis), particularly in specimens where light activation is impractical.
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Alkan, Ferhat, Joana Silva, Eric Pintó Barberà, and William J. Faller. "Ribo-ODDR: oligo design pipeline for experiment-specific rRNA depletion in Ribo-seq." Bioinformatics 37, no. 17 (March 15, 2021): 2659–67. http://dx.doi.org/10.1093/bioinformatics/btab171.
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Abstract Motivation Ribosome Profiling (Ribo-seq) has revolutionized the study of RNA translation by providing information on ribosome positions across all translated RNAs with nucleotide-resolution. Yet several technical limitations restrict the sequencing depth of such experiments, the most common of which is the overabundance of rRNA fragments. Various strategies can be employed to tackle this issue, including the use of commercial rRNA depletion kits. However, as they are designed for more standardized RNAseq experiments, they may perform suboptimally in Ribo-seq. In order to overcome this, it is possible to use custom biotinylated oligos complementary to the most abundant rRNA fragments, however currently no computational framework exists to aid the design of optimal oligos. Results Here, we first show that a major confounding issue is that the rRNA fragments generated via Ribo-seq vary significantly with differing experimental conditions, suggesting that a ‘one-size-fits-all’ approach may be inefficient. Therefore we developed Ribo-ODDR, an oligo design pipeline integrated with a user-friendly interface that assists in oligo selection for efficient experiment-specific rRNA depletion. Ribo-ODDR uses preliminary data to identify the most abundant rRNA fragments, and calculates the rRNA depletion efficiency of potential oligos. We experimentally show that Ribo-ODDR designed oligos outperform commercially available kits and lead to a significant increase in rRNA depletion in Ribo-seq. Availability and implementation Ribo-ODDR is freely accessible at https://github.com/fallerlab/Ribo-ODDR. Supplementary information Supplementary data are available at Bioinformatics online.
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Rubenstein, Marvin, Courtney M. P. Hollowell, and Patrick Guinan. "Relationship of alterations in the expression of nontargeted genes and suppression of bcl-2 by antisense oligonucleotides." Journal of Clinical Oncology 30, no. 15_suppl (May 20, 2012): e13513-e13513. http://dx.doi.org/10.1200/jco.2012.30.15_suppl.e13513.
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e13513 Background: Antisense oligos have been employed against prostate cancer models targeting proteins associated with growth/apoptosis. However gene therapy may not be totally specific. Oligos against bcl-2 are in clinical trials and it was of interest: 1) To see whether therapy produces non-specific effects compromising efficacy; 2) To identify genes whose activity may have to be maintained/replaced. Methods: In LNCaP cells we evaluated monospecific (directed against bcl-2) and bispecific (directed against bcl-2 & epidermal growth factor receptor) oligos which comparably suppressed bcl-2. Cells were evaluated by PCR for expression of non-targeted genes associated with apoptosis (caspase-3, clusterin); androgen regulation (androgen receptor [AR], p300, creb binding protein [CBP]); cytokines (interleukins 2 [IL-2], 4 [IL-4], interferon [IFN]); antigen expression (prostate specific antigen [PSA], prostate membrane antigen [PSMA], prostatic acid phosphatase [PAP]); and autocrine growth (insulin like growth factor [IGF1]). Results: Most non-targeted genes were unaffected. However following suppression of bcl-2 activity by mono- and bispecific oligos, cells compensated by suppressing caspase-3 (apoptosis promoter) and enhancing AR and coactivator p300 expression. This suggests an ability to reverse bcl-2 suppression of apoptosis through decreased expression of a promoter and increased androgen sensitivity. It identifies caspase-3 as an essential gene whose expression must be either maintained/replaced when bcl-2 is therapeutically suppressed. Among the differentiation antigens, cell surface PSMA expression was increased by bispecific oligos; secretory PSA and PAP were not. Increased PSMA may to be due to induced IFN expression produced by bispecific oligos, attributed to a 2X intrastrand conformation not seen in the monospecific oligo. Increased PSMA expression could make prostate cancer cells more recognizable to cytotoxic T cells and potentiate prostate cancer vaccines. Conclusions: If gene therapy is to be effective, the mechanisms for compensatory changes which contribute to tumor resistance must be further identified/controlled.
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Jiang, Jiming. "Development and applications of fluorescence in situ hybridization using oligonucleotide-based probes." Semina: Ciências Biológicas e da Saúde 38, no. 1supl (February 16, 2018): 58. http://dx.doi.org/10.5433/1679-0367.2017v38n1suplp58.
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Fluorescence in situ hybridization (FISH) has been the most important technique in plant cytogenetic research. However, application of FISH techniques in most plant species has been hindered by the lack of cloned probes that generate distinct signals on chromosomes. We have recently developed a procedure to develop FISH probes by selecting a large number of oligonucleotides (oligos) derived from single copy DNA sequences. The bioinformatically selected oligos are then massively synthesized de novo in parallel, amplified, and labeled as FISH probes. The “oligo-FISH probes” designed from conserved DNA sequences generate distinct FISH signals on related plant species that have diverged for more than 10 million years. We have conducted oligo-FISH in several distantly related species in the Solanaceae family. This comparative FISH mapping effort has revealed karyotype evolution and discovered species-specific chromosomal translocations in several Solanum species.
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Krasnodębski, Cezary, Agnieszka Sawuła, Urszula Kaźmierczak, and Magdalena Żuk. "Oligo—Not Only for Silencing: Overlooked Potential for Multidirectional Action in Plants." International Journal of Molecular Sciences 24, no. 5 (February 24, 2023): 4466. http://dx.doi.org/10.3390/ijms24054466.
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Oligo technology is a low-cost and easy-to-implement method for direct manipulation of gene activity. The major advantage of this method is that gene expression can be changed without requiring stable transformation. Oligo technology is mainly used for animal cells. However, the use of oligos in plants seems to be even easier. The oligo effect could be similar to that induced by endogenous miRNAs. In general, the action of exogenously introduced nucleic acids (Oligo) can be divided into a direct interaction with nucleic acids (genomic DNA, hnRNA, transcript) and an indirect interaction via the induction of processes regulating gene expression (at the transcriptional and translational levels) involving regulatory proteins using endogenous cellular mechanisms. Presumed mechanisms of oligonucleotides’ action in plant cells (including differences from animal cells) are described in this review. Basic principles of oligo action in plants that allow bidirectional changes in gene activity and even those that lead to heritable epigenetic changes in gene expression are presented. The effect of oligos is related to the target sequence at which they are directed. This paper also compares different delivery methods and provides a quick guide to using IT tools to help design oligonucleotides.
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Jayaraman, Pushkala, Timothy Mosbruger, Taishan Hu, Nikolaos G. Tairis, Chao Wu, Peter M. Clark, Monica D’Arcy, et al. "AnthOligo: automating the design of oligonucleotides for capture/enrichment technologies." Bioinformatics 36, no. 15 (June 2, 2020): 4353–56. http://dx.doi.org/10.1093/bioinformatics/btaa552.
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Abstract Summary A number of methods have been devised to address the need for targeted genomic resequencing. One of these methods, region-specific extraction (RSE) is characterized by the capture of long DNA fragments (15–20 kb) by magnetic beads, after enzymatic extension of oligonucleotides hybridized to selected genomic regions. Facilitating the selection of the most appropriate capture oligos for targeting a region of interest, satisfying the properties of temperature (Tm) and entropy (ΔG), while minimizing the formation of primer-dimers in a pooled experiment, is therefore necessary. Manual design and selection of oligos becomes very challenging, complicated by factors such as length of the target region and number of targeted regions. Here we describe, AnthOligo, a web-based application developed to optimally automate the process of generation of oligo sequences used to target and capture the continuum of large and complex genomic regions. Apart from generating oligos for RSE, this program may have wider applications in the design of customizable internal oligos to be used as baits for gene panel analysis or even probes for large-scale comparative genomic hybridization array processes. AnthOligo was tested by capturing the Major Histocompatibility Complex (MHC) of a random sample. The application provides users with a simple interface to upload an input file in BED format and customize parameters for each task. The task of probe design in AnthOligo commences when a user uploads an input file and concludes with the generation of a result-set containing an optimal set of region-specific oligos. AnthOligo is currently available as a public web application with URL: http://antholigo.chop.edu. Supplementary information Supplementary data are available at Bioinformatics online.
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Reynaga Franco, Felipe, José Manuel Grijalva Chon, Jorge Eduardo Chávez Villalba, Reina Castro Longoria, José Alfredo Arreola Lizárraga, and Ramón Héctor Barraza Guardado. "Are 45 years of reproductive isolation enough to prevent the amplification of mitochondrial genes in the Pacific oyster?" AquaTechnica: Revista Iberoamericana de Acuicultura. 1, no. 1 (December 31, 2019): 22. http://dx.doi.org/10.33936/at.v1i1.2147.
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The Pacific oyster culture in Mexico began 45 years ago, first with spat imported from the USA and now with spat produced in several local hatcheries. Oyster farmers do not know the parameters that define the quality of the spat they buy, among them the level of genetic variability available in the lots offered. In order to evaluate and compare the genetic variability in spat produced by four Mexican hatcheries, an attempt was made to amplify and sequence the non-coding region and the ND5 gene of the oyster mitochondrial DNA with oligos reported in the scientific literature. The amplification of the non-coding region was not possible due to the bad design of the oligos. Despite the integrity of the extracted oyster DNA, the ND5 gene was not able to be amplified possibly due to the modification of the oligo recognition site in the gene. The generational separation of the oyster cultivated in Mexico from its original source population makes it necessary to obtain new mitochondrial sequences in order to design new oligos suitable for the populations established in Mexico.
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David, Benjamin M., Ryan M. Wyllie, Ramdane Harouaka, and Paul A. Jensen. "A reinforcement learning framework for pooled oligonucleotide design." Bioinformatics 38, no. 8 (February 10, 2022): 2219–25. http://dx.doi.org/10.1093/bioinformatics/btac073.
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Abstract Motivation The goal of oligonucleotide (oligo) design is to select oligos that optimize a set of design criteria. Oligo design problems are combinatorial in nature and require computationally intensive models to evaluate design criteria. Even relatively small problems can be intractable for brute-force approaches that test every possible combination of oligos, so heuristic approaches must be used to find near-optimal solutions. Results We present a general reinforcement learning (RL) framework, called OligoRL, to solve oligo design problems with complex constraints. OligoRL allows ‘black-box’ design criteria and can be adapted to solve many oligo design problems. We highlight the flexibility of OligoRL by building tools to solve three distinct design problems: (i) finding pools of random DNA barcodes that lack restriction enzyme recognition sequences (CutFreeRL); (ii) compressing large, non-degenerate oligo pools into smaller degenerate ones (OligoCompressor) and (iii) finding Not-So-Random hexamer primer pools that avoid rRNA and other unwanted transcripts during RNA-seq library preparation (NSR-RL). OligoRL demonstrates how RL offers a general solution for complex oligo design problems. Availability and implementation OligoRL and all simulation codes are available as a Julia package at http://jensenlab.net/tools and archived at https://archive.softwareheritage.org/browse/origin/directory/?origin_url=https://github.com/bmdavid2/OligoRL. Supplementary information Supplementary data are available at Bioinformatics online.
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Guinan, Patrick, Marvin Rubenstein, and Courtney M. P. Hollowell. "Potential increase in androgen sensitivity following antisense oligonucleotide suppression of Bcl-2 in a prostate cancer model." Journal of Clinical Oncology 30, no. 15_suppl (May 20, 2012): e13532-e13532. http://dx.doi.org/10.1200/jco.2012.30.15_suppl.e13532.
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e13532 Background: Antisense oligonucleotides (oligos) have been employed against in vivo and in vitro prostate cancer models targeting growth stimulatory gene products. While most oligos have targeted growth factors or their receptors, others have been directed against inhibitors of apoptosis and mediators of androgen action. In LNCaP cells we evaluated a set of oligos which targeted and comparably suppressed the expression of the apoptosis inhibitor protein bcl-2. To evaluate the specificity of this type of gene therapy, targeted and non-targeted genes were evaluated for their expression. The purpose was to identify whether additional (non-targeted) genes altered their expression in a manner which could circumvent or compensate for the suppression of bcl-2, promoting growth through increased androgen sensitivity. Methods: LNCaP prostate cells were treated with mono- and bispecific oligos directed against bcl-2. Employing RT-PCR the expression of both targeted and non-targeted genes (androgen receptor [AR], coactivators p300 and creb binding protein [CREB]) was determined. Results: LNCaP cells adapted to the suppression of bcl-2 (an apoptosis inhibitor) with enhanced expression of both AR and p300. This suggests an increased sensitivity to androgens. Conclusions: In this model, oligo treatment directed against bcl-2, may be evaded through a compensatory increase in both AR and p300 expression. This promotion of tumor growth, and the altered expression of AR coactivators normally seen in advanced disease, suggests a tumor transition to a more aggressive phenotype following suppressive treatment directed against bcl-2.
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Meng, Yuesheng, Wei Liu, Xiaoxia Ma, Xiuqin Meng, Gongwen Ai, and Yanxiang Zhang. "Decreased Proliferation of Myeloid Leukemia Cells through Down-Regulating LYL1 Expression with Small Interference RNA." Blood 110, no. 11 (November 16, 2007): 4158. http://dx.doi.org/10.1182/blood.v110.11.4158.4158.
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Abstract Ectopic expression of the basic helix-loop-helix transcription factor LYL1 has been implicated in T-cell acute lymphoblastic leukemia (T-ALL). It has also been found to be over-expressed in cells of acute myeloid leukemia (AML). Myeloid leukemia cells over-expressing LYL1 cDNA had accelerated growth rates, increased plating efficiency and a blockade of differentiation. To further investigate its role in the pathogenesis of leukemia, we used small interference RNA (siRNA) to silence the expression of LYL1 in human leukemia cell line K562, which expresses a moderate level of endogenous LYL1 protein. Three LYL1-specific RNA oligos, the Stealth Select RNAi HSS142834, HSS142835, and HSS142836, purchased from Invitrogen, were introduced into K562 cells by using Invitrogen transfection reagent Lipofectamine RNAiMAX. Two successive transfections at day 1 and day 2 were made according to manufacturer’s manual. Expression levels of LYL1 in LYL1 siRNA transfected cells and control cells (transfected with the Stealth RNAi Negative Controls) were determined with fluorescence real-time quantitative polymerase chain reaction assay. Our result showed that the application of any single RNAi oligo achieved observable inhibition of LYL1 expression levels (30–40%) while a combination of the three RNAi oligos remarkable inhibition (70.4%). The growth rates of K562 cells were not affected by any single RNAi oligo. However, a combination of three RNAi oligos did induce noticeable growth inhibition of cells. Plating efficiency assay showed that the clonogenic recovery rate of K562 cells treated with a combination of thee RNAi oligos was inhibited by 32.5% (P<0.05). The reduced growth rate and clonogenicity of cells was supposed to be secondary to the repressed expression of LYL1 because all other factors were controlled in our experiments. Further experiments are underway to define the changes of other genes in the LYL1-suppressed cells. We also tested the effect of specific siRNA on the expression of LYL1 and clonogenecity of leukemia cells in patient samples. Mononuclear cells separated from nine newly-diagnosed AML patients whose cells expressed comparatively higher levels of LYL1 were transfected with a combination of three LYL1 specific siRNA oligos for twice. We found that the siRNA oligos suppressed the expression of LYL1 in leukemia cells in most of the patients (7/9, decreased by 2 times or more) when compared with controls. Remarkably, the clonogenicity of AML cells in 3 patients was also inhibited by siRNA (P<0.05). In conclusion, the specific siRNA was effective to downregulate the expression of LYL1 in myeloid leukemia cells. It was also effective to affect cell proliferation in some cases. The data demonstrates that LYL1 plays a role for the malignant genotypes of leukemia cells and suggests that the RNA interference therapy targeting specific oncogenes might be clinically useful in the management of hematological malignancies.
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Rubenstein, M., P. Tsui, K. A. Christensen, and P. Guinan. "Effect of bispecific antisense oligos on prostate cancer cell growth." Journal of Clinical Oncology 25, no. 18_suppl (June 20, 2007): 14034. http://dx.doi.org/10.1200/jco.2007.25.18_suppl.14034.
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14034 Background: Antisense oligos against TGF-a (MR1), EGFR (MR2), and bcl-2 (MR4) are efficacious against prostate tumors. Methods: To enhance activity “bispecifics” were constructed. A pair recognized TGF-a and EGFR mRNA binding sites (TGF-a/EGFR [MR12] and EGFR/TGF-a [MR21]), another pair EGFR and bcl-2 (EGFR/bcl-2 [MR24] and bcl-2/EGFR [MR42]). Pairs differ in 5’ to 3’ binding site orientation, and were tested in vitro against prostate tumor cells. Following cell attachment, incubations were for 2 days with the agents followed by 2 days in their absence. Results: Bispecifics (6.25uM) are at least as effective as monospecifics and EGFR contributed to most first pair activity. Against PC-3 and LNCaP cells, MR2, MR4, MR12, MR21, MR24 and MR42 significantly inhibited growth. PC-3 cells were then incubated ± a chemotherapeutic agent. With LD50 Cytoxan, MR2, MR4, MR24, MR42 significantly inhibited 47.3, 45.7, 68.3 and 64.9%; with LD50 Taxol MR2, MR4, MR24, MR42 significantly inhibited 49.8, 45.8, 64.1 and 59.2%; and with LD50 DES MR2, MR4, MR24, MR42 significantly inhibited 66.6, 67.6, 64.3 and 67.2% respectively. Each agent significantly increased the inhibition produced by either oligo alone. LNCaP cells were also incubated with mono- and bispecific oligos ± chemotherapeutics. MR2, MR4, MR24, MR42 produced significant inhibitions of 57.4, 58.4, 69.4 and 68.6% for Cytoxan; 70.4, 70.1, 73.6 and 74.0% for Taxol; and 49.8, 50.1, 59.6 and 53.9% respectively for DES. A complete PC-3 experiment compared MR1, MR2, MR4, MR12, MR21, MR24 and MR42 in the presence of LD50 Cytoxan. Each oligo combined with Cytoxan significantly inhibited: MR1 by 51.0, MR2 by 55.0, MR4 by 58.0; MR12 by 56.0; MR21 by 61.1, MR24 by 65.5 and MR42 by 66.0%. Bispecifics directed against two different pathways, MR24 and MR42 were the most effective. A complete LNCaP experiment compared the same series of oligos in the presence of LD50 Cytoxan. Each oligo combined with Cytoxan significantly inhibited: MR1 by 49.0, MR2 by 50.0, MR4 by 53.0; MR12 by 52.0; MR21 by 58.6, MR24 by 53.9 and MR42 by 58.0%. Conclusions: Bispecific oligos significantly advance antisense technology and could play a role treating prostate cancer, particularly when combined with chemotherapy. Bispecifics against proteins associated with different growth pathways may be best. No significant financial relationships to disclose.
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Mata-Montero, Manrique, Nabil Shalaby, and Bradley Sheppard. "Efficient Serial and Parallel Algorithms for Selection of Unique Oligos in EST Databases." Advances in Bioinformatics 2013 (April 8, 2013): 1–6. http://dx.doi.org/10.1155/2013/793130.
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Obtaining unique oligos from an EST database is a problem of great importance in bioinformatics, particularly in the discovery of new genes and the mapping of the human genome. Many algorithms have been developed to find unique oligos, many of which are much less time consuming than the traditional brute force approach. An algorithm was presented by Zheng et al. (2004) which finds the solution of the unique oligos search problem efficiently. We implement this algorithm as well as several new algorithms based on some theorems included in this paper. We demonstrate how, with these new algorithms, we can obtain unique oligos much faster than with previous ones. We parallelize these new algorithms to further improve the time of finding unique oligos. All algorithms are run on ESTs obtained from a Barley EST database.
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MCCOY, MICHAEL. "PAUSE FOR OLIGOS." Chemical & Engineering News 82, no. 48 (November 29, 2004): 12–13. http://dx.doi.org/10.1021/cen-v082n048.p012.
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Tsvetkov, A., M. Jantsch, Z. Wu, C. Murphy, and J. G. Gall. "Transcription on lampbrush chromosome loops in the absence of U2 snRNA." Molecular Biology of the Cell 3, no. 3 (March 1992): 249–61. http://dx.doi.org/10.1091/mbc.3.3.249.
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The five small nuclear RNAs (snRNAs) involved in splicing occur on the loops of amphibian lampbrush chromosomes and in hundreds to thousands of extrachromosomal granules called B snurposomes. To assess the role of these snRNAs during transcription and to explore possible relationships between the loops and B snurposomes, we injected single-stranded antisense oligodeoxynucleotides (oligos) against U1 and U2 snRNA into toad and newt oocytes. As shown before, antisense U1 and U2 oligos caused truncation of U1 and complete destruction of U2 snRNAs, respectively. However, injection of any oligo, regardless of sequence, brought on dramatic cytological changes, including shortening of the chromosomes and retraction of the lateral loops, with concomitant shutdown of polymerase II transcription, as well as disappearance of some or all of the B snurposomes. When injected oocytes were incubated for 12 h or longer in physiological saline, these changes were reversible; that is, the chromosomes lengthened, transcription (detected by 3H-UTP incorporation) resumed on newly extended lateral loops, and B snurposomes reappeared. In situ hybridization showed that loops and B snurposomes had negligible amounts of U2 snRNA after recovery from injection of the anti-U2 oligo, whereas these structures had normal levels of U2 snRNA after recovery from a control oligo. Thus, the morphological integrity of B snurposomes and lampbrush chromosome loops is not dependent on the presence of U2 snRNA. Because transcription occurs in the absence of U2 snRNA, we conclude that splicing is not required for transcription on lampbrush chromosome loops.
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Romanov, Dmitry V., Gennady I. Karlov, and Mikhail G. Divashuk. "Developing Oligo Probes for Chromosomes Identification in Hemp (Cannabis sativa L.)." Plants 11, no. 15 (July 22, 2022): 1900. http://dx.doi.org/10.3390/plants11151900.
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Hemp (Cannabis sativa L., 2n = 20) is a valuable crop that is successfully used as a food, technical and medicinal crop. It is a dioecious plant with an XX\XY sex determination system. Some chromosomes of C. sativa have almost the same lengths and centromeric indexes. Cytogenetic markers help to distinguish similar plant chromosomes, including sex chromosomes, which is important for the breeding process. Two repeats (CS-1 and CS-237) were used to develop labeled oligo-probes for rapid and low-cost oligo-FISH. These oligos can be recommended for use as cytological markers to distinguish sex chromosomes (X and Y) and somatic chromosome pairs 3, 6, and 8 by rapid oligo-FISH in a short time.
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Nagel, Stefan, Michaela Scherr, Klaus Hornischer, Alexander Kel, Maren Kaufmann, Hans G. Drexler, and Roderick A. F. MacLeod. "Functional Characterization of the BCL11B Breakpoint Region Reveals Multiple Enhancers at Dnase-I Hypersensitive Sites Some of Which Control NK-Family Homeobox Genes in T-ALL Cells with t(5;14)(q35;q32)." Blood 106, no. 11 (November 16, 2005): 845. http://dx.doi.org/10.1182/blood.v106.11.845.845.
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Abstract The zinc-finger transcription factor BCL11B (14q32) is a key translocation target in pediatric T-cell acute lymphoblastic leukemia (T-ALL) where it ectopically activates NK-family homeobox genes, chiefly TLX3, or NKX2-5, via the recurrent t(5;14)(q35;q32). However, the mechanism underlying leukemic activation by BCL11B remains obscure. Breakpoints at 14q32 are dispersed over about 1.2 Mbp downstream of BCL11B amid a non-coding genomic “desert”. Detailed cytogenetic analysis of T-ALL cell lines, including one carrying a complex double-insertion enabled the putative breakpoint target zone to be narrowed to ~300 kbp covering the central and distal parts of the 3′-BCL11B region. Interestingly, Crawford et al. (PNAS101: 992–7, 2004) have identified a series of DNase-I hypersensitive sites (DHS) in T-cells amid this genomic desert including a unique cluster near the most distal breakpoint to serve as candidate BCL11B transcriptional enhancers. Accordingly, we used the TRANSFAC database to identify multiple transcription factor (TF) binding site sequences nearby these DHS. To investigate the role of DHS in activating homeobox transcription in T-ALL, we designed double-stranded 26-mer oligos matching each of 9 DHS which were used to transfect a T-ALL cell line (PEER) in which NKX2-5 is inserted about 1 Mbp downstream of BCL11B and thereby activated. Such oligos may inhibit TF binding by directly blocking access to DHS or act as decoys to sequester TF. We found that oligos targeting DHS in the central and distal regions of 3′-BCL11B, close to the insertion junctions in PEER cells, were effective in down-regulating NKX2-5 transcription in a dose dependent manner. In contrast, oligos targeting DHS near 3′-BCL11B were able to down-regulate BCL11B but not NKX2-5. Treatments with neither mutated DHS oligos, nor other control oligos caused inhibition. Transcription of ESTs present at 3′-BCL11B was unaffected by DHS-oligo transfection indicating specific targeting of BCL11B or NKX2-5 by their respective DHS. Analysis of t(5;14) T-ALL cell lines by Halo-FISH, showed the selective homing of 3′-BCL11B chromatin to the nuclear matrix when juxtaposed with NKX2-5, whereas 3′-BCL11B chromatin present on non-participant chromosomes was extruded to surrounding halos inimical to transcription. Taken together, our data show the presence of multiple DHS covering the ~1.2 Mbp breakpoint dispersal region at 3′-BCL11B in T-ALL cells which appear to serve as enhancers of BCL11B or nearby translocated NK-family homeobox genes. These multiple enhancers may be required for the precise timing of BCL11B transcription which is critical to thymocyte development - a question which will be addressed by planned future studies. As well as revealing novel aspects underlying the transcriptional control of BCL11B in T-cells, our data highlight a potential therapeutic target in leukemia within “junk DNA”.
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Guinan, Patrick, Marvin Rubenstein, and Courtney M. P. Hollowell. "Effect of suppression of bcl-2 with antisense oligonucleotides on p53 expression." Journal of Clinical Oncology 31, no. 15_suppl (May 20, 2013): e16085-e16085. http://dx.doi.org/10.1200/jco.2013.31.15_suppl.e16085.
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e16085 Background: In theory gene therapy is specific but difficulties are encounted in practice. Tumors express altered patterns of expression and regulatory pathways provide many targets. However the actual activity of most genes are similar to normal. Resistance develops because pathways are complex, regulated by stimulatory and inhibitory factors, each affected by therapy. Tumors alter dependence on targeted gene products for growth by relying upon others, through compensation. Antisense oligos have targeted regulatory proteins in both in vivo and in vitro prostate cancer models. Cells treated with antisense directed against bcl-2 compensated by suppressing caspase-3 (an apoptosis promoter) and enhancing androgen receptor (AR), (co-activating) p300 and IL-6 expression. This suggests that in LNCaP a progression to increased androgen sensitivity accompanies bcl-2 suppression with a pattern of co-activation associated with more advanced prostate tumors. Methods: We evaluated mono- and bispecific oligos which targeted and equally suppressed bcl-2 expression in LNCaP cells. To further evaluate compensatory mechanisms related to tumor resistance we evaluated the level of the suppressor gene p53 employing RT-PCR and agarose gel quantification. Bands representing pcr product were photographed, converted to black and white and assessed by MIPAV software. Results: Comparable amounts of RNA from LNCaP cells treated with either mono- or bispecific oligos directed against bcl-2 (and EGFR in the bispecifics) were evaluated by RT-PCR using primers directed against p53. When background intensity was subtracted, the relative intensity of all bands corresponding to p53 and representing cells treated with MR4, MR24 and MR42 (compared to controls) were respectively increased 47.5% ± 42.3 (p = 0.02), 86.5% ± 35.3 (p = 0.00013) and 58.0% ± 42.0 (p = 0.0077). These results were pooled from both duplicate PCR runs and gels, and indicate each oligo targeting bcl-2 significantly enhanced p53 expression. Conclusions: Inhibition of bcl-2 activity mediated via antisense oligos enhances suppressor gene p53 expression. In contrast to the effects noted above, p53 enhancement would appear beneficial.
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Wells, William. "Mutating mice with oligos." Genome Biology 1 (2000): spotlight—20001023–02. http://dx.doi.org/10.1186/gb-spotlight-20001023-02.
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Rick Mullin. "Agilent to boost oligos." C&EN Global Enterprise 98, no. 32 (August 24, 2020): 14. http://dx.doi.org/10.1021/cen-09832-buscon6.
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Slodzinski, Martin K., and Mordecai P. Blaustein. "Na+/Ca2+exchange in neonatal rat heart cells: antisense inhibition and protein half-life." American Journal of Physiology-Cell Physiology 275, no. 2 (August 1, 1998): C459—C467. http://dx.doi.org/10.1152/ajpcell.1998.275.2.c459.
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Cardiac Na+/Ca2+exchanger (NCX) protein half-life ( t ½) and antisense knockdown were studied in primary cultured neonatal rat cardiomyocytes. Protein t ½ was determined using [35S]methionine with a pulse-chase protocol. The 35S signal in NCX was identified by immunoprecipitation and Western blotting. The t ½ of NCX protein was 33 h. Low concentrations (0.5 μM) of chimeric, phosphorothioated antisense oligodeoxynucleotides (AS-oligos) targeted to the region around the start codon of NCX1 transcript were used to knock down NCX protein and activity. Control myocytes (no oligos or scrambled oligos for at least 4 days) exhibited spontaneous Ca2+ transients (measured with fura 2). The sustained (“diastolic”) Ca2+ concentration in the cytosol ([Ca2+]cyt) of control cells was unaffected by cyclopiazonic acid (CPA) plus caffeine (Caf), which promote depletion of sarcoplasmic reticular Ca2+ stores, but [Ca2+]cytrose in control cells when external Na+ was removed. In contrast, ∼60% of cells treated with AS-oligos for at least 4 days did not exhibit spontaneous Ca2+transients or respond to Na+-free medium; however, CPA + Caf did induce a prolonged elevation in [Ca2+]cytin these cells. In all cells, 50 mM K+ increased [Ca2+]cyt. NCX protein was reduced by ∼50% in cells treated with AS-oligos for 7 days but was not reduced after only 2 days. These biochemical data are consistent with the physiological evidence of NCX knockdown in ∼60% of cells.
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Dubey, Raghvendra K., Delbert G. Gillespie, and Edwin K. Jackson. "A2B Adenosine Receptors Mediate the Anti-Mitogenic Effects of Adenosine in Cardiac Fibroblasts." Hypertension 36, suppl_1 (October 2000): 708. http://dx.doi.org/10.1161/hyp.36.suppl_1.708-b.
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P85 Adenosine inhibits growth of CFs; however, the adenosine receptor subtype that mediates this anti-mitogenic effect remains undefined. Using specific ADE receptor antagonists and agonists and antisense oligonucleotides (OLIGO) against A2B receptors, we investigated the role of A2B receptors in inhibiting cardiac fibroblast growth. PDGF (25ng/ml)-induced DNA synthesis, cell number and collagen synthesis in CFs were inhibited by A2 (chloroadenosine [Cl-Ad]and MECA), but not by A1 (CPA), A2a ( CGS21680 ) or A3 (AB-MECA),receptor agonists.The inhibitory effects of 1μM MECA and Cl-Ad were reversed by A1/A2 (DPSPX; 10nM), but not by A1 (DPCPX; 10nM), receptor antagonists. In CFs treated with antisense, but not sense or scrambled, OLIGOs to the A2B receptor, both basal and PDGF-induced DNA synthesis was enhanced by 70±4% and 64±5% respectively. Moreover, the inhibitory effects of Cl-Ad and MECA were completely abolished in CFs treated with antisense, but not sense and scrambled, OLIGOs. In conclusion, A2B receptors mediate the anti-mitogenic effects of adenosine suggesting that A2B receptors are importantly involved in the regulation of CF biology. Thus, A2B receptors may play a critical role in regulating cardiac remodeling associated with CF proliferation.
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Du, Pei, Lifang Zhuang, Yanzhi Wang, Li Yuan, Qing Wang, Danrui Wang, Dawadondup, et al. "Development of oligonucleotides and multiplex probes for quick and accurate identification of wheat and Thinopyrum bessarabicum chromosomes." Genome 60, no. 2 (February 2017): 93–103. http://dx.doi.org/10.1139/gen-2016-0095.
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In comparison with general FISH for preparing probes in terms of time and cost, synthesized oligonucleotide (oligo hereafter) probes for FISH have many advantages such as ease of design, synthesis, and labeling. Low cost and high sensitivity and resolution of oligo probes greatly simplify the FISH procedure as a simple, fast, and efficient method of chromosome identification. In this study, we developed new oligo and oligo multiplex probes to accurately and efficiently distinguish wheat (Triticum aestivum, 2n = 6x, AABBDD) and Thinopyrum bessarabicum (2n = 2x = 14, JJ) chromosomes. The oligo probes contained more nucleotides or more repeat units that produced stronger signals for more efficient chromosome painting. Four Th. bessarabicum-specific oligo probes were developed based on genomic DNA sequences of Th. bessarabicum chromosome arm 4JL, and one of them (oligo DP4J27982) was pooled with the oligo multiplex #1 to simultaneously detect wheat and Th. bessarabicum chromosomes for quick and accurate identification of Chinese Spring (CS) – Th. bessarabicum alien chromosome introgression lines. Oligo multiplex #4 revealed chromosome variations among CS and eight wheat cultivars by a single round of FISH analysis. This research demonstrated the high efficiency of using oligos and oligo multiplexes in chromosome identification and manipulation.
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Nagata, Tetsuya, and Shinichi Takeda. "Antisense Oligos for Muscular Dystrophy." Rinsho Shinkeigaku 50, no. 11 (2010): 843. http://dx.doi.org/10.5692/clinicalneurol.50.843.
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Lin, H., Z. Zhang, M. Q. Zhang, B. Ma, and M. Li. "ZOOM! Zillions of oligos mapped." Bioinformatics 24, no. 21 (August 6, 2008): 2431–37. http://dx.doi.org/10.1093/bioinformatics/btn416.
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Michael McCoy. "BioSpring plans expansion in oligos." C&EN Global Enterprise 101, no. 1 (January 2, 2023): 10–11. http://dx.doi.org/10.1021/cen-10101-buscon13.
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Rubenstein, Marvin, Courtney M. P. Hollowell, and Patrick Guinan. "Involvement of compensatory CD44+ stem cells following BCL-2 suppression by antisense oligonucleotides." Journal of Clinical Oncology 31, no. 15_suppl (May 20, 2013): 2590. http://dx.doi.org/10.1200/jco.2013.31.15_suppl.2590.
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2590 Background: Gene therapy is in theory specific but encounters difficulties in practice. Suitable targets are found in many pathways and tumors do express altered patterns of expression. However the actual activity of most regulatory genes are similar to normal. Resistance develops because biochemical pathways are complex, regulated by stimulatory and inhibitory factors, each possibly affected by therapy. It’s suggested that tumors alter dependence on targeted gene products for growth by relying upon others, through compensation. Antisense oligos have targeted regulatory proteins in both in vivo and in vitro prostate cancer models. Cells treated with antisense directed against bcl-2 compensated by suppressing caspase-3 (an apoptosis promoter) and enhancing androgen receptor (AR), (co-activating) p300 and IL-6 expression. This suggests that in LNCaP a progression to increased androgen sensitivity accompanies bcl-2 suppression with a pattern of co-activation associated with more advanced prostate tumors. Methods: We evaluated mono- and bispecific oligos which targeted and equally suppressed bcl-2 expression in LNCaP cells. To further evaluate compensatory mechanisms related to tumor resistance we evaluated the level of CD44 expression employing RT-PCR and agarose gel quantification. Bands representing pcr product were photographed, converted to black and white and assessed by MIPAV software. Results: Comparable amounts of RNA from LNCaP cells treated with either mono- or bispecific oligos directed against bcl-2 (and EGFR in the bispecifics) were evaluated by RT-PCR using primers directed against CD44. When background intensity was subtracted, the relative intensity of the bands corresponding to CD44, and representing cells treated with MR4, MR24 and MR42 (compared to controls) were respectively increased 3.0% ± 33.6 (NS), suppressed 16.4% ± 49.1 (NS) and suppressed 9.2% ± 26.5 (NS). These results were pooled from both duplicate PCR runs and gels, and indicate no significant changes in CD44 expression was produced by any oligo type. Conclusions: Stem cells expressing this marker were unaffected by treatment, suggesting this population is not altered by suppressive bcl-2 therapy.
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Lee, David, Yan Liang, Chris Merritt, Fiona Pakiam, Giang Ong, Shaobu Weng, Dwayne Dunaway, et al. "A new approach for immuno-oncology biomarker discovery: High-plex, spatial protein profiling based on NanoString digital quantification." Journal of Clinical Oncology 35, no. 7_suppl (March 1, 2017): 27. http://dx.doi.org/10.1200/jco.2017.35.7_suppl.27.
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27 Background: The immune response to cancer is shaped by the abundance and localization of immune cell populations, their activation status, and expression of immunomodulatory factors. To detect proteins at high multiplex with spatial resolution, NanoString optical barcoding technology was used to digitally profile protein expression in formalin fixed paraffin embedded (FFPE) samples and compared to traditional IHC. Methods: NanoString has enabled digital profiling of immuno-oncology protein targets, including immune cell markers and checkpoint proteins. Protein detection is enabled via primary antibodies (Abs) which are attached via a UV cleavable linker to DNA indexing oligos. FFPE samples are stained with a multiplex cocktail of labeled Abs, then DNA oligos are released by UV light exposure. Liberated oligos are then hybridized to optical barcodes for quantitation on a NanoString instrument. This technique enables quantitative, multiplex protein detection over 5 logs of dynamic range. IHC and NanoString spatial protein profiling were performed on alternating sections from blocks of tonsil, melanoma, and colorectal cancer. Sections were fluorescently labeled with panCK, Ki67, and Syto-83 to visualize morphology, and regions of interest (ROI) were selected for profiling using up to 30 oligo-tagged Abs. Results: NanoString counts strongly correlated with quantification of CD3, CD4, CD8, PanCK, Ki67, PD-1, and PD-L1 derived from IHC. To explore limits of detection, ROIs of 1, 2, 4, or 8 cells were profiled. Digital counts were detected above background at the single cell level and linearly correlated with cell count. Furthermore, quantification with two cell lineage markers and double positive cells were demonstrated using a 30-plex Ab cocktail. Conclusions: Multiplex, digital protein profiling with spatial resolution will enable deep characterization of immune responses in tumors. Additionally, single cell profiling enables inter-cellular characterization of variations in immune response. The strong correlation of NanoString data to IHC indicates the feasibility to spatially profile multiple key proteins with minimal consumption of patient tissue.
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Yuan, Xudong, Ling Li, Appu Rathinavelu, Jinsong Hao, Madhusudhanan Narasimhan, Matthew He, Viviene Heitlage, Linda Tam, Sana Viqar, and Mojgan Salehi. "siRNA Drug Delivery by Biodegradable Polymeric Nanoparticles." Journal of Nanoscience and Nanotechnology 6, no. 9 (September 1, 2006): 2821–28. http://dx.doi.org/10.1166/jnn.2006.436.
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RNA interference (RNAi) is an emerging technology in which the introduction of double-stranded RNA (dsRNA) into a diverse range of organisms and cell types causes degradation of the complementary mRNA. It offers a broad spectrum of applications in both biological and medical research. Small interference RNA (siRNA) was recently explored for its therapeutical potential. However, the drug delivery of siRNA oligos is very novel and is in great need of future research. To this end, a biodegradable poly(D,L-lactide-co-glycolide) (PLGA) nanoparticle drug carrier system was prepared to load siRNA oligos with desired physicochemical properties. The nanoparticles were characterized by scanning electron microscopy and laser diffraction particle sizer. The delivery of siRNA into the targeted 293T cells was observed using fluorescent-labeled double-stranded Cy3-oligos. The model siRNA oligos, si-GFP-RNA, were also successfully loaded into PLGA nanoparticles and delivered in 293T cells. The gene silencing effect and the inhibition of GFP expression were investigated using fluorescent microscopy. Both positive and negative controls were used to compare with the new siRNA nanoparticle delivery system. It was found that nanoparticles offered both effective delivery of siRNA and prominent GFP gene silencing effect. Compared to conventional carrier systems, the new biodegradable polymeric nanoparticle system may also offer improved formulation stability, which is practically beneficial and may be used in the future clinical studies of siRNA therapeutics.
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Alizadehmojarad, Ali A., Sergei M. Bachilo, Anatoly Kolomeisky, and R. Bruce Weisman. "(Digital Presentation) Realistic Molecular Dynamics Modeling of ssDNA/SWCNT Hybrids." ECS Meeting Abstracts MA2022-01, no. 9 (July 7, 2022): 715. http://dx.doi.org/10.1149/ma2022-019715mtgabs.
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Despite the importance of single-wall carbon nanotubes (SWCNTs) coated with short oligos of single-stranded DNA (ssDNA), the structure-specific interactions in these hybrids remain poorly understood. It is known that the interactions can depend on the DNA base sequence and length, and on the nanotube diameter and roll-up angle. To study these phenomena, we are applying a combination of computational and experimental methods. A major goal for guiding and validating molecular dynamics simulations of the hybrid structures is finding the average length of nanotube covered by each ssDNA oligo. We have quantified this by carefully preparing dialyzed aqueous dispersions of SWCNTs in specific oligos and then measuring the absolute mass concentrations of both components using total organic carbon analysis. Corresponding absorption spectra were also measured to deduce ultraviolet SWCNT molar absorptivities (structurally averaged), which in combination with known ssDNA nucleobase absorptivities allow quicker determinations of mass ratios in the hybrids. Our results for a library of hybrids indicate that purine nucleobases on average cover a larger region on the nanotube surface than do pyrimidine nucleobases, as is consistent with the sizes of those aromatic structures. This average coverage is key to developing realistic atomistic molecular dynamics models for the conformations of ssDNA adsorbed on SWCNT sidewalls. Examples of such computed hybrid structures and their significance will be presented.
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Yu, Zhihui, Hongjin Wang, Ennian Yang, Guangrong Li, and Zujun Yang. "Precise Identification of Chromosome Constitution and Rearrangements in Wheat–Thinopyrum intermedium Derivatives by ND-FISH and Oligo-FISH Painting." Plants 11, no. 16 (August 13, 2022): 2109. http://dx.doi.org/10.3390/plants11162109.
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Thinopyrum intermedium possesses many desirable agronomic traits that make it a valuable genetic source for wheat improvement. The precise identification of individual chromosomes of allohexaploid Th. intermedium is a challenge due to its three sub-genomic constitutions with complex evolutionary ancestries. The non-denaturing fluorescent in situ hybridization (ND-FISH) using tandem-repeat oligos, including Oligo-B11 and Oligo-pDb12H, effectively distinguished the St, J and JS genomes, while Oligo-FISH painting, based on seven oligonucleotide pools derived from collinear regions between barley (Hordeum vulgare L.) and wheat (Triticum aestivum L.), was able to identify each linkage group of the Th. intermedium chromosomes. We subsequently established the first karyotype of Th. intermedium with individual chromosome recognition using sequential ND-FISH and Oligo-FISH painting. The chromosome constitutions of 14 wheat–Th. intermedium partial amphiploids and addition lines were characterized. Distinct intergenomic chromosome rearrangements were revealed among Th. intermedium chromosomes in these amphiploids and addition lines. The precisely defined karyotypes of these wheat–Th. intermedium derived lines may be helpful for further study on chromosome evolution, chromatin introgression and wheat breeding programs.
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Torres, Milton Luiz. "CONSIDERAÇÕES SOBRE A PALAVRA “POUCO” EM APOCALIPSE 17:10." PRÁXIS TEOLÓGICA 16, no. 1 (December 23, 2020): e1589. http://dx.doi.org/10.25194/2317-0573.2020v16n1.e1589.
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Em anos recentes, algumas discussões vêm ocorrendo, no meio teológico adventista, com respeito ao significado exato da palavra grega oligon no verso “São também sete reis. Cinco já caíram, um ainda existe, e o outro ainda não surgiu; mas, quando surgir, deverá permanecer durante pouco tempo” (Ap 17:10). Os estudiosos já perceberam que a expressão “durante pouco tempo” traduz esta única palavra grega, que significa simplesmente “pouco”. O termo “tempo” fica subentendido pelo contexto, enquanto a tradução “durante” é exigida pelo fato de que o adjetivo oligos aparece no caso acusativo (oligon), o que lhe concede valor adverbial e lhe acrescenta a ideia de duração, como acontece, por exemplo, na tradução da passagem na Nova Versão Internacional. Obviamente, a intenção aqui não é ser dogmático. É simplesmente propor alguns aspectos relevantes para a discussão de uma passagem que ultimamente tem se tornado tão capital para as discussões escatológicas.
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Stellwagen, Earle. "TBA Markedly Alters A-Tract Oligos." Biophysical Journal 118, no. 3 (February 2020): 64a. http://dx.doi.org/10.1016/j.bpj.2019.11.526.
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Heasman, Janet. "Morpholino Oligos: Making Sense of Antisense?" Developmental Biology 243, no. 2 (March 2002): 209–14. http://dx.doi.org/10.1006/dbio.2001.0565.
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Cui, Yun-Xi, Xue-Nan Feng, Ya-Xin Wang, Hui-Yu Pan, Hua Pan, and De-Ming Kong. "An integrated-molecular-beacon based multiple exponential strand displacement amplification strategy for ultrasensitive detection of DNA methyltransferase activity." Chemical Science 10, no. 8 (2019): 2290–97. http://dx.doi.org/10.1039/c8sc05102j.
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Chalapati, Sachin, Conor A. Crosbie, Dixita Limbachiya, and Nimesh Pinnamaneni. "Direct oligonucleotide sequencing with nanopores." Open Research Europe 1 (August 24, 2021): 47. http://dx.doi.org/10.12688/openreseurope.13578.2.
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Third-generation DNA sequencing has enabled sequencing of long, unamplified DNA fragments with minimal steps. Direct sequencing of ssDNA or RNA gives valuable insights like base-level modifications, phosphoramidite synthesis yield estimates and strand quality analysis, without the need to add the complimentary strand. Direct sequencing of single-stranded nucleic acid species is challenging as they are non-compatible to the double-stranded sequencing adapters used by manufacturers. The MinION platform from Oxford Nanopore Technologies performs sequencing by passing single-strands of DNA through a layer of biological nanopore sensors; although sequencing is performed on single-strands, the recommended template by the manufacturer is double-stranded. We have identified that the MinION platform can perform sequencing of short, single-strand oligonucleotides directly without amplification or second-strand synthesis by performing a single annealing step before library preparation. Short 5’ phosphorylated oligos when annealed to an adapter sequence can be directly sequenced in the 5' to 3' direction via nanopores. Adapter sequences were designed to bind to the 5’ end of the oligos and to leave a 3’ adenosine overhang after binding to their target. The 3’ adenosine overhang of the adapter and the terminal phosphate makes the 5’ end of the oligo analogous to an end-prepared dsDNA, rendering it compatible with ligation-based library preparation for sequencing. An oligo-pool containing 42,000, 120 nt orthogonal sequences was phosphorylated and sequenced using this method and ~90% of these sequences were recovered with high accuracy using BLAST. In the nanopore raw data, we have identified that empty signals can be wrongly identified as a valid read by the MinION platform and sometimes multiple signals containing several strands can be fused into a single raw sequence file due to segmentation faults in the software. This direct oligonucleotide sequencing method enables novel applications in DNA data storage systems where short oligonucleotides are the primary information carriers.
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Chalapati, Sachin, Conor A. Crosbie, Dixita Limbachiya, and Nimesh Pinnamaneni. "Direct oligonucleotide sequencing with nanopores." Open Research Europe 1 (May 12, 2021): 47. http://dx.doi.org/10.12688/openreseurope.13578.1.
Full textAbstract:
Third-generation DNA sequencing has enabled sequencing of long, unamplified DNA fragments with minimal steps. Direct sequencing of ssDNA or RNA gives valuable insights like base-level modifications, phosphoramidite synthesis yield estimates and strand quality analysis, without the need to add the complimentary strand. Direct sequencing of single-stranded nucleic acid species is challenging as they are non-compatible to the double-stranded sequencing adapters used by manufacturers. The MinION platform from Oxford Nanopore Technologies performs sequencing by passing single-strands of DNA through a layer of biological nanopore sensors; although sequencing is performed on single-strands, the recommended template by the manufacturer is double-stranded. We have identified that the MinION platform can perform sequencing of short, single-strand oligonucleotides directly without amplification or second-strand synthesis by performing a single annealing step before library preparation. Short 5’ phosphorylated oligos when annealed to an adapter sequence can be directly sequenced in the 5' to 3' direction via nanopores. Adapter sequences were designed to bind to the 5’ end of the oligos and to leave a 3’ adenosine overhang after binding to their target. The 3’ adenosine overhang of the adapter and the terminal phosphate makes the 5’ end of the oligo analogous to an end-prepared dsDNA, rendering it compatible with ligation-based library preparation for sequencing. An oligo-pool containing 42,000, 120 nt orthogonal sequences was phosphorylated and sequenced using this method and ~90% of these sequences were recovered with high accuracy using BLAST. In the nanopore raw data, we have identified that empty signals can be wrongly identified as a valid read by the MinION platform and sometimes multiple signals containing several strands can be fused into a single raw sequence file due to segmentation faults in the software. This direct oligonucleotide sequencing method enables novel applications in DNA data storage systems where short oligonucleotides are the primary information carriers.
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Le, Bao T., Suxiang Chen, Mikhail Abramov, Piet Herdewijn, and Rakesh N. Veedu. "Evaluation of anhydrohexitol nucleic acid, cyclohexenyl nucleic acid andd-altritol nucleic acid-modified 2′-O-methyl RNA mixmer antisense oligonucleotides for exon skipping in vitro." Chemical Communications 52, no. 92 (2016): 13467–70. http://dx.doi.org/10.1039/c6cc07447b.
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Karwowski, Boleslaw T. "The Influence of Spirodi(Iminohydantoin) on Charge Transfer through ds-DNA Containing 8-OXO-dG: A Theoretical Approach." International Journal of Molecular Sciences 24, no. 10 (May 10, 2023): 8570. http://dx.doi.org/10.3390/ijms24108570.
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Genetic information stored in a DNA base sequence is continuously exposed to harmful factors. It has been determined that 9 × 104 different DNA damage events occur in a single human cell every 24 h. Of these, 7,8-dihydro-8-oxo-guanosine (OXOG) is one of the most abundant and can undergo further transformations towards spirodi(iminohydantoin) (Sp). Sp is highly mutagenic in comparison to its precursor if not repaired. In this paper, the influence of both Sp diastereomers 4R and 4S as well as their anti and syn conformers on charge transfer through the double helix was taken into theoretical consideration. In addition, the electronic properties of four modelled double-stranded oligonucleotides (ds-oligos) were also discussed, i.e., d[A1Sp2A3oxoG4A5] * [T5C4T3C2T1]. Throughout the study, the M06—2X/6—31++G** level theory was used. Solvent–solute non-equilibrated and equilibrated interactions were also considered. The subsequent results elucidated that the 7,8-dihydro-8-oxo-guanosine:cytidine (OXOGC) base pair is the settled point of a migrated radical cation in each of the discussed cases, due to its low adiabatic ionization potential, i.e., ~5.55 [eV]. The opposite was noted for excess electron transfer through ds-oligos containing anti (R)-Sp or anti (S)-Sp. The radical anion was found on the OXOGC moiety, whereas in the presence of syn (S)-Sp or syn (R)-Sp, an excess electron was found on the distal A1T5 or A5T1 base pair, respectively. Furthermore, a spatial geometry analysis of the discussed ds-oligos revealed that the presence of syn (R)-Sp in the ds-oligo caused only a slight deformation to the double helix, while syn (S)-Sp formed an almost ideal base pair with a complementary dC. The above results are in strong agreement with the final charge transfer rate constant, as calculated according to Marcus’ theory. In conclusion, DNA damage such as spirodi(iminohydantoin), especially when becoming part of clustered DNA damage, can affect the effectiveness of other lesion recognition and repair processes. This can lead to the acceleration of undesired and deleterious processes such as carcinogenesis or aging. However, in terms of anticancer radio-/chemo- or combined therapy, the slowing down of the repair machinery can result in increased effectiveness. With this in mind, the influence of clustered damage on charge transfer and its subsequent effect on single-damage recognition by glycosylases justifies future investigation.
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ZHANG, ZEFENG, HAO LIN, and MING LI. "MANGO: MULTIPLE ALIGNMENT WITH N GAPPED OLIGOS." Journal of Bioinformatics and Computational Biology 06, no. 03 (June 2008): 521–41. http://dx.doi.org/10.1142/s0219720008003527.
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Multiple sequence alignment is a classical and challenging task. The problem is NP-hard. The full dynamic programming takes too much time. The progressive alignment heuristics adopted by most state-of-the-art works suffer from the "once a gap, always a gap" phenomenon. Is there a radically new way to do multiple sequence alignment? In this paper, we introduce a novel and orthogonal multiple sequence alignment method, using both multiple optimized spaced seeds and new algorithms to handle these seeds efficiently. Our new algorithm processes information of all sequences as a whole and tries to build the alignment vertically, avoiding problems caused by the popular progressive approaches. Because the optimized spaced seeds have proved significantly more sensitive than the consecutive k-mers, the new approach promises to be more accurate and reliable. To validate our new approach, we have implemented MANGO: Multiple Alignment with N Gapped Oligos. Experiments were carried out on large 16S RNA benchmarks, showing that MANGO compares favorably, in both accuracy and speed, against state-of-the-art multiple sequence alignment methods, including ClustalW 1.83, MUSCLE 3.6, MAFFT 5.861, ProbConsRNA 1.11, Dialign 2.2.1, DIALIGN-T 0.2.1, T-Coffee 4.85, POA 2.0, and Kalign 2.0. We have further demonstrated the scalability of MANGO on very large datasets of repeat elements. MANGO can be downloaded at and is free for academic usage.