Journal articles: 'Random sequence DNA'

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Sperling, Linda, Philippe Dessen, Marek Zagulski, Ron E. Pearlman, Andrzey Migdalski, Robert Gromadka, Marine Froissard, Anne-Marie Keller, and Jean Cohen. "Random Sequencing of Paramecium Somatic DNA." Eukaryotic Cell 1, no. 3 (June 2002): 341–52. http://dx.doi.org/10.1128/ec.1.3.341-352.2002.

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ABSTRACT We report a random survey of 1 to 2% of the somatic genome of the free-living ciliate Paramecium tetraurelia by single-run sequencing of the ends of plasmid inserts. As in all ciliates, the germ line genome of Paramecium (100 to 200 Mb) is reproducibly rearranged at each sexual cycle to produce a somatic genome of expressed or potentially expressed genes, stripped of repeated sequences, transposons, and AT-rich unique sequence elements limited to the germ line. We found the somatic genome to be compact (>68% coding, estimated from the sequence of several complete library inserts) and to feature uniformly small introns (18 to 35 nucleotides). This facilitated gene discovery: 722 open reading frames (ORFs) were identified by similarity with known proteins, and 119 novel ORFs were tentatively identified by internal comparison of the data set. We determined the phylogenetic position of Paramecium with respect to eukaryotes whose genomes have been sequenced by the distance matrix neighbor-joining method by using random combined protein data from the project. The unrooted tree obtained is very robust and in excellent agreement with accepted topology, providing strong support for the quality and consistency of the data set. Our study demonstrates that a random survey of the somatic genome of Paramecium is a good strategy for gene discovery in this organism.

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Banfalvi, Gaspar. "Origin of Coding RNA from Random-Sequence RNA." DNA and Cell Biology 38, no. 3 (March 2019): 223–28. http://dx.doi.org/10.1089/dna.2018.4389.

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Hsu, Tai-Hsin, and Su-Long Nyeo. "Simple Deviation Analysis of Two-Dimensional Viral DNA Walks." Journal of Biological Systems 11, no. 03 (September 2003): 221–43. http://dx.doi.org/10.1142/s0218339003000841.

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We consider the method of two-dimensional DNA walks based on three independent groups of mapping rules for 21 DNA sequences of animal and plant viruses, and for the sequences of irrational and random numbers. This method provides a visualization tool for the determination of the regional abundance of nucleotides in DNA sequences. By defining a statistical deviation and a maximum-deviation ratio for a DNA walk, we find that the maximum-deviation ratios for the 21 viral DNA sequences are generally larger than those of the random-number sequences of same lengths. It is shown that the viral DNA sequences generally have the smallest maximum-deviations with the same mapping group, and that greater difference between CG and AT contents is associated with larger maximum-deviation ratio. Also it is possible to distinguish a viral DNA sequence from a random-number sequence if the lengths of the sequences are longer than 2000 base-pairs. Other possible applications of the two-dimensional DNA walks are mentioned.

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Liu, Chang, Vladimir Vigdorovich, Vivek Kapur, and Mitchell S. Abrahamsen. "A Random Survey of the Cryptosporidium parvum Genome." Infection and Immunity 67, no. 8 (August 1, 1999): 3960–69. http://dx.doi.org/10.1128/iai.67.8.3960-3969.1999.

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ABSTRACT Cryptosporidium parvum is an obligate intracellular pathogen responsible for widespread infections in humans and animals. The inability to obtain purified samples of this organism’s various developmental stages has limited the understanding of the biochemical mechanisms important for C. parvum development or host-parasite interaction. To identify C. parvum genes independent of their developmental expression, a random sequence analysis of the 10.4-megabase genome of C. parvum was undertaken. Total genomic DNA was sheared by nebulization, and fragments between 800 and 1,500 bp were gel purified and cloned into a plasmid vector. A total of 442 clones were randomly selected and subjected to automated sequencing by using one or two primers flanking the cloning site. In this way, 654 genomic survey sequences (GSSs) were generated, corresponding to >320 kb of genomic sequence. These sequences were assembled into 408 contigs containing >250 kb of unique sequence, representing ∼2.5% of the C. parvum genome. Comparison of the GSSs with sequences in the public DNA and protein databases revealed that 107 contigs (26%) displayed similarity to previously identified proteins and rRNA and tRNA genes. These included putative genes involved in the glycolytic pathway, DNA, RNA, and protein metabolism, and signal transduction pathways. The repetitive sequence elements identified included a telomere-like sequence containing hexamer repeats, 57 microsatellite-like elements composed of dinucleotide or trinucleotide repeats, and a direct repeat sequence. This study demonstrates that large-scale genomic sequencing is an efficient approach to analyze the organizational characteristics and information content of the C. parvum genome.

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Lee, Suk-Hwan. "DNA sequence watermarking based on random circular angle." Digital Signal Processing 25 (February 2014): 173–89. http://dx.doi.org/10.1016/j.dsp.2013.11.010.

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Schriefer, Lawrence A., Beth K. Gebauer, Lisa Q. Q. Qiu, Robert H. Waterston, and Richard K. Wilson. "Low pressure DNA shearing: a method for random DNA sequence analysis." Nucleic Acids Research 18, no. 24 (1990): 7455–56. http://dx.doi.org/10.1093/nar/18.24.7455.

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Oliphant, A. R., C. J. Brandl, and K. Struhl. "Defining the sequence specificity of DNA-binding proteins by selecting binding sites from random-sequence oligonucleotides: analysis of yeast GCN4 protein." Molecular and Cellular Biology 9, no. 7 (July 1989): 2944–49. http://dx.doi.org/10.1128/mcb.9.7.2944-2949.1989.

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We describe a new method for accurately defining the sequence recognition properties of DNA-binding proteins by selecting high-affinity binding sites from random-sequence DNA. The yeast transcriptional activator protein GCN4 was coupled to a Sepharose column, and binding sites were isolated by passing short, random-sequence oligonucleotides over the column and eluting them with increasing salt concentrations. Of 43 specifically bound oligonucleotides, 40 contained the symmetric sequence TGA(C/G)TCA, whereas the other 3 contained sequences matching six of these seven bases. The extreme preference for this 7-base-pair sequence suggests that each position directly contacts GCN4. The three nucleotide positions on each side of this core heptanucleotide also showed sequence preferences, indicating their effect on GCN4 binding. Interestingly, deviations in the core and a stronger sequence preference in the flanking region were found on one side of the central C . G base pair. Although GCN4 binds as a dimer, this asymmetry supports a model in which interactions on each side of the binding site are not equivalent. The random selection method should prove generally useful for defining the specificities of other DNA-binding proteins and for identifying putative target sequences from genomic DNA.

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Oliphant, A. R., C. J. Brandl, and K. Struhl. "Defining the sequence specificity of DNA-binding proteins by selecting binding sites from random-sequence oligonucleotides: analysis of yeast GCN4 protein." Molecular and Cellular Biology 9, no. 7 (July 1989): 2944–49. http://dx.doi.org/10.1128/mcb.9.7.2944.

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We describe a new method for accurately defining the sequence recognition properties of DNA-binding proteins by selecting high-affinity binding sites from random-sequence DNA. The yeast transcriptional activator protein GCN4 was coupled to a Sepharose column, and binding sites were isolated by passing short, random-sequence oligonucleotides over the column and eluting them with increasing salt concentrations. Of 43 specifically bound oligonucleotides, 40 contained the symmetric sequence TGA(C/G)TCA, whereas the other 3 contained sequences matching six of these seven bases. The extreme preference for this 7-base-pair sequence suggests that each position directly contacts GCN4. The three nucleotide positions on each side of this core heptanucleotide also showed sequence preferences, indicating their effect on GCN4 binding. Interestingly, deviations in the core and a stronger sequence preference in the flanking region were found on one side of the central C . G base pair. Although GCN4 binds as a dimer, this asymmetry supports a model in which interactions on each side of the binding site are not equivalent. The random selection method should prove generally useful for defining the specificities of other DNA-binding proteins and for identifying putative target sequences from genomic DNA.

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MAVROTHALASSITIS, GEORGE, GREGORY BEAL, and TAKIS S. PAPAS. "Defining Target Sequences of DNA-Binding Proteins by Random Selection and PCR: Determination of the GCN4 Binding Sequence Repertoire." DNA and Cell Biology 9, no. 10 (December 1990): 783–88. http://dx.doi.org/10.1089/dna.1990.9.783.

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Bellini, T., G. Zanchetta, T. P. Fraccia, R. Cerbino, E. Tsai, G. P. Smith, M. J. Moran, D. M. Walba, and N. A. Clark. "Liquid crystal self-assembly of random-sequence DNA oligomers." Proceedings of the National Academy of Sciences 109, no. 4 (January 10, 2012): 1110–15. http://dx.doi.org/10.1073/pnas.1117463109.

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11

Loomis, William F., and Michael E. Gilpin. "Neutral mutations and repetitive DNA." Bioscience Reports 7, no. 7 (July 1, 1987): 599–606. http://dx.doi.org/10.1007/bf01119778.

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We have previously shown that computer simulations of processes that generate selectively advantageous changes together with random duplications and deletions give rise to genomes with many different genes embedded in a large amount of dispensable DNA sequence. We now explore the consequences of neutral changes on the evolution of genomes. We follow the consequences of sequence divergences that are neutral when they occur in dispensable sequences or extra copies of genes present in multigene families. We find that when divergence occurs at about the same frequency as duplication/deletion events, genomes carry repetitive sequences in proportion to their size. Inspection of the genomes as they evolved showed that multigene families were generated by relatively recent duplications of single genes and so would be expected to be highly homogeneous.

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Sakakibara, Stacey M., and John E. Carlson. "DNA FINGERPRINTING IN RHODODENDRONS USING RANDOM AMPLIFIED POLYMORPHIC DNA." HortScience 31, no. 3 (June 1996): 323g—324. http://dx.doi.org/10.21273/hortsci.31.3.323g.

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Random amplified polymorphic DNA (RAPD) markers were evaluated for use in DNA fingerprinting of commercial Rhododendron cultivars. DNA was isolated from Rhododendron leaves and subjected to PCR amplification with single primers, 10 nucleotides in length, and of arbitrary sequence. Amplification products were visualized by agarose gel electrophoresis and ethidium bromide staining. Fingerprints were readily identifiable for a number of cultivars, and a high level of polymorphism was observed among clones of 10 rhododendron varieties. The technique was consistently reproducible in different trials using the thermocycler, between different thermocyclers, and using different DNA isolation from the same plant. This method will be applied to large-scale fingerprinting of Rhododendron cultivars and for distinguishing material propagated in tissue culture.

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13

CHEN, YAW-HWANG, SU-LONG NYEO, and JUI-PING YU. "POWER-LAWS IN THE COMPLETE SEQUENCES OF HUMAN GENOME." Journal of Biological Systems 13, no. 02 (June 2005): 105–15. http://dx.doi.org/10.1142/s0218339005001434.

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The distance distributions of the four types of bases A, C, G and T in the complete sequences of human genome are shown to have long-tail power-law but short-distance exponential behaviors. However, the random sequences with identical numbers of bases show only short-distance exponential behaviors. The DNA sequence of E. coli, which is much shorter than human's, is shown to exhibit essentially exponential behavior as its corresponding random sequence. Also, DNA sequence of human's with smaller C + G content is seen to enjoy longer power-law tail in its distributions of C and G. The coefficient in the exponential decaying function shows a linear dependent with the C + G content but the decay exponent in the power-law shows no such dependence.

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14

Huang, J., T. K. Blackwell, L. Kedes, and H. Weintraub. "Differences between MyoD DNA binding and activation site requirements revealed by functional random sequence selection." Molecular and Cellular Biology 16, no. 7 (July 1996): 3893–900. http://dx.doi.org/10.1128/mcb.16.7.3893.

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A method has been developed for selecting functional enhancer/promoter sites from random DNA sequences in higher eukaryotic cells. Of sequences that were thus selected for transcriptional activation by the muscle-specific basic helix-loop-helix protein MyoD, only a subset are similar to the preferred in vitro binding consensus, and in the same promoter context an optimal in vitro binding site was inactive. Other sequences with full transcriptional activity instead exhibit sequence preferences that, remarkably, are generally either identical or very similar to those found in naturally occurring muscle-specific promoters. This first systematic examination of the relation between DNA binding and transcriptional activation by basic helix-loop-helix proteins indicates that binding per se is necessary but not sufficient for transcriptional activation by MyoD and implies a requirement for other DNA sequence-dependent interactions or conformations at its binding site.

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15

Cohen, Dana. "General Designs Reveal Distinct Codes in Protein-Coding and Non-Coding Human DNA." Genes 13, no. 11 (October 28, 2022): 1970. http://dx.doi.org/10.3390/genes13111970.

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This study seeks to investigate distinct signatures and codes within different genomic sequence locations of the human genome. The promoter and other non-coding regions contain sites for the binding of biological particles, for processes such as transcription regulation. The specific rules and sequence codes that govern this remain poorly understood. To derive these (codes), the general designs of sequence are investigated. Genomic signatures are a powerful tool for assessing the general designs of sequence, and cross-comparing different genomic regions for their distinct sequence properties. Through these genomic signatures, the relative non-random properties of sequences are also assessed. Furthermore, a binary components analysis is carried out making use of information theory ideas, to study the RY (purine/pyrimidine), WS (weak/strong) and KM (keto/amino) signatures in the sequences. From this comparison, it is possible to identify the relative importance of these properties within the various protein-coding and non-coding genomic locations. The results show that coding DNA has a strongly non-random WS signature, which reflects the genetic code, and the hydrogen-bond base pairing of codon–anti-codon interactions. In contrast, non-coding locations, such as the promoter, contain a distinct genomic signature. A prominent feature throughout non-coding DNA is a highly non-random RY signature, which is very different in nature to coding DNA, and suggests a structural-based RY code. This marks progress towards deciphering the unknown code(s) in non-protein-coding DNA, and a further understanding of the coding DNA. Additionally, it unravels how DNA carries information. These findings have implications for the most fundamental principles of biology, including knowledge of gene regulation, development and disease.

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Syahrani, Iswaya Maalik. "ANALISIS PEMBANDINGAN TEKNIK ENSEMBLE SECARA BOOSTING(XGBOOST) DAN BAGGING (RANDOMFOREST) PADA KLASIFIKASI KATEGORI SAMBATAN SEKUENS DNA." Jurnal Penelitian Pos dan Informatika 9, no. 1 (October 1, 2019): 27. http://dx.doi.org/10.17933/jppi.2019.090103.

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<p class="JGI-AbstractIsi">Bioinformatics research currently supported by rapid growth of computation technology and algorithm. Ensemble decision tree is common method for classifying large and complex dataset such as DNA sequence. By implementing two classification methods with ensemble technique like xgboost and random Forest might improve the accuracy result on classifying DNA Sequence splice junction type. With 96,24% of xgboost accuracy and 95,11% of Random Forest accuracy, our conclusions the xgboost and random forest methods using right parameter setting are highly effective tool for classifying small example dataset. Analyzing both methods with their characteristics will give an overview on how they work to meet the needs in DNA splicing.</p>

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Siegel, Andrew F., Barbara Trask, Jared C. Roach, Gregory G. Mahairas, Leroy Hood, and Ger van den Engh. "Analysis of Sequence-Tagged-Connector Strategies for DNA Sequencing." Genome Research 9, no. 3 (March 1, 1999): 297–307. http://dx.doi.org/10.1101/gr.9.3.297.

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The BAC-end sequencing, or sequence-tagged-connector (STC), approach to genome sequencing involves sequencing the ends of BAC inserts to scatter sequence tags (STCs) randomly across the genome. Once any BAC or other large segment of DNA is sequenced to completion by conventional shotgun approaches, these STC tags can be used to identify a minimum tiling path of BAC clones overlapping the nucleation sequence for sequence extension. Here, we explore the properties of STC-sequencing strategies within a mathematical model of a random target with homologous repeats and imperfect sequencing technology to understand the consequences of varying various parameters on the incidence of problem clones and the cost of the sequencing project. Problem clones are defined as clones for which either (A) there is no identifiable overlapping STC to extend the sequence in a particular direction or (B) the identified STC with minimum overlap comes from a nonoverlapping clone, either owing to random false matches or repeat-family homology. Based on the minimum overlap, we estimate the number of clones to be entirely sequenced and, then, using cost estimates, identify the decision rule (the degree of sequence similarity required before a match is declared between an STC and a clone) to minimize overall sequencing cost. A method to optimize the overlap decision rule is highly desirable, because both the total cost and the number of problem clones are shown to be highly sensitive to this choice. For a target of 3 Gb containing ∼800 Mb of repeats with 85%–90% identity, we expect <10 problem clones with 15 times coverage by 150-kb clones. We derive the optimal redundancy and insert sizes of clone libraries for sequencing genomes of various sizes, from microbial to human. We estimate that establishing the resource of STCs as a means of identifying minimally overlapping clones represents only 1%–3% of the total cost of sequencing the human genome, and, up to a point of diminishing returns, a larger STC resource is associated with a smaller total sequencing cost.

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LIANG, S., M. P. SAMANTA, and B. A. BIEGEL. "cWINNOWER ALGORITHM FOR FINDING FUZZY DNA MOTIFS." Journal of Bioinformatics and Computational Biology 02, no. 01 (March 2004): 47–60. http://dx.doi.org/10.1142/s0219720004000466.

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The cWINNOWER algorithm detects fuzzy motifs in DNA sequences rich in proteinbinding signals. A signal is defined as any short nucleotide pattern having up to d mutations differing from a motif of length l. The algorithm finds such motifs if a clique consisting of a suffciently large number of mutated copies of the motif (i.e., the signals) is present in the DNA sequence. The cWINNOWER algorithm substantially improves the sensitivity of the winnower method of Pevzner and Sze by imposing a consensus constraint, enabling it to detect much weaker signals. We studied the minimum detectable clique size qc as a function of sequence length N for random sequences. We found that qc increases linearly with N for a fast version of the algorithm based on counting threemember sub-cliques. Imposing consensus constraints reduces qc by a factor of three in this case, which makes the algorithm dramatically more sensitive. Our most sensitive algorithm, which counts four-member sub-cliques, needs a minimum of only 13 signals to detect motifs in a sequence of length N=12,000 for (l,d)=(15,4).

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Gao, Jianbo, Yan Qi, Yinhe Cao, and Wen-wen Tung. "Protein Coding Sequence Identification by Simultaneously Characterizing the Periodic and Random Features of DNA Sequences." Journal of Biomedicine and Biotechnology 2005, no. 2 (2005): 139–46. http://dx.doi.org/10.1155/jbb.2005.139.

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Most codon indices used today are based on highly biased nonrandom usage of codons in coding regions. The background of a coding or noncoding DNA sequence, however, is fairly random, and can be characterized as a random fractal. When a gene-finding algorithm incorporates multiple sources of information about coding regions, it becomes more successful. It is thus highly desirable to develop new and efficient codon indices by simultaneously characterizing the fractal and periodic features of a DNA sequence. In this paper, we describe a novel way of achieving this goal. The efficiency of the new codon index is evaluated by studying all of the 16 yeast chromosomes. In particular, we show that the method automatically and correctly identifies which of the three reading frames is the one that contains a gene.

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PROVATA, A., and Y. ALMIRANTIS. "FRACTAL CANTOR PATTERNS IN THE SEQUENCE STRUCTURE OF DNA." Fractals 08, no. 01 (March 2000): 15–27. http://dx.doi.org/10.1142/s0218348x00000044.

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The coding parts of DNA sequences are regarded as clusters of connected sites of a random Cantor-like set, while the non-coding parts are regarded as the empty regions of the same set. Under this representation, we find that higher eucaryotes are mapped on random Cantor sets with fractal dimension around 0.85, while lower organisms are mapped on Cantor sets with fractal dimension 1. This result indicates that the coding/non-coding partition in the DNA sequences of lower organisms is homogeneous-like, while in the higher eucaryotes the partition is fractal. This result agrees with the power law distribution observed in the non-coding parts of higher eucaryotes.

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Kumar, K. Krishna, Ganesan Pugalenthi, and P. N. Suganthan. "DNA-Prot: Identification of DNA Binding Proteins from Protein Sequence Information using Random Forest." Journal of Biomolecular Structure and Dynamics 26, no. 6 (June 2009): 679–86. http://dx.doi.org/10.1080/07391102.2009.10507281.

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Plohl, Miroslav, Branko Borˇstnik, Vlatka Lucijanić-Justić, and ÐurÐica Ugarković. "Evidence for random distribution of sequence variants in Tenebrio molitor satellite DNA." Genetical Research 60, no. 1 (August 1992): 7–13. http://dx.doi.org/10.1017/s0016672300030615.

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SummaryTenebrio molitor satellite DNA has been analysed in order to study sequential organization of tandemly repeated monomers, i.e. to see whether different monomer variants are distributed randomly over the whole satellite, or clustered locally. Analysed sequence variants are products of single base substitutions in a consensus satellite sequence, producing additional restriction sites. The ladder of satellite multimers obtained after digestion with restriction enzymes was compared with theoretical calculations and revealed the distribution pattern of particular monomer variants within the satellite. A defined higher order repeating structure, indicating the existence of satellite subfamilies, could not be observed. Our results show that some sequence variants are very abundant, being present in nearly 50 % of the monomers, while others are very rare (0-1 % of monomers). However, the distribution of either very frequent, or very rare sequence variants in T. molitor satellite DNA is always random. Monomer variants are randomly distributed in the total satellite DNA and thus spread across all chromosomes, indicating a relatively high rate of sequence homogenization among different chromosomes. Such a distribution of monomer variants represents a transient stage in the process of sequence homogenization, indicating the high rate of spreading in comparison with the rate of sequence variant amplification.

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Parent, Jean-Guy, and Danièle Pagé. "Identification of Raspberry Cultivars by Sequence Characterized Amplified Region DNA Analysis." HortScience 33, no. 1 (February 1998): 140–42. http://dx.doi.org/10.21273/hortsci.33.1.140.

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Five polymorphic random amplified polymorphic DNA (RAPD) markers for 13 red raspberry (Rubus idaeus L.) and two purple raspberry (R. idaeus L. × R. occidentalis L.) cultivars were cloned and their termini sequenced. Sequence-specific 24-mer primer pairs were synthesized as extended RAPD primers and used in sequence characterized amplified region (SCAR) DNA analysis. All primer pairs generated polymorphic SCAR markers of the original RAPD marker sizes and length variants. Markers from four of the primer pairs could be easily scored and were adequate to identify the raspberry cultivars of the certification program of the province of Quebec.

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Choi, In-Geol, Sang Suk Kim, Jae-Ryeon Ryu, Ye Sun Han, Won-Gi Bang, Sung-Hou Kim, and Yeon Gyu Yu. "Random sequence analysis of genomic DNA of a hyperthermophile: Aquifex pyrophilus." Extremophiles 1, no. 3 (August 1, 1997): 125–34. http://dx.doi.org/10.1007/s007920050025.

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Sullivan, Richard, Mary Catherine Adams, Rajesh R. Naik, and Valeria T. Milam. "Analyzing Secondary Structure Patterns in DNA Aptamers Identified via CompELS." Molecules 24, no. 8 (April 21, 2019): 1572. http://dx.doi.org/10.3390/molecules24081572.

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In contrast to sophisticated high-throughput sequencing tools for genomic DNA, analytical tools for comparing secondary structure features between multiple single-stranded DNA sequences are less developed. For single-stranded nucleic acid ligands called aptamers, secondary structure is widely thought to play a pivotal role in driving recognition-based binding activity between an aptamer sequence and its specific target. Here, we employ a competition-based aptamer screening platform called CompELS to identify DNA aptamers for a colloidal target. We then analyze predicted secondary structures of the aptamers and a large population of random sequences to identify sequence features and patterns. Our secondary structure analysis identifies patterns ranging from position-dependent score matrixes of individual structural elements to position-independent consensus domains resulting from global alignment.

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Nelson, Adin, Ivelise Rijo, Zhigang Zhang, Andrew D. Zelenetz, and Ariela Noy. "Feasiblity and Implication of Bidirectional Sequencing Using a Multiplex Framework 2 Region Primer for Somatic Mutation Analysis of the Immunoglobulin (IgH) Heavy Chain in Chronic Lymphocytic Leukemia (CLL)." Blood 110, no. 11 (November 16, 2007): 4706. http://dx.doi.org/10.1182/blood.v110.11.4706.4706.

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Abstract Background: A somatic mutation rate of >2% of the immunoglobulin (IgH) heavy chain gene, in comparison to germline DNA, is a positive prognostic indicator in chronic lymphocytic leukemia (CLL). Genomic DNA is amplified using the Biomed-2 multiplex PCR primer set, sequenced in the reverse direction only using a 3′ JH primer, and compared to the germline sequence in VBase, a comprehensive directory of all human germline variable region sequences compiled from over a thousand published sequences. It is unknown whether forward sequencing using the multiplex 5′ Biomed-2 primers in a single reaction is feasible or whether doing so improves the accuracy of the mutational analysis. Methods: DNA was extracted from peripheral blood or bone marrow mononuclear cells from patients with CLL using the QIAGEN QIAspin DNA mini-kit. The FR2 region of the IgH gene was amplified using tube B of the Biomed-2 multiplex PCR primer set, separated in 2% agarose gel, excised, and prepared for sequencing using the QIAGEN QIAquick gel extraction kit. Bidirectional DNA sequencing was performed with the full set of multiplex 5′ FR2 primers combined in one reaction for the forward sequence and in a second reaction with the Biomed-2 3′ JH primer for the reverse sequence. A consensus sequence was obtained and mutation rates were calculated based on the consensus sequence and the reverse sequence separately. Results: The FR2 region was amplified from 30 CLL patients. 20 samples produced bidirectional consensus DNA sequences, 2 sequenced only with multiplex FR2 primers, 6 sequenced only with a JH primer, and 2 produced no sequences. Compared with unidirectional JH sequencing, bidirectional sequencing did not reassign any patient in the germline IgH group to the mutated category. In 15 patients, the uni- and bi-directional sequencing were identical. In 4 patients, a single basepair difference was noted. A random permutation test yields a two-sided p-value as 12.5%, indicating that no significant difference was detected between the uni- and bi-directional sequencing. Multiplex bidirectional sequencing did provide sequence information within the CDR3 region at the 3′ terminus of the amplimer which is partially truncated when using the JH primer alone. Conclusion: Bidirectional sequencing does not provide a somatic IgH mutation rate that differs significantly from that obtained from the reverse sequence alone and does not likely influence the IgH mutational prognostic assignment. Nonetheless, the bidirectional consensus sequence adds bases in the CDR3 region which can be used for research applications such as the generation of patient-specific primers for PCR. It is also noteworthy that multiplex PCR using the Biomed-2 primers is feasible.

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Karlin, S., and V. Brendel. "Patchiness and correlations in DNA sequences." Science 259, no. 5095 (January 29, 1993): 677–80. http://dx.doi.org/10.1126/science.8430316.

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The highly nonrandom character of genomic DNA can confound attempts at modeling DNA sequence variation by standard stochastic processes (including random walk or fractal models). In particular, the mosaic character of DNA consisting of patches of different composition can fully account for apparent long-range correlations in DNA.

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van Belkum, Alex, Stewart Scherer, Loek van Alphen, and Henri Verbrugh. "Short-Sequence DNA Repeats in Prokaryotic Genomes." Microbiology and Molecular Biology Reviews 62, no. 2 (June 1, 1998): 275–93. http://dx.doi.org/10.1128/mmbr.62.2.275-293.1998.

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SUMMARY Short-sequence DNA repeat (SSR) loci can be identified in all eukaryotic and many prokaryotic genomes. These loci harbor short or long stretches of repeated nucleotide sequence motifs. DNA sequence motifs in a single locus can be identical and/or heterogeneous. SSRs are encountered in many different branches of the prokaryote kingdom. They are found in genes encoding products as diverse as microbial surface components recognizing adhesive matrix molecules and specific bacterial virulence factors such as lipopolysaccharide-modifying enzymes or adhesins. SSRs enable genetic and consequently phenotypic flexibility. SSRs function at various levels of gene expression regulation. Variations in the number of repeat units per locus or changes in the nature of the individual repeat sequences may result from recombination processes or polymerase inadequacy such as slipped-strand mispairing (SSM), either alone or in combination with DNA repair deficiencies. These rather complex phenomena can occur with relative ease, with SSM approaching a frequency of 10−4 per bacterial cell division and allowing high-frequency genetic switching. Bacteria use this random strategy to adapt their genetic repertoire in response to selective environmental pressure. SSR-mediated variation has important implications for bacterial pathogenesis and evolutionary fitness. Molecular analysis of changes in SSRs allows epidemiological studies on the spread of pathogenic bacteria. The occurrence, evolution and function of SSRs, and the molecular methods used to analyze them are discussed in the context of responsiveness to environmental factors, bacterial pathogenicity, epidemiology, and the availability of full-genome sequences for increasing numbers of microorganisms, especially those that are medically relevant.

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Mehes-Smith, Melanie, Paul Michael, and Kabwe Nkongolo. "Species-diagnostic and species-specific DNA sequences evenly distributed throughout pine and spruce chromosomes." Genome 53, no. 10 (October 2010): 769–77. http://dx.doi.org/10.1139/g10-065.

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Genome organization in the family Pinaceae is complex and largely unknown. The main purpose of the present study was to develop and physically map species-diagnostic and species-specific molecular markers in pine and spruce. Five RAPD (random amplified polymorphic DNA) and one ISSR (inter-simple sequence repeat) species-diagnostic or species-specific markers for Picea mariana , Picea rubens , Pinus strobus , or Pinus monticola were identified, cloned, and sequenced. In situ hybridization of these sequences to spruce and pine chromosomes showed the sequences to be present in high copy number and evenly distributed throughout the genome. The analysis of centromeric and telomeric regions revealed the absence of significant clustering of species-diagnostic and species-specific sequences in all the chromosomes of the four species studied. Both RAPD and ISSR markers showed similar patterns.

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Wright, W. E., M. Binder, and W. Funk. "Cyclic amplification and selection of targets (CASTing) for the myogenin consensus binding site." Molecular and Cellular Biology 11, no. 8 (August 1991): 4104–10. http://dx.doi.org/10.1128/mcb.11.8.4104-4110.1991.

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The consensus binding site for the muscle regulatory factor myogenin was determined from an unbiased set of degenerate oligonucleotides using CASTing (cyclic amplification and selection of targets). Stretches of totally random sequence flanked by polymerase chain reaction priming sequences were mixed with purified myogenin or myotube nuclear extracts, DNA-protein complexes were immunoprecipitated with an antimyogenin antibody, and the DNA was amplified by polymerase chain reaction. Specific binding was obtained after four to six cycles of CASTing. The population of selected binding sites was then cloned, and a consensus was determined from sequencing individual isolates. Starting from a pool with 14 random bases, purified myogenin yielded a consensus binding site of AACAG[T/C]TGTT, while nuclear extracts retrieved the sequence TTGCACCTGTTNNTT from a pool containing 35 random bases. The latter sequence is consistent with that predicted from combining an E12/E47 half-site (N[not T]CAC) with the purified myogenin half-site ([T/C] TGTT). The presence of paired E boxes in many of the sequences isolated following CASTing with nuclear extracts proves that myogenin can bind cooperatively with other E-box-binding factors.

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31

Wright, W. E., M. Binder, and W. Funk. "Cyclic amplification and selection of targets (CASTing) for the myogenin consensus binding site." Molecular and Cellular Biology 11, no. 8 (August 1991): 4104–10. http://dx.doi.org/10.1128/mcb.11.8.4104.

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The consensus binding site for the muscle regulatory factor myogenin was determined from an unbiased set of degenerate oligonucleotides using CASTing (cyclic amplification and selection of targets). Stretches of totally random sequence flanked by polymerase chain reaction priming sequences were mixed with purified myogenin or myotube nuclear extracts, DNA-protein complexes were immunoprecipitated with an antimyogenin antibody, and the DNA was amplified by polymerase chain reaction. Specific binding was obtained after four to six cycles of CASTing. The population of selected binding sites was then cloned, and a consensus was determined from sequencing individual isolates. Starting from a pool with 14 random bases, purified myogenin yielded a consensus binding site of AACAG[T/C]TGTT, while nuclear extracts retrieved the sequence TTGCACCTGTTNNTT from a pool containing 35 random bases. The latter sequence is consistent with that predicted from combining an E12/E47 half-site (N[not T]CAC) with the purified myogenin half-site ([T/C] TGTT). The presence of paired E boxes in many of the sequences isolated following CASTing with nuclear extracts proves that myogenin can bind cooperatively with other E-box-binding factors.

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32

Tajima, F. "Relationship between DNA polymorphism and fixation time." Genetics 125, no. 2 (June 1, 1990): 447–54. http://dx.doi.org/10.1093/genetics/125.2.447.

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Abstract When there is no recombination among nucleotide sites in DNA sequences, DNA polymorphism and fixation of mutants at nucleotide sites are mutually related. Using the method of gene genealogy, the relationship between the DNA polymorphism and the fixation of mutant nucleotide was quantitatively investigated under the assumption that mutants are selectively neutral, that there is no recombination among nucleotide sites, and that the population is a random mating population with N diploid individuals. The results obtained indicate that the expected number of nucleotide differences between two DNA sequences randomly sampled from the population is 42% less when a mutant at a particular nucleotide site reaches fixation than at a random time, and that heterozygosity is also expected to be less when fixation takes place than at a random time, but the amount of reduction depends on the value of 4Nv in this case, where v is the mutation rate per DNA sequence per generation. The formula for obtaining the expected number of nucleotide differences between the two DNA sequences for a given fixation time is also derived, and indicates that, even when it takes a large number of generations for a mutant to reach fixation, this number is 33% less than at a random time. The computer simulation conducted suggests that the expected number of nucleotide differences between the two DNA sequences at the time when an advantageous mutant becomes fixed is essentially the same as that of neutral mutant if the fixation time is the same. The effect of recombination on the amount of DNA polymorphism was also investigated by using computer simulation.

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33

Banerjee, Monica, and Terence A. Brown. "Non-random DNA damage resulting from heat treatment: implications for sequence analysis of ancient DNA." Journal of Archaeological Science 31, no. 1 (January 2004): 59–63. http://dx.doi.org/10.1016/s0305-4403(03)00099-2.

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34

Bradley, Richard C. "On a ‘Replicating Character String’ Model." Journal of Applied Probability 51, no. 2 (June 2014): 512–27. http://dx.doi.org/10.1239/jap/1402578640.

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In Chaudhuri and Dasgupta's 2006 paper a certain stochastic model for ‘replicating character strings’ (such as in DNA sequences) was studied. In their model, a random ‘input’ sequence was subjected to random mutations, insertions, and deletions, resulting in a random ‘output’ sequence. In this paper their model will be set up in a slightly different way, in an effort to facilitate further development of the theory for their model. In their 2006 paper, Chaudhuri and Dasgupta showed that, under certain conditions, strict stationarity of the ‘input’ sequence would be preserved by the ‘output’ sequence, and they proved a similar ‘preservation’ result for the property of strong mixing with exponential mixing rate. In our setup, we will in spirit slightly extend their ‘preservation of stationarity’ result, and also prove a ‘preservation’ result for the property of absolute regularity with summable mixing rate.

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Bradley, Richard C. "On a ‘Replicating Character String’ Model." Journal of Applied Probability 51, no. 02 (June 2014): 512–27. http://dx.doi.org/10.1017/s0021900200011396.

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In Chaudhuri and Dasgupta's 2006 paper a certain stochastic model for ‘replicating character strings’ (such as in DNA sequences) was studied. In their model, a random ‘input’ sequence was subjected to random mutations, insertions, and deletions, resulting in a random ‘output’ sequence. In this paper their model will be set up in a slightly different way, in an effort to facilitate further development of the theory for their model. In their 2006 paper, Chaudhuri and Dasgupta showed that, under certain conditions, strict stationarity of the ‘input’ sequence would be preserved by the ‘output’ sequence, and they proved a similar ‘preservation’ result for the property of strong mixing with exponential mixing rate. In our setup, we will in spirit slightly extend their ‘preservation of stationarity’ result, and also prove a ‘preservation’ result for the property of absolute regularity with summable mixing rate.

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36

Javahery, R., A. Khachi, K. Lo, B. Zenzie-Gregory, and S. T. Smale. "DNA sequence requirements for transcriptional initiator activity in mammalian cells." Molecular and Cellular Biology 14, no. 1 (January 1994): 116–27. http://dx.doi.org/10.1128/mcb.14.1.116-127.1994.

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A transcriptional initiator (Inr) for mammalian RNA polymerase II can be defined as a DNA sequence element that overlaps a transcription start site and is sufficient for (i) determining the start site location in a promoter that lacks a TATA box and (ii) enhancing the strength of a promoter that contains a TATA box. We have prepared synthetic promoters containing random nucleotides downstream of Sp1 binding sites to determine the range of DNA sequences that convey Inr activity. Numerous sequences behaved as functional Inrs in an in vitro transcription assay, but the Inr activities varied dramatically. An examination of the functional elements revealed loose but consistent sequence requirements, with the approximate consensus sequence Py Py A+1 N T/A Py Py. Most importantly, almost every functional Inr that has been described fits into the consensus sequence that we have defined. Although several proteins have been reported to bind to specific Inrs, manipulation of those elements failed to correlate protein binding with Inr activity. The simplest model to explain these results is that all or most Inrs are recognized by a universal binding protein, similar to the functional recognition of all TATA sequences by the same TATA-binding protein. The previously reported proteins that bind near specific Inr elements may augment the strength of an Inr or may impart transcriptional regulation through an Inr.

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37

Javahery, R., A. Khachi, K. Lo, B. Zenzie-Gregory, and S. T. Smale. "DNA sequence requirements for transcriptional initiator activity in mammalian cells." Molecular and Cellular Biology 14, no. 1 (January 1994): 116–27. http://dx.doi.org/10.1128/mcb.14.1.116.

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A transcriptional initiator (Inr) for mammalian RNA polymerase II can be defined as a DNA sequence element that overlaps a transcription start site and is sufficient for (i) determining the start site location in a promoter that lacks a TATA box and (ii) enhancing the strength of a promoter that contains a TATA box. We have prepared synthetic promoters containing random nucleotides downstream of Sp1 binding sites to determine the range of DNA sequences that convey Inr activity. Numerous sequences behaved as functional Inrs in an in vitro transcription assay, but the Inr activities varied dramatically. An examination of the functional elements revealed loose but consistent sequence requirements, with the approximate consensus sequence Py Py A+1 N T/A Py Py. Most importantly, almost every functional Inr that has been described fits into the consensus sequence that we have defined. Although several proteins have been reported to bind to specific Inrs, manipulation of those elements failed to correlate protein binding with Inr activity. The simplest model to explain these results is that all or most Inrs are recognized by a universal binding protein, similar to the functional recognition of all TATA sequences by the same TATA-binding protein. The previously reported proteins that bind near specific Inr elements may augment the strength of an Inr or may impart transcriptional regulation through an Inr.

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38

Choi, Woo Suk, and Miguel Garcia-Diaz. "A minimal motif for sequence recognition by mitochondrial transcription factor A (TFAM)." Nucleic Acids Research 50, no. 1 (December 20, 2021): 322–32. http://dx.doi.org/10.1093/nar/gkab1230.

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Abstract Mitochondrial transcription factor A (TFAM) plays a critical role in mitochondrial transcription initiation and mitochondrial DNA (mtDNA) packaging. Both functions require DNA binding, but in one case TFAM must recognize a specific promoter sequence, while packaging requires coating of mtDNA by association with non sequence-specific regions. The mechanisms by which TFAM achieves both sequence-specific and non sequence-specific recognition have not yet been determined. Existing crystal structures of TFAM bound to DNA allowed us to identify two guanine-specific interactions that are established between TFAM and the bound DNA. These interactions are observed when TFAM is bound to both specific promoter sequences and non-sequence specific DNA. These interactions are established with two guanine bases separated by 10 random nucleotides (GN10G). Our biochemical results demonstrate that the GN10G consensus is essential for transcriptional initiation and contributes to facilitating TFAM binding to DNA substrates. Furthermore, we report a crystal structure of TFAM in complex with a non sequence-specific sequence containing a GN10G consensus. The structure reveals a unique arrangement in which TFAM bridges two DNA substrates while maintaining the GN10G interactions. We propose that the GN10G consensus is key to facilitate the interaction of TFAM with DNA.

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39

Pierrou, S., S. Enerback, and P. Carlsson. "Selection of High-Affinity Binding Sites for Sequence-Specific, DNA Binding Proteins from Random Sequence Oligonucleotides." Analytical Biochemistry 229, no. 1 (July 1995): 99–105. http://dx.doi.org/10.1006/abio.1995.1384.

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40

Wang, Xingyuan, Hongyu Zhao, Yutao Hou, Chao Luo, Yingqian Zhang, and Chunpeng Wang. "Chaotic image encryption algorithm based on pseudo-random bit sequence and DNA plane." Modern Physics Letters B 33, no. 22 (August 7, 2019): 1950263. http://dx.doi.org/10.1142/s0217984919502634.

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In this paper, a new chaotic image encryption algorithm based on pseudo-random bit sequence and DNA plane is proposed. The coupled map lattice (CML) is applied to design a pseudo-random bit sequence generation (PBSG) system and use the system to generate the random sequence needed in the encryption process. The initial values and parameters of the system are generated by the SHA-256 hash algorithm combined with given keys. Firstly, the plane image is decomposed into four DNA planes in combination with the DNA encoding rules, and then the four DNA planes are subjected to row circular permutation and column circular permutation. After that, the diffusion operation on each DNA plane is performed. Finally, the four DNA planes are decoded and then combined into a pixel matrix, that is, the final cipher image is obtained. Throughout the encryption process, the choice of DNA encoding and decoding rules is determined by the PBSG system. Simulation results and security analysis show that the algorithm not only has good encryption effect, but also can resist various classic attacks, and has excellent security performance.

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41

Bakalinsky, Alan T., Hong Xu, Diane J. Wilson, and S. Arulsekar. "666 PB 110 RANDOM AMPLIFIED POLYMORPHIC DNA MARKERS ARE INADEQUATE FOR FINGERPRINTING GRAPE ROOTSTOCKS." HortScience 29, no. 5 (May 1994): 528c—528. http://dx.doi.org/10.21273/hortsci.29.5.528c.

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A total of eight random amplified polymorphic DNA (RAPD) markers were generated in a screen of 77 primers of 10-base length and were detected reproducibly among nine different grape (Vitis) rootstocks. Occasional failed amplifications could not be explained rationally nor easily corrected by systematic replacement of individual reaction components. In an effort to improve their reliability, the RAPD markers were cloned, their termini sequenced, and new sequence-specific primer pairs were synthesized based on addition of 10 to 14 bases to the 3' termini of the original 10-mers. Six pairs of the new primers were evaluated at their optimal and higher-than optimal annealing temperatures. One primer pair amplified a product the same size as the original RAPD marker in all rootstocks, resulting in loss of polymorphism. Post-amplification digestion with 7 different restriction endonucleases failed to reveal restriction site differences. Three primer pairs amplified an unexpected length variant in some accessions. Two other pairs of primers amplified a number of unexpected bands. Better approaches for exploiting the sequence differences that account for the RAPD phenomenon will be discussed.

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SKOTNICKI, M. L., A. M. MACKENZIE, M. A. CLEMENTS, and P. M. SELKIRK. "DNA sequencing and genetic diversity of the 18S–26S nuclear ribosomal internal transcribed spacers (ITS) in nine Antarctic moss species." Antarctic Science 17, no. 3 (August 17, 2005): 377–84. http://dx.doi.org/10.1017/s0954102005002816.

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We have sequenced the 18S–26S nuclear ribosomal DNA ITS region from the genome of nine different moss species from the Ross Sea region of Antarctica. This relatively quick and simple technique enables these species to be readily distinguished, facilitating their taxonomic identification. Only a single moss shoot is required, and for identification of these bryophytes it is only necessary to determine a few hundred nucleotides of the DNA sequence in a single sequencing reaction. Several previously unidentified Antarctic moss specimens were readily characterized by comparison with ITS sequences of known moss species. The relationships between species and locations previously detected by the RAPD (Random Amplified Polymorphic DNA) technique were confirmed by DNA sequencing, demonstrating that the two techniques can be complementary for molecular analysis of the ecology of mosses in Antarctica.

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43

Brooks, Steven A., Li Huang, Bikram S. Gill, and John P. Fellers. "Analysis of 106 kb of contiguous DNA sequence from the D genome of wheat reveals high gene density and a complex arrangement of genes related to disease resistance." Genome 45, no. 5 (October 1, 2002): 963–72. http://dx.doi.org/10.1139/g02-049.

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Vast differences exist in genome sizes of higher plants; however, gene count remains relatively constant among species. Differences observed in DNA content can be attributed to retroelement amplification leading to genome expansion. Cytological and genetic studies have demonstrated that genes are clustered in islands rather than distributed at random in the genome. Analysis of gene islands within highly repetitive genomes of plants like wheat remains largely unstudied. The objective of our work was to sequence and characterize a contiguous DNA sequence from chromosome 1DS of Aegilops tauschii. An RFLP probe that maps to the Lr21 region of 1DS was used to isolate a single BAC. The BAC was sequenced and is 106 kb in length. The contiguous DNA sequence contains a 46-kb retroelement-free gene island containing seven coding sequences. Within the gene island is a complex arrangement of resistance and defense response genes. Overall gene density in this BAC is 1 gene per 8.9 kb. This report demonstrates that wheat and its relatives do contain regions with gene densities similar to that of Arabidopsis.Key words: resistance gene block, nucleotide-binding site, pathogenesis-related genes.

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44

Wang, Liangjiang, Mary Yang, and Jack Y. Yang. "Prediction of DNA-binding residues from protein sequence information using random forests." BMC Genomics 10, Suppl 1 (2009): S1. http://dx.doi.org/10.1186/1471-2164-10-s1-s1.

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45

Zhu, Y. L., Q. J. Song, D. L. Hyten, C. P. Van Tassell, L. K. Matukumalli, D. R. Grimm, S. M. Hyatt, E. W. Fickus, N. D. Young, and P. B. Cregan. "Single-Nucleotide Polymorphisms in Soybean." Genetics 163, no. 3 (March 1, 2003): 1123–34. http://dx.doi.org/10.1093/genetics/163.3.1123.

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Abstract Single-nucleotide polymorphisms (SNPs) provide an abundant source of DNA polymorphisms in a number of eukaryotic species. Information on the frequency, nature, and distribution of SNPs in plant genomes is limited. Thus, our objectives were (1) to determine SNP frequency in coding and noncoding soybean (Glycine max L. Merr.) DNA sequence amplified from genomic DNA using PCR primers designed to complete genes, cDNAs, and random genomic sequence; (2) to characterize haplotype variation in these sequences; and (3) to provide initial estimates of linkage disequilibrium (LD) in soybean. Approximately 28.7 kbp of coding sequence, 37.9 kbp of noncoding perigenic DNA, and 9.7 kbp of random noncoding genomic DNA were sequenced in each of 25 diverse soybean genotypes. Over the >76 kbp, mean nucleotide diversity expressed as Watterson’s θ was 0.00097. Nucleotide diversity was 0.00053 and 0.00111 in coding and in noncoding perigenic DNA, respectively, lower than estimates in the autogamous model species Arabidopsis thaliana. Haplotype analysis of SNP-containing fragments revealed a deficiency of haplotypes vs. the number that would be anticipated at linkage equilibrium. In 49 fragments with three or more SNPs, five haplotypes were present in one fragment while four or less were present in the remaining 48, thereby supporting the suggestion of relatively limited genetic variation in cultivated soybean. Squared allele-frequency correlations (r2) among haplotypes at 54 loci with two or more SNPs indicated low genome-wide LD. The low level of LD and the limited haplotype diversity suggested that the genome of any given soybean accession is a mosaic of three or four haplotypes. To facilitate SNP discovery and the development of a transcript map, subsets of four to six diverse genotypes, whose sequence analysis would permit the discovery of at least 75% of all SNPs present in the 25 genotypes as well as 90% of the common (frequency >0.10) SNPs, were identified.

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Agüero, Fernán, Ramiro E. Verdún, Alberto Carlos C. Frasch, and Daniel O. Sánchez. "A Random Sequencing Approach for the Analysis of the Trypanosoma cruzi Genome: General Structure, Large Gene and Repetitive DNA Families, and Gene Discovery." Genome Research 10, no. 12 (November 21, 2000): 1996–2005. http://dx.doi.org/10.1101/gr.146300.

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A random sequence survey of the genome of Trypanosoma cruzi, the agent of Chagas disease, was performed and 11,459 genomic sequences were obtained, resulting in ∼4.3 Mb of readable sequences or ∼10% of the parasite haploid genome. The estimated total GC content was 50.9%, with a high representation of A and T di- and trinucleotide repeats. Out of the estimated 5000 parasite genes, 947 putative new genes were identified. Another 1723 sequences corresponded to genes detected previously in T. cruzi through expression sequence tag analysis. 7735 sequences had no matches in the database, but the presence of open reading frames that passed Fickett's test suggests that some might contain coding DNA. The survey was highly redundant, with ∼35% of the sequences included in a few large sequence families. Some of them code for protein families present in dozens of copies, including proteins essential for parasite survival and retrotransposons. Other sequence families include repetitive DNA present in thousands of copies per haploid genome. Some families in the latter group are new, parasite-specific, repetitive DNAs. These results suggest that T. cruzi could constitute an interesting model to analyze gene and genome evolution due to its plasticity in terms of sequence amplification and divergence. Additional information can be found at http://www.iib.unsam.edu.ar/tcruzi.gss.html.[The sequence data described in this paper have been submitted to the dbGSS database under the following GenBank accession nos.:AQ443439–AQ443513, AQ443743–AQ445667, AQ902981–AQ911366,AZ049857–AZ051184, and AZ302116–AZ302563.]

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47

Okinaka, R. T., K. Cloud, O. Hampton, A. R. Hoffmaster, K. K. Hill, P. Keim, T. M. Koehler, et al. "Sequence and Organization of pXO1, the Large Bacillus anthracis Plasmid Harboring the Anthrax Toxin Genes." Journal of Bacteriology 181, no. 20 (October 15, 1999): 6509–15. http://dx.doi.org/10.1128/jb.181.20.6509-6515.1999.

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ABSTRACT The Bacillus anthracis Sterne plasmid pXO1 was sequenced by random, “shotgun” cloning. A circular sequence of 181,654 bp was generated. One hundred forty-three open reading frames (ORFs) were predicted using GeneMark and GeneMark.hmm, comprising only 61% (110,817 bp) of the pXO1 DNA sequence. The overall guanine-plus-cytosine content of the plasmid is 32.5%. The most recognizable feature of the plasmid is a “pathogenicity island,” defined by a 44.8-kb region that is bordered by inverted IS1627 elements at each end. This region contains the three toxin genes (cya, lef, and pagA), regulatory elements controlling the toxin genes, three germination response genes, and 19 additional ORFs. Nearly 70% of the ORFs on pXO1 do not have significant similarity to sequences available in open databases. Absent from the pXO1 sequence are homologs to genes that are typically required to drive theta replication and to maintain stability of large plasmids in Bacillus spp. Among the ORFs with a high degree of similarity to known sequences are a collection of putative transposases, resolvases, and integrases, suggesting an evolution involving lateral movement of DNA among species. Among the remaining ORFs, there are three sequences that may encode enzymes responsible for the synthesis of a polysaccharide capsule usually associated with serotype-specific virulent streptococci.

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Beyer, Stefan, Wendy U. Dittmer, Andreas Reuter, and Friedrich C. Simmel. "Controlled Release of Thrombin Using Aptamer-Based Nanodevices." Advances in Science and Technology 53 (October 2006): 116–21. http://dx.doi.org/10.4028/www.scientific.net/ast.53.116.

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Aptamers are DNA or RNA single strands that have been selected from random pools based on their ability to bind ligands. Like antibodies, aptamers are highly specific to their targets, and thus have many potential uses in biomedicine and biotechnology. We report here on the construction of a protein-binding molecular device based on a DNA aptamer, which can be instructed to hold or release the human blood-clotting factor, α-thrombin, depending on an operator DNA sequence addressing it. In the operation of this DNA nanodevice, the thrombin-binding DNA aptamer is switched between a binding and a non-binding form. This is achieved by sequentially hybridizing and removing a DNA single strand to the protein binding region of the aptamer. This principle of operation is limited as the switching sequence is determined by the protein-binding sequence. To overcome this limitation we introduce a DNA signal translation device that allows the operation of aptamers with arbitrary sequences. The function of the translator is based on branch migration and the action of the endonuclease FokI. The modular design of the translator facilitates the adaptation of the device to various input or output sequences.

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Lin, Jun Sheng, Alexia Kauff, Yong Diao, Huiyong Yang, Steve Lawrence, and Jennifer L. Juengel. "Creation of DNA aptamers against recombinant bone morphogenetic protein 15." Reproduction, Fertility and Development 28, no. 8 (2016): 1164. http://dx.doi.org/10.1071/rd14409.

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The oocyte-derived growth factor bone morphogenetic protein (BMP) 15 plays important roles in fertility, but its mechanism of action differs between species. Generation of BMP15-binding molecules, as an essential investigation tool, would be helpful to provide valuable insight into the underlying biological features of BMP15. The BMP15-binding molecules could be antibodies or aptamers. Aptamers have many advantages over antibodies as macromolecular ligands for target proteins. DNA aptamers can be obtained by a method of Systematic Evolution of Ligands by EXponential enrichment (SELEX) beginning with a pool of random sequences. However, the success of this technique cannot be guaranteed if the initial pool lacks candidate sequences. Herein, we report on the creation of DNA aptamers by means of modified SELEX. The modification included enhanced mutation and progressive selection during an in vitro evolutionary process. As a proof-of-principle, we started from a single sequence instead of a multiple-sequence pool. Functional aptamers against the recombinant BMP15 were successfully created and identified.

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Syahrani, Iswaya Maalik. "Comparation Analysis of Ensemble Technique With Boosting(Xgboost) and Bagging (Randomforest) For Classify Splice Junction DNA Sequence Category." Jurnal Penelitian Pos dan Informatika 9, no. 1 (October 1, 2019): 27–36. http://dx.doi.org/10.17933/jppi.v9i1.249.

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Bioinformatics research currently supported by rapid growth of computation technology and algorithm. Ensemble decision tree is common method for classifying large and complex dataset such as DNA sequence. By implementing two classification methods with ensemble technique like xgboost and random Forest might improve the accuracy result on classifying DNA Sequence splice junction type. With 96,24% of xgboost accuracy and 95,11% of Random Forest accuracy, our conclusions the xgboost and random forest methods using right parameter setting are highly effective tool for classifying small example dataset. Analyzing both methods with their characteristics will give an overview on how they work to meet the needs in DNA splicing.

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Journal articles on the topic 'Random sequence DNA'

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