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Journal articles on the topic 'DNA hybrid'

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Author: Grafiati

Published: 9 March 2023

Last updated: 1 April 2023

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1

Kawashima, Etsuko, Yusuke Ohba, Yusuke Terui, and Kazuo Kamaike. "Design, Synthesis, and Analysis of Minor Groove Binder Pyrrolepolyamide-2′-Deoxyguanosine Hybrids." Journal of Nucleic Acids 2010 (2010): 1–13. http://dx.doi.org/10.4061/2010/235240.

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Pyrrolepolyamide-2′-deoxyguanosine hybrids (Hybrid2and Hybrid3) incorporating the 3-aminopropionyl or 3-aminopropyl linker were designed and synthesized on the basis of previously reported results of a pyrrolepolyamide-adenosine hybrid (Hybrid1). Evaluation of the DNA binding sequence selectivity of pyrrolepolyamide-2′-deoxyguanosine hybrids was performed by CD spectral andTmanalyses. It was shown that Hybrid3possessed greater binding specificity than distamycin A, Hybrid1and Hybrid2.

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2

Tseng, Yu-Hsin, and Jer-Ming Hu. "A new hybrid from Taiwan, Elatostema ×hybrida (Urticaceae), is the first confirmed natural hybrid for Urticaceae." Phytotaxa 161, no. 1 (February 20, 2014): 43. http://dx.doi.org/10.11646/phytotaxa.161.1.2.

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Explosive pollen dispersal is common in Urticaceae and they are thought to be wind-pollinated. Despite a lack of obvious mechanism for preventing cross-species pollination, putative hybrid species in Urticaceae are rarely documented. Here we described the first natural hybrid in Urticaceae Elatostema ×hybrida from Taiwan. Morphological characters in E. ×hybrida are intermediate between putative parental species: E. lineolatum var. majus and E. platyphylloides. Six hybrid populations of E. ×hybrida were found in Taiwan that exhibited largely overlapping distribution patterns with its putative parents. Phylogenetic analysis of chloroplast DNA showed that the hybrid species is more closely related to E. lineolatum var. majus suggesting that the latter is the maternal parent and that hybridization is unidirectional. The chromosome number of E. ×hybrida remains the same as its putative parents (2n = 26). We speculate that the examined hybrids are natural first-generation results of independent hybridization events. Based on the morphology, spatial distribution, DNA sequence data, pollen viability and cytological observations, we hypothesize that E. ×hybrida is derived from natural hybridization events between E. lineolatum var. majus (♀) and E. platyphylloides (♂).

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3

KAPER, Thijs, Stan J. J. BROUNS, Ans C. M. GEERLING, Willem M. DE VOS, and John VAN der OOST. "DNA family shuffling of hyperthermostable β-glycosidases." Biochemical Journal 368, no. 2 (December 1, 2002): 461–70. http://dx.doi.org/10.1042/bj20020726.

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The structural compatibility of two hyperthermostable family 1 glycoside hydrolases, Pyrococcus furiosus CelB and Sulfolobus solfataricus LacS, as well as their kinetic potential were studied by construction of a library of 2048 hybrid β-glycosidases using DNA family shuffling. The hybrids were tested for their thermostability, ability to hydrolyse lactose and sensitivity towards inhibition by glucose. Three screening rounds at 70°C led to the isolation of three high-performance hybrid enzymes (hybrid 11, 18 and 20) that had 1.5—3.5-fold and 3.5—8.6-fold increased lactose hydrolysis rates compared with parental CelB and LacS respectively. The three variants were the result of a single crossover event, which gave rise to hybrids with a LacS N-terminus and a main CelB sequence. Constructed three-dimensional models of the hybrid enzymes revealed that the catalytic (βα)8-barrel was composed of both LacS and CelB elements. In addition, an extra intersubunit hydrogen bond in hybrids 18 and 20 might explain their superior stability over hybrid 11. This study demonstrates that extremely thermostable enzymes with limited homology and different mechanisms of stabilization can be efficiently shuffled to form stable hybrids with improved catalytic features.

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4

Xu, B., and D. A. Clayton. "A persistent RNA-DNA hybrid is formed during transcription at a phylogenetically conserved mitochondrial DNA sequence." Molecular and Cellular Biology 15, no. 1 (January 1995): 580–89. http://dx.doi.org/10.1128/mcb.15.1.580.

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Critical features of the mitochondrial leading-strand DNA replication origin are conserved from Saccharomyces cerevisiae to humans. These include a promoter and a downstream GC-rich sequence block (CSBII) that encodes rGs within the primer RNA. During in vitro transcription at yeast mitochondrial replication origins, there is stable and persistent RNA-DNA hybrid formation that begins at the 5' end of the rG region. The short rG-dC sequence is the necessary and sufficient nucleic acid element for establishing stable hybrids, and the presence of rGs within the RNA strand of the RNA-DNA hybrid is required. The efficiency of hybrid formation depends on the length of RNA synthesized 5' to CSBII and the type of RNA polymerase employed. Once made, the RNA strand of an RNA-DNA hybrid can serve as an effective primer for mitochondrial DNA polymerase. These results reveal a new mechanism for persistent RNA-DNA hybrid formation and suggest a step in priming mitochondrial DNA replication that requires both mitochondrial RNA polymerase and an rG-dC sequence-specific event to form an extensive RNA-DNA hybrid.

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5

Koroma, Alie Patrick, Raymond Jones, and Pawel Michalak. "Snapshot of DNA methylation changes associated with hybridization in Xenopus." Physiological Genomics 43, no. 22 (November 2011): 1276–80. http://dx.doi.org/10.1152/physiolgenomics.00110.2011.

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Hybridization often results in dramatic genome reconfigurations including epigenetic changes that control gene expression. Here we survey methylation patterns of interspecific Xenopus F1 hybrids relative to parental species X. laevis and X. muelleri, using methyl-sensitive amplification polymorphisms (MSAPs). Out of a total of 546 MSAP markers, 364 were effective in elucidating the difference in methylation patterns between the hybrids and the parental species. Principal coordinate analysis of methylated fragments revealed four distinct clusters with the two parental species separate from hybrid males and females. On average, hybrids were characterized by a higher proportion (70.6%) of methylated fragments compared with the parental species (64.5%), and this difference was consistent with previously observed disruptions of hybrid transcriptomes. The proportion of methylated fragments did not correlate with variation in genome size, as measured with flow cytometry. The levels of methylation in sterile hybrid males (73.8%) were higher than in fertile hybrid females (68.6%), but this difference was not statistically significant. A total of 76 methylated fragments (20.9%) were hybrid-unique, presumably originating from methylation alterations in hybrid genomes.

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6

Mangalam, Anand P., John Simonsen, and Albert S. Benight. "Cellulose/DNA Hybrid Nanomaterials." Biomacromolecules 10, no. 3 (March 9, 2009): 497–504. http://dx.doi.org/10.1021/bm800925x.

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7

Cheng, Enjun, Yulin Li, Zhongqiang Yang, Zhaoxiang Deng, and Dongsheng Liu. "DNA-SWNT hybrid hydrogel." Chemical Communications 47, no. 19 (2011): 5545. http://dx.doi.org/10.1039/c1cc11028d.

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8

Rioz-Martínez, Ana, and Gerard Roelfes. "DNA-based hybrid catalysis." Current Opinion in Chemical Biology 25 (April 2015): 80–87. http://dx.doi.org/10.1016/j.cbpa.2014.12.033.

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9

KONSTANTINOVIC, MIROSLAV, VESNA MAKSIMOVIC, GORDANA NIKCEVIC, and VLADIMIR GLISIN. "Hybrid PLtl Promoter with Dual Regulation Control." DNA and Cell Biology 10, no. 5 (June 1991): 389–95. http://dx.doi.org/10.1089/dna.1991.10.389.

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10

SUYAMA, AKIRA. "DNA Computing. 4. Hardware of Hybrid DNA Computer." Journal of the Institute of Electrical Engineers of Japan 122, no. 3 (2002): 160–63. http://dx.doi.org/10.1541/ieejjournal.122.160.

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11

Barati Farimani, Amir, Payam Dibaeinia, and Narayana R. Aluru. "DNA Origami–Graphene Hybrid Nanopore for DNA Detection." ACS Applied Materials & Interfaces 9, no. 1 (December 22, 2016): 92–100. http://dx.doi.org/10.1021/acsami.6b11001.

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12

Kawanabe, Takahiro, Sonoko Ishikura, Naomi Miyaji, Taku Sasaki, Li Min Wu, Etsuko Itabashi, Satoko Takada, et al. "Role of DNA methylation in hybrid vigor in Arabidopsis thaliana." Proceedings of the National Academy of Sciences 113, no. 43 (October 7, 2016): E6704—E6711. http://dx.doi.org/10.1073/pnas.1613372113.

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Hybrid vigor or heterosis refers to the superior performance of F1 hybrid plants over their parents. Heterosis is particularly important in the production systems of major crops. Recent studies have suggested that epigenetic regulation such as DNA methylation is involved in heterosis, but the molecular mechanism of heterosis is still unclear. To address the epigenetic contribution to heterosis in Arabidopsis thaliana, we used mutant genes that have roles in DNA methylation. Hybrids between C24 and Columbia-0 (Col) without RNA polymerase IV (Pol IV) or methyltransferase I (MET1) function did not reduce the level of biomass heterosis (as evaluated by rosette diameter). Hybrids with a mutation in decrease in dna methylation 1 (ddm1) showed a decreased heterosis level. Vegetative heterosis in the ddm1 mutant hybrid was reduced but not eliminated; a complete reduction could result if there was a change in methylation at all loci critical for generating the level of heterosis, whereas if only a proportion of the loci have methylation changes there may only be a partial reduction in heterosis.

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13

Arnott, Struther, R. Chandrasekaran, R. P. Millane, and Hye-Shin Park. "DNA-RNA hybrid secondary structures." Journal of Molecular Biology 188, no. 4 (April 1986): 631–40. http://dx.doi.org/10.1016/s0022-2836(86)80011-0.

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14

Eleutério Jr., José, Ivna Cavalcante Barros, Diane Isabelle Magno Cavalcante, Renata Mirian Nunes Eleutério, and Paulo César Giraldo. "HPV-DNA Hybrid Capture Test." Acta Cytologica 54, no. 4 (2010): 546–50. http://dx.doi.org/10.1159/000325175.

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15

Lorenz, Ronny, Ivo L. Hofacker, and Stephan H. Bernhart. "Folding RNA/DNA hybrid duplexes." Bioinformatics 28, no. 19 (July 24, 2012): 2530–31. http://dx.doi.org/10.1093/bioinformatics/bts466.

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16

Cui, Chunzhi, Dong Hyuk Park, and Dong June Ahn. "Organic Semiconductor–DNA Hybrid Assemblies." Advanced Materials 32, no. 51 (October 9, 2020): 2002213. http://dx.doi.org/10.1002/adma.202002213.

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17

E, Beeram. "Mini review on Protein – Protein and DNA/RNA – protein interactions in biology." Asploro Journal of Biomedical and Clinical Case Reports 2, no. 2 (October 29, 2019): 82–83. http://dx.doi.org/10.36502/2019/asjbccr.6165.

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RNase H1 generally processes the RNA- DNA hybrids through non specific interaction between HBD and the ds RNA/DNA hybrid. There are no direct protein- protein interactions between the hybrid and HBD of RNase H1. The DNA binding region is highly conserved compared to RNA binding region and the Kd for RNA/DNA hybrid is less compared to ds RNA than to that of ds DNA [1]. HBD increases the processivity of RNase H1 and mutations in RNA binding region is tolerated compared to DBR. The RNA interacts between ɑ2 and β3 region with in the loop and with the protein in shallower minor groove.

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18

Trucco, Federico, Tatiana Tatum, Kenneth R. Robertson, A. Lane Rayburn, and Patrick J. Tranel. "Characterization of Waterhemp (Amaranthus tuberculatus) × Smooth Pigweed (A. hybridus) F1Hybrids." Weed Technology 20, no. 1 (March 2006): 14–22. http://dx.doi.org/10.1614/wt-05-018r.1.

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In the state of Illinois, waterhemp and smooth pigweed are among the worst agricultural weeds. Previous research shows high potential for hybridization between these two species. However, the actual occurrence of hybrids in natural settings is still uncertain. Morphological similarity between hybrids and waterhemp makes field surveys of hybrids difficult to conduct. The main purpose of this study was to characterize the morphology of waterhemp × smooth pigweed F1hybrids, emphasizing evaluation of characters that may allow for hybrid discrimination in fieldAmaranthuscommunities. Concurrently, the study characterized hybrid reproductive fitness, chromosome number, and DNA content. To accomplish this, hybrids were obtained from field crosses. A species-specific polymorphism in theALSgene was used to verify hybrid identity. Significant differences (α = 0.05) between hybrids and individuals of the parental species were observed for five staminate and five carpellate characters. Of these, five characters differentiated hybrids from waterhemp. However, clustering analyses using these characters indicated that morphological differences were not reliable enough, by themselves, for unambiguous hybrid identification. Also, hybrid homoploidy (2n= 32) with respect to parental species excluded chromosome counts in hybridity determinations. However, DNA content analysis may be used for such purpose. Hybrids had an average of 1.21 pg of DNA per 2C nucleus, a value intermediate to that of parental species. Hybrids produced 3.3 or 0.7% the seed output of parental and sibling waterhemp individuals, respectively. Percent micropollen in hybrids was 95-times greater than in parental species. Hybrid sterility appears to be the most reliable feature for hybrid discrimination when conducting field surveys. However, molecular and cytogenetic analyses as employed in this study may be desired for ultimate identity corroboration.

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19

Schütt, Sabine, Andrea R. Florl, Wei Shi, Myriam Hemberger, Annie Orth, Sabine Otto, Wolfgang A. Schulz, and Reinald H. Fundele. "DNA Methylation in Placentas of Interspecies Mouse Hybrids." Genetics 165, no. 1 (September 1, 2003): 223–28. http://dx.doi.org/10.1093/genetics/165.1.223.

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Abstract Interspecific hybridization in the genus Mus results in several hybrid dysgenesis effects, such as male sterility and X-linked placental dysplasia (IHPD). The genetic or molecular basis for the placental phenotypes is at present not clear. However, an extremely complex genetic system that has been hypothesized to be caused by major epigenetic changes on the X chromosome has been shown to be active. We have investigated DNA methylation of several single genes, Atrx, Esx1, Mecp2, Pem, Psx1, Vbp1, Pou3f4, and Cdx2, and, in addition, of LINE-1 and IAP repeat sequences, in placentas and tissues of fetal day 18 mouse interspecific hybrids. Our results show some tendency toward hypomethylation in the late gestation mouse placenta. However, no differential methylation was observed in hyper- and hypoplastic hybrid placentas when compared with normal-sized littermate placentas or intraspecific Mus musculus placentas of the same developmental stage. Thus, our results strongly suggest that generalized changes in methylation patterns do not occur in trophoblast cells of such hybrids.

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20

Warner, Darya. "Hybrid Matters: Art and Science as a New Epistemology." DNA and Cell Biology 41, no. 1 (January 1, 2022): 16–18. http://dx.doi.org/10.1089/dna.2021.0527.

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21

Rougerie, R., Jean Haxaire, Ian J. Kitching, and Paul D. N. Hebert. "DNA barcodes and morphology reveal a hybrid hawkmoth in Tahiti (Lepidoptera : Sphingidae)." Invertebrate Systematics 26, no. 6 (2012): 445. http://dx.doi.org/10.1071/is12029.

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Interspecific hybridisation is a rare but widespread phenomenon identified as a potential complicating factor for the identification of species through DNA barcoding. Hybrids can, however, also deceive morphology-based taxonomy, resulting in the description of invalid species based on hybrid specimens. As the result of an unexpected case of discordance between barcoding results and current morphology-based taxonomy, we discovered an example of such a hybrid ‘species’ in hawkmoths. By combining barcodes, morphology and a nuclear marker, we show that Gnathothlibus collardi Haxaire, 2002 is actually an F1 hybrid between two closely related species that co-occur on Tahiti. In accordance with the International Code of Zoological Nomenclature, the taxon G. collardi is thus invalid as a species. This study demonstrates the potential of DNA barcodes to detect overlooked hybrid taxa. With the growth of sequence libraries, we anticipate that more unsuspected hybrid species will be detected, particularly among those taxa that are very rare, such as those known from only the type specimen.

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22

Ma, Xuan, Feng Xing, Qingxiao Jia, Qinglu Zhang, Tong Hu, Baoguo Wu, Lin Shao, Yu Zhao, Qifa Zhang, and Dao-Xiu Zhou. "Parental variation in CHG methylation is associated with allelic-specific expression in elite hybrid rice." Plant Physiology 186, no. 2 (February 23, 2021): 1025–41. http://dx.doi.org/10.1093/plphys/kiab088.

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Abstract Heterosis refers to the superior performance of hybrid lines over inbred parental lines. Besides genetic variation, epigenetic differences between parental lines are suggested to contribute to heterosis. However, the precise nature and extent of differences between the parental epigenomes and the reprograming in hybrids that govern heterotic gene expression remain unclear. In this work, we analyzed DNA methylomes and transcriptomes of the widely cultivated and genetically studied elite hybrid rice (Oryza sativa) SY63, the reciprocal hybrid, and the parental varieties ZS97 and MH63, for which high-quality reference genomic sequences are available. We showed that the parental varieties displayed substantial variation in genic methylation at CG and CHG (H = A, C, or T) sequences. Compared with their parents, the hybrids displayed dynamic methylation variation during development. However, many parental differentially methylated regions (DMRs) at CG and CHG sites were maintained in the hybrid. Only a small fraction of the DMRs displayed non-additive DNA methylation variation, which, however, showed no overall correlation relationship with gene expression variation. In contrast, most of the allelic-specific expression (ASE) genes in the hybrid were associated with DNA methylation, and the ASE negatively associated with allelic-specific methylation (ASM) at CHG. These results revealed a specific DNA methylation reprogramming pattern in the hybrid rice and pointed to a role for parental CHG methylation divergence in ASE, which is associated with phenotype variation and hybrid vigor in several plant species.

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23

Zhang, Steven B., David Maguire, Mei Zhang, Yeping Tian, Shanmin Yang, Amy Zhang, Katherine Casey-Sawicki, et al. "Mitochondrial DNA and Functional Investigations into the Radiosensitivity of Four Mouse Strains." International Journal of Cell Biology 2014 (2014): 1–8. http://dx.doi.org/10.1155/2014/850460.

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We investigated whether genetic radiosensitivity-related changes in mtDNA/nDNA ratios are significant to mitochondrial function and if a material effect on mtDNA content and function exists. BALB/c (radiosensitive), C57BL/6 (radioresistant), and F1 hybrid mouse strains were exposed to total body irradiation. Hepatic genomic DNA was extracted, and mitochondria were isolated. Mitochondrial oxygen consumption, ROS, and calcium-induced mitochondrial swelling were measured. Radiation influenced strain-specific survivalin vivo. F1 hybrid survival was influenced by maternal input. Changes in mitochondrial content corresponded to survivalin vivoamong the 4 strains. Calcium-induced mitochondrial swelling was strain dependent. Isolated mitochondria from BALB/c mice were significantly more sensitive to calcium overload than mitochondria from C57BL/6 mice. Maternal input partially influenced the recovery effect of radiation on calcium-induced mitochondrial swelling in F1 hybrids; the hybrid with a radiosensitive maternal lineage exhibited a lower rate of recovery. Hybrids had a survival rate that was biased toward maternal input. mtDNA content and mitochondrial permeability transition pores (MPTP) measured in these strains before irradiation reflected a dominant input from the parent. After irradiation, the MPTP opened sooner in radiosensitive and hybrid strains, likely triggering intrinsic apoptotic pathways. These findings have important implications for translation into predictors of radiation sensitivity/resistance.

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24

Islam, M. M., M. E. Hoque, S. M. H. A. Rabbi, and M. S. Ali. "DNA Fingerprinting and Diversity Analysis of BRRI Hybrid Varieties and their Corresponding Parents." Plant Tissue Culture and Biotechnology 21, no. 2 (December 31, 2011): 189–98. http://dx.doi.org/10.3329/ptcb.v21i2.10242.

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DNA fingerprinting and genetic diversity of four Bangladesh Rice Research Institute (BRRI) hybrid varieties and their parental lines were carried out. A total of 73 microsatellite markers were tested for screening the genotypes. Among the 73 amplified products, 37% had polymorphic bands showing 81 alleles. The number of alleles per locus ranged from two (RM10) to eight (RM327), where average allele number was 4.333. The Polymorphism Information Contents (PIC) lied between 0.337 (RM10) and 0.852 (RM327). RM327 was the most robust marker providing the highest PIC value (0.852). Pair-wise genetic dissimilarity coefficient interaction showed that BRRI hybrids two was the most genetically distant from each other whereas BRRI hybrids one, three, four and their respective parents were very close. Cluster analysis based on Dices similarity coefficient UPGMA system grouped BRRI hybrid and their parental lines into four major clusters at 0.41 cut off similarity coefficient. Four BRRI hybrid varieties grouped into four distinct clusters along with their component lines indicating their genetic closeness. Key words: Hybrid rice, Diversity analysis, Microsatellite markers, DNA fingerprinting D. O. I. 10.3329/ptcb.v21i2.10242 Plant Tissue Cult. & Biotech. 21(2): 189-198, 2011 (December)

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25

Pettigrew, John D., and John A. W. Kirsch. "Base–compositional biases and the bat problem. I. DNA–hybridization melting curves based on AT– and GC–enriched tracers." Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences 353, no. 1367 (March 29, 1998): 369–79. http://dx.doi.org/10.1098/rstb.1998.0215.

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We explored the interordinal relationships of mammals using DNA–DNA hybridization, with particular reference to the much–debated problem of whether the megabats and microbats are more closely related to each other than the megabats are to primates. To try to improve resolution when taxa are distantly related and the melting points of hybrids are low and difficult to distinguish, we increased the GC–content of DNA by a fractionation method that used the same melting–point apparatus also used in the hybridization studies. When we used GC–rich DNA as the tracer to make hybrids, the melting point of the self–hybrid shifted to a higher temperature as expected, but the behaviour of heterologous hybrids varied with the taxa being compared. When the melting point of the heterologous hybrid also shifted to a higher temperature so that the two compared taxa maintained the same or proportional distance, we called this ‘following behaviour’, because the heterologous hybrid made with GC– tracer ‘followed’ the GC– self– to higher temperatures. We also commonly saw anomalous behaviour, where the melting point of the heterologous hybrid shifted to a lower temperature when compared with an AT– hybrid. In these anomalous cases, the distance measured between the taxa increased markedly as a result of GC–, indicating that an underestimate of distance may have resulted from AT– in DNA. This inference was supported by the finding that it was rare to observe a decrease in measured distance between taxa using GC– DNA, but very common to find an increase as would be expected from the generally higher AT–contents of eutherian DNAs. Moreover, the most extreme cases, where distances changed most using GC–rich DNA, were usually those involving comparisons between taxa known to have the most extreme AT–biases among mammals, such as the megabats and rhinolophoid (including megadermatid) microbats. Our results show that AT–bias in eutherian DNA leads to consistent underestimates of measured differences between taxa with extreme AT–biases.

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26

Suresh, Gorle, and U. Deva Priyakumar. "DNA–RNA hybrid duplexes with decreasing pyrimidine content in the DNA strand provide structural snapshots for the A- to B-form conformational transition of nucleic acids." Phys. Chem. Chem. Phys. 16, no. 34 (2014): 18148–55. http://dx.doi.org/10.1039/c4cp02478h.

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27

Wang, Lijun, Shusuke Oura, and Yongbo Wu. "Antioxidant potential of tea assessed by optical absorption spectroscopy in DNA-encased carbon nanotubes." Czech Journal of Food Sciences 39, No. 1 (February 26, 2021): 23–28. http://dx.doi.org/10.17221/135/2020-cjfs.

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It is essential to develop a simple method to assess food quality quantitatively. Available methods primarily rely on nanotechnology and offer high selectivity and sensitivity. In this study, we aimed to develop a sensitive nanoprobe, and, to this end, a double-stranded DNA-encased HiPco carbon nanotube (dsDNA-HiPco) hybrid was prepared and used to evaluate the antioxidant potential of a Chinese tea against hydrogen peroxide (H2O2) with a range of irradiation wavelengths. The morphology and dispersion of the hybrids were analysed using atomic force microscopy, which showed that dsDNA wrapped on the SWCNT surface well and homogeneous dispersion of the rod-shaped tubes while the concentration of dsDNA was 1 mg mL–1. The antioxidant effect of Chinese tea was evaluated by using near-infrared absorption and photoluminescence of the hybrid. Experimental results revealed that the tea exerted excellent antioxidant effects when the hybrid was pre-treated with 0.03% wt H2O2. Catechin present in the Chinese tea played a pivotal role in exerting the antioxidant effects. Therefore, a simple detection method proposed herein can be successfully applied in various fields, including biology, medicine, and the food industry.

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28

Zhi, Chengxin, Zheng-yu Long, Andrzej Manikowski, Jeanne Comstock, Wei-Chu Xu, Neal C. Brown, Paul M. Tarantino,, et al. "Hybrid Antibacterials. DNA Polymerase−Topoisomerase Inhibitors." Journal of Medicinal Chemistry 49, no. 4 (February 2006): 1455–65. http://dx.doi.org/10.1021/jm0510023.

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29

RAWLS, REBECCA. "Hybrid DNA-RNA efficiently repairs gene." Chemical & Engineering News 74, no. 37 (September 9, 1996): 11. http://dx.doi.org/10.1021/cen-v074n037.p011.

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30

Balasubramanian, Ramkumar, Sohini Pal, Himanshu Joshi, Anjana Rao, Akshay Naik, Manoj Varma, Banani Chakraborty, and Prabal K. Maiti. "DNA Translocation through Hybrid Bilayer Nanopores." Journal of Physical Chemistry C 123, no. 18 (April 23, 2019): 11908–16. http://dx.doi.org/10.1021/acs.jpcc.9b00399.

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31

Praetorius, Florian, and Hendrik Dietz. "Genetically Encoded DNA-Protein Hybrid Origami." Biophysical Journal 112, no. 3 (February 2017): 25a. http://dx.doi.org/10.1016/j.bpj.2016.11.171.

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32

Cassell, Alan M., Walter A. Scrivens, and James M. Tour. "Assembly of DNA/Fullerene Hybrid Materials." Angewandte Chemie International Edition 37, no. 11 (June 19, 1998): 1528–31. http://dx.doi.org/10.1002/(sici)1521-3773(19980619)37:11<1528::aid-anie1528>3.0.co;2-q.

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33

Cassell, Alan M, Walter A Scrivens, and James M Tour. "Aufbau von DNA/Fulleren-Hybrid-materialien." Angewandte Chemie 110, no. 11 (June 5, 1998): 1670–72. http://dx.doi.org/10.1002/(sici)1521-3757(19980605)110:11<1670::aid-ange1670>3.0.co;2-8.

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34

Allan, Norman. "Ultradilute hybrid DNA dot-blot phenomenon." Homeopathy 96, no. 2 (April 2007): 134. http://dx.doi.org/10.1016/j.homp.2007.02.005.

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35

Kim, Eunjung, Shweta Agarwal, Nayoung Kim, Fredrik Sydow Hage, Vincent Leonardo, Amy Gelmi, and Molly M. Stevens. "Bioinspired Fabrication of DNA–Inorganic Hybrid Composites Using Synthetic DNA." ACS Nano 13, no. 3 (February 11, 2019): 2888–900. http://dx.doi.org/10.1021/acsnano.8b06492.

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36

Yoo, Chang-Hyuk, Seungwon Jung, Jaehyun Bae, Gunn Kim, Jisoon Ihm, and Junghoon Lee. "DNA aptamer release from the DNA–SWNT hybrid by protein recognition." Chemical Communications 52, no. 13 (2016): 2784–87. http://dx.doi.org/10.1039/c5cc07726e.

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37

Hewitt, Sarah K., Kobchai Duangrattanalert, Tim Burgis, Leo A. H. Zeef, Samina Naseeb, and Daniela Delneri. "Plasticity of Mitochondrial DNA Inheritance and its Impact on Nuclear Gene Transcription in Yeast Hybrids." Microorganisms 8, no. 4 (March 31, 2020): 494. http://dx.doi.org/10.3390/microorganisms8040494.

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Mitochondrial DNA (mtDNA) in yeast is biparentally inherited, but colonies rapidly lose one type of parental mtDNA, thus becoming homoplasmic. Therefore, hybrids between the yeast species possess two homologous nuclear genomes, but only one type of mitochondrial DNA. We hypothesise that the choice of mtDNA retention is influenced by its contribution to hybrid fitness in different environments, and the allelic expression of the two nuclear sub-genomes is affected by the presence of different mtDNAs in hybrids. Saccharomyces cerevisiae/S. uvarum hybrids preferentially retained S. uvarum mtDNA when formed on rich media at colder temperatures, while S. cerevisiae mtDNA was primarily retained on non-fermentable carbon source, at any temperature. Transcriptome data for hybrids harbouring different mtDNA showed a strong environmentally dependent allele preference, which was more important in respiratory conditions. Co-expression analysis for specific biological functions revealed a clear pattern of concerted allelic transcription within the same allele type, which supports the notion that the hybrid cell works preferentially with one set of parental alleles (or the other) for different cellular functions. Given that the type of mtDNA retained in hybrids affects both nuclear expression and fitness, it might play a role in driving hybrid genome evolution in terms of gene retention and loss.

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Tamura, Mihoko, Ryutaro Tao, and Akira Sugiura. "Production of Interspecific Hybrids of Persimmon by Protoplast Fusion." HortScience 32, no. 3 (June 1997): 442A—442. http://dx.doi.org/10.21273/hortsci.32.3.442a.

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Interspecific hybrids between Diospyros glandulosa (2n = 2x = 30) and D. kaki cv. Jiro (2n = 6x = 90) were produced by electrofusion of protoplasts. Protoplasts were isolated from calli derived from leaf primordia, fused electrically, and cultured by agarose-bead culture using modified KM8p medium. Relative nuclear DNA contents of calli derived from fusion-treated protoplasts were determined by flow cytometry. One-hundred-forty-nine of 166 calli obtained had the nuclear DNA content of the sum of those of D. glandulosa and D. kaki cv. Jiro. RAPD analysis showed that the 149 callus lines yielded specific bands for both D. glandulosa and D. kaki cv. Jiro and they appeared to be interspecific somatic hybrid calli. Shoots were regenerated from 63 of the 149 interspecific hybrid calli. PCR-RFLP of chloroplast DNA analysis, flow cytometric determination of nuclear DNA content, and RAPD analysis revealed that the 63 interspecific hybrid shoot lines contained nuclear genome from both the parents but only chloroplast genome from D. glandulosa. Microscopic observation of root tip cells confirmed that somatic chromosome numbers of the interspecific hybrids were 2n = 8x = 120.

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Kondratskaya, I. P., A. N. Yukhimuk, V. A. Stolepchenko, O. V. Chizhik, Z. G. Kozlovskaya, P. P. Vasko, and V. N. Reshetnikov. "The creating of intergenetic hybrids of festulolium of Festuca arundinacea morphotipe with the use of post-genomic technologies and DNA-marking." Faktori eksperimental'noi evolucii organizmiv 25 (August 30, 2019): 253–59. http://dx.doi.org/10.7124/feeo.v25.1172.

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Aim. To form the varietal population of festulolium intergeneric hybrids of Festuca arundinacea morphotype. To carry out DNA-labeling of created festulolium hybrid plants and parental forms. Methods. The festulolium intergeneric hybrid’s creation was carried out by embryo culture method from an immature caryopsis by growing on a nutrient medium. For the plant genotypes labeling the multilocus primers associated with coding DNA regions (Start Codon Targeted (SCoT) Polymorphism), SRAP (Sequence-related amplified polymorphism) have been selected. Results. The viable plants of intergeneric festulolium hybrids of Festuca arundinacea morphotype have been obtained. To select the best festulolium biotypes for variety populations with high feed and seed productivity formation. A system for hybrid plants genotypes and their parental forms registration in the form of molecular genetic passports have been elaborated. The genetic passports reflects the allele’s composition in loci associated with DNA coding sequences. Conclusions. The best biotypes with economically valuable traits were selected and included in the further selection process. The molecular genetic passports of hybrid festulolium plants and parental forms were composed. Keywords: festulolium, immature caryopsis, biotypes, DNA, PCR, molecular genetic passports.

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N'soukpoé-Kossi, Christophe N., Caroline Descôteaux, Éric Asselin, Joseph Bariyanga, Heidar-Ali Tajmir-Riahi, and Gervais Bérubé. "Transfer RNA Bindings to Antitumor Estradiol-Platinum(II) Hybrid and Cisplatin." DNA and Cell Biology 27, no. 6 (June 2008): 337–43. http://dx.doi.org/10.1089/dna.2008.0727.

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Lohman, Gregory J. S., Yinhua Zhang, Alexander M. Zhelkovsky, Eric J. Cantor, and Thomas C. Evans. "Efficient DNA ligation in DNA–RNA hybrid helices by Chlorella virus DNA ligase." Nucleic Acids Research 42, no. 3 (November 6, 2013): 1831–44. http://dx.doi.org/10.1093/nar/gkt1032.

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Lohman, G. J., Y. Zhang, A. M. Zhelkovsky, E. J. Cantor, and T. C. Evans. "Efficient DNA ligation in DNA-RNA hybrid helices by Chlorella virus DNA ligase." Nucleic Acids Research 42, no. 18 (October 7, 2014): 11846. http://dx.doi.org/10.1093/nar/gku792.

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Reis, Gabriela Barreto dos, Larissa Fonseca Andrade-Vieira, José Marcello Salabert de Campos, Antonio Vander Pereira, and Lisete Chamma Davide. "KARYOTYPE ALTERATIONS AFTER HYBRIDIZATION BETWEEN Pennisetum purpureum AND Pennisetum glaucum." Ciência e Agrotecnologia 39, no. 5 (October 2015): 443–54. http://dx.doi.org/10.1590/s1413-70542015000500003.

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ABSTRACTNapier grass and pearl millet are tropical forages from the genus Pennisetum. The variability in those species is explored in breeding programs of forages, as well as in the production of interspecific hybrids. Hybridization is a phenomenon that leads to intergenomic conflicts following the elimination of genomic sequences. In this sense, the present work aimed to study the genomic alterations occurring after interspecific hybridization of pearl millet and Napier grass with the use of cytogenetics and flow cytometry tools. These methods allowed the evaluation of chromosome morphometry, DNA content and genomic ratio in pearl millet, Napier grass and hybrids. It was observed that pearl millet and Napier grass have chromosomes with superposed size. The hybrid presents chromosomes that are smaller than expected, leading to karyotype alterations. Additionally, comparing the DNA content of parents and hybrids, loss of DNA content was demonstrated. Further, changes in the pearl millet and Napier grass genome ratio were also verified in the hybrid nucleus. Moreover, genomic rearrangements were shown to occur through karyotype alterations in the hybrid.

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Ojasalo, Sofia, Petteri Piskunen, Boxuan Shen, Mauri A. Kostiainen, and Veikko Linko. "Hybrid Nanoassemblies from Viruses and DNA Nanostructures." Nanomaterials 11, no. 6 (May 27, 2021): 1413. http://dx.doi.org/10.3390/nano11061413.

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Viruses are among the most intriguing nanostructures found in nature. Their atomically precise shapes and unique biological properties, especially in protecting and transferring genetic information, have enabled a plethora of biomedical applications. On the other hand, structural DNA nanotechnology has recently emerged as a highly useful tool to create programmable nanoscale structures. They can be extended to user defined devices to exhibit a wide range of static, as well as dynamic functions. In this review, we feature the recent development of virus-DNA hybrid materials. Such structures exhibit the best features of both worlds by combining the biological properties of viruses with the highly controlled assembly properties of DNA. We present how the DNA shapes can act as “structured” genomic material and direct the formation of virus capsid proteins or be encapsulated inside symmetrical capsids. Tobacco mosaic virus-DNA hybrids are discussed as the examples of dynamic systems and directed formation of conjugates. Finally, we highlight virus-mimicking approaches based on lipid- and protein-coated DNA structures that may elicit enhanced stability, immunocompatibility and delivery properties. This development also paves the way for DNA-based vaccines as the programmable nano-objects can be used for controlling immune cell activation.

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Chen, Liangyu, Yanyu Zhu, Xiaobo Ren, Dan Yao, Yang Song, Sujie Fan, Xueying Li, et al. "Heterosis and Differential DNA Methylation in Soybean Hybrids and Their Parental Lines." Plants 11, no. 9 (April 22, 2022): 1136. http://dx.doi.org/10.3390/plants11091136.

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Heterosis is an important biological phenomenon and is widely applied to increase agricultural productivity. However, the underlying molecular mechanisms of heterosis are still unclear. Here we constructed three combinations of reciprocal hybrids of soybean, and subsequently used MethylRAD-seq to detect CCGG and CCWGG (W = A or T) methylation in the whole genome of these hybrids and their parents at the middle development period of contemporary seed. We were able to prove that changes in DNA methylation patterns occurred in immature hybrid seeds and the parental variation was to some degree responsible for differential expression between the reciprocal hybrids. Non-additive differential methylation sites (DMSs) were also identified in large numbers in hybrids. Interestingly, most of these DMSs were hyper-methylated and were more concentrated in gene regions than the natural distribution of the methylated sites. Further analysis of the non-additive DMSs located in gene regions exhibited their participation in various biological processes, especially those related to transcriptional regulation and hormonal function. These results revealed DNA methylation reprogramming pattern in the hybrid soybean, which is associated with phenotypic variation and heterosis initiation.

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Gillespie, F. P., T. H. Hong, and J. M. Eisenstadt. "Transcription and translation of mitochondrial DNA in interspecific somatic cell hybrids." Molecular and Cellular Biology 6, no. 6 (June 1986): 1951–57. http://dx.doi.org/10.1128/mcb.6.6.1951-1957.1986.

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We examined the mitochondrial transcription and translation products of somatic cell hybrids constructed by the fusion of Chinese hamster and mouse cells. The hybrid cell lines OAC-k, OAC-l, and OAC-m contain approximately equal amounts of hamster and mouse mitochondrial DNA and produced mitochondrial rRNA from both parental species in the same ratio. Cell lines OAC-k, OAC-l, and OAC-m also produced poly(A)+ mouse mitochondrial RNA transcripts comparable in complexity and quantity to poly(A)+ RNA from the mouse parent. However, the overall level of poly(A)+ hamster mitochondrial RNA from these hybrids was significantly reduced compared with that from the hamster parent. The hybrid cells also lacked several poly(A)+ RNA species found in the hamster parent, but contained additional minor transcripts. The mitochondrially coded proteins of the OAC-k, OAC-l, and OAC-m cells were predominantly encoded by the mouse mitochondrial DNA.

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Gillespie, F. P., T. H. Hong, and J. M. Eisenstadt. "Transcription and translation of mitochondrial DNA in interspecific somatic cell hybrids." Molecular and Cellular Biology 6, no. 6 (June 1986): 1951–57. http://dx.doi.org/10.1128/mcb.6.6.1951.

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We examined the mitochondrial transcription and translation products of somatic cell hybrids constructed by the fusion of Chinese hamster and mouse cells. The hybrid cell lines OAC-k, OAC-l, and OAC-m contain approximately equal amounts of hamster and mouse mitochondrial DNA and produced mitochondrial rRNA from both parental species in the same ratio. Cell lines OAC-k, OAC-l, and OAC-m also produced poly(A)+ mouse mitochondrial RNA transcripts comparable in complexity and quantity to poly(A)+ RNA from the mouse parent. However, the overall level of poly(A)+ hamster mitochondrial RNA from these hybrids was significantly reduced compared with that from the hamster parent. The hybrid cells also lacked several poly(A)+ RNA species found in the hamster parent, but contained additional minor transcripts. The mitochondrially coded proteins of the OAC-k, OAC-l, and OAC-m cells were predominantly encoded by the mouse mitochondrial DNA.

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Zimmer, Anjali D., and Douglas Koshland. "Differential roles of the RNases H in preventing chromosome instability." Proceedings of the National Academy of Sciences 113, no. 43 (October 10, 2016): 12220–25. http://dx.doi.org/10.1073/pnas.1613448113.

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DNA:RNA hybrids can lead to DNA damage and genome instability. This damage can be prevented by degradation of the RNA in the hybrid by two evolutionarily conserved enzymes, RNase H1 and H2. Indeed, RNase H-deficient cells have increased chromosomal rearrangements. However, the quantitative and spatial contributions of the individual enzymes to hybrid removal have been unclear. Additionally, RNase H2 can remove single ribonucleotides misincorporated into DNA during replication. The relative contribution of DNA:RNA hybrids and misincorporated ribonucleotides to chromosome instability also was uncertain. To address these issues, we studied the frequency and location of loss-of-heterozygosity (LOH) events on chromosome III in Saccharomyces cerevisiae strains that were defective for RNase H1, H2, or both. We showed that RNase H2 plays the major role in preventing chromosome III instability through its hybrid-removal activity. Furthermore, RNase H2 acts pervasively at many hybrids along the chromosome. In contrast, RNase H1 acts to prevent LOH within a small region of chromosome III where the instability is dependent upon two hybrid-prone sequences. This restriction of RNase H1 activity to a subset of hybrids is not the result of its constrained localization, because we found it at hybrids genome-wide. This result suggests that the genome-protection activity of RNase H1 is regulated at a step after hybrid recognition. The global function of RNase H2 and the region-specific function of RNase H1 provide insight into why these enzymes with overlapping hybrid-removal activities have been conserved throughout evolution.

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Sun, Lanlan, Yonghai Song, Li Wang, Yujing Sun, Cunlan Guo, Zhelin Liu, and Zhuang Li. "DNA-Templated Gold Nanoparticles Formation." Journal of Nanoscience and Nanotechnology 8, no. 9 (September 1, 2008): 4415–23. http://dx.doi.org/10.1166/jnn.2008.270.

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The interaction between HAuCl4 and DNA has enabled creation of DNA-templated gold nanoparticles without formation of large nanoparticles. It was found that spheral DNA-HAuCl4 hybrid of 8.7nm in diameter, flower-like DNA-HAuCl4 hybrid, nanoparticles chains and nanoparticles network of DNA-HAuCl4 hybrid could be obtained by varying the reaction conditions, including DNA concentration and reaction temperature. The intermediate product was investigated by shortening the reaction time of DNA and HAuCl4, and the obtained nanoparticles preserved a small DNA segment, which indicated that the reaction between DNA and HAuCl4 had a process. The addition of reduction reagent resulted in DNA-templated gold nanoparticles and nanoflowers, respectively. UV-vis absorption spectra were used to characterize the DNA-HAuCl4 hybrid and the gold nanostructures templated on DNA, and XPS spectra were used to compare the composition of DNA-Au(III) complex and gold nanoparticles. AFM and TEM results revealed that the spheral gold nanoparticles of about 11 nm in size and flower-like gold nanoparticles were formed after the addition of NaBH4.

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Guzzo-Pernell, Nancy, and Geoffrey W. Tregear. "Triple helical DNA formation by a hydrophobic oligonucleotide-peptide hybrid molecule." Australian Journal of Chemistry 53, no. 8 (2000): 699. http://dx.doi.org/10.1071/ch00114.

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Stable triple helical DNA formation with triplex forming oligonucleotide–peptide hybrids, containing hydrophobic peptides, has previously been difficult to achieve. We report hereon stable triplexation with an oligonucleotide–peptide hybrid containing a hydrophobic peptide. The peptide of interest is the gp41b peptide, which is derived from the hydrophobic terminal domain of the HIV transmembrane glycoprotein gp41. Triplex forming oligonucleotides conjugated to the gp41b peptide were prepared with and without intramolecular spacer linkers. Hybrids with appropriate spacers formed stable triplexes whereas those without the linkers did not. Oligonucleotide–peptide conjugates have several applications mainly in control of gene expression, with the peptide enhancing intracellular delivery of the oligonucleotide. The gp41b peptide is one of a number of candidate peptides considered to be potential delivery vectors. Hence, the data presented here may prove to be useful in designing such conjugates. Our data also extend the list of DNA structures known to stabilize triplexes and suggest that triplexation by oligonucleotide–peptide hybrids may be peptide sequence dependent.

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