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Journal articles on the topic 'DNA strand'

Author: Grafiati

Published: 7 July 2024

Last updated: 31 July 2025

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1

Maslowska, Katarzyna H., Karolina Makiela-Dzbenska, Jin-Yao Mo, Iwona J. Fijalkowska, and Roel M. Schaaper. "High-accuracy lagging-strand DNA replication mediated by DNA polymerase dissociation." Proceedings of the National Academy of Sciences 115, no. 16 (2018): 4212–17. http://dx.doi.org/10.1073/pnas.1720353115.

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The fidelity of DNA replication is a critical factor in the rate at which cells incur mutations. Due to the antiparallel orientation of the two chromosomal DNA strands, one strand (leading strand) is replicated in a mostly processive manner, while the other (lagging strand) is synthesized in short sections called Okazaki fragments. A fundamental question that remains to be answered is whether the two strands are copied with the same intrinsic fidelity. In most experimental systems, this question is difficult to answer, as the replication complex contains a different DNA polymerase for each str

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Shi, Jiezhong, Ben Zhang, Tianyi Zheng, et al. "DNA Materials Assembled from One DNA Strand." International Journal of Molecular Sciences 24, no. 9 (2023): 8177. http://dx.doi.org/10.3390/ijms24098177.

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Due to the specific base-pairing recognition, clear nanostructure, programmable sequence and responsiveness of the DNA molecule, DNA materials have attracted extensive attention and been widely used in controlled release, drug delivery and tissue engineering. Generally, the strategies for preparing DNA materials are based on the assembly of multiple DNA strands. The construction of DNA materials using only one DNA strand can not only save time and cost, but also avoid defects in final assemblies generated by the inaccuracy of DNA ratios, which potentially promote the large-scale production and

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Jensen, Sarah Ø., Nadia Øgaard, Hans Jørgen Nielsen, Jesper B. Bramsen, and Claus L. Andersen. "Enhanced Performance of DNA Methylation Markers by Simultaneous Measurement of Sense and Antisense DNA Strands after Cytosine Conversion." Clinical Chemistry 66, no. 7 (2020): 925–33. http://dx.doi.org/10.1093/clinchem/hvaa100.

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Abstract Background Most existing DNA methylation-based methods for detection of circulating tumor DNA (ctDNA) are based on conversion of unmethylated cytosines to uracil. After conversion, the 2 DNA strands are no longer complementary; therefore, targeting only 1 DNA strand merely utilizes half of the available input DNA. We investigated whether the sensitivity of methylation-based ctDNA detection strategies could be increased by targeting both DNA strands after bisulfite conversion. Methods Dual-strand digital PCR assays were designed for the 3 colorectal cancer (CRC)–specific methylation ma

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Fan, Xinqing, and Carolyn Mary Price. "Coordinate Regulation of G- and C Strand Length during New Telomere Synthesis." Molecular Biology of the Cell 8, no. 11 (1997): 2145–55. http://dx.doi.org/10.1091/mbc.8.11.2145.

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We have used the ciliate Euplotes to study the role of DNA polymerase in telomeric C strand synthesis.Euplotes provides a unique opportunity to study C strand synthesis without the complication of simultaneous DNA replication because millions of new telomeres are made at a stage in the life cycle when no general DNA replication takes place. Previously we showed that the C-strands of newly synthesized telomeres have a precisely controlled length while the G-strands are more heterogeneous. This finding suggested that, although synthesis of the G-strand (by telomerase) is the first step in telome

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Ma, Jingjing. "Molecular Logic Gate Based on DNA Strand Displacement Reaction." Journal of Nanoelectronics and Optoelectronics 16, no. 6 (2021): 974–77. http://dx.doi.org/10.1166/jno.2021.3037.

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In this paper, I construct an XOR logic gate based on DNA strand displacement reaction, and verify our design through corresponding biochemical experiment. I designed several different DNA strands. Based on two basic DNA strand displacement reaction mechanisms, by adding different input strands and taking the signal of FAM fluorescent group as the output, the XOR logic gate is realized. The result shows that DNA strand displacement technology has important application value in DNA computing, especially in the construction of DNA molecular logic gates.

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6

Sugiman-Marangos, Seiji N., Yoni M. Weiss, and Murray S. Junop. "Mechanism for accurate, protein-assisted DNA annealing by Deinococcus radiodurans DdrB." Proceedings of the National Academy of Sciences 113, no. 16 (2016): 4308–13. http://dx.doi.org/10.1073/pnas.1520847113.

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Accurate pairing of DNA strands is essential for repair of DNA double-strand breaks (DSBs). How cells achieve accurate annealing when large regions of single-strand DNA are unpaired has remained unclear despite many efforts focused on understanding proteins, which mediate this process. Here we report the crystal structure of a single-strand annealing protein [DdrB (DNA damage response B)] in complex with a partially annealed DNA intermediate to 2.2 Å. This structure and supporting biochemical data reveal a mechanism for accurate annealing involving DdrB-mediated proofreading of strand compleme

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7

Bolt, Edward L., and Thorsten Allers. "New enzymes, new mechanisms?: DNA repair by recombination in the Archaea." Biochemist 26, no. 3 (2004): 19–21. http://dx.doi.org/10.1042/bio02603019.

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DNA repair by homologous recombination is highly accurate, since it uses an intact DNA strand to guide repair of its damaged homologue. This article focuses on two key steps in recombination: unwinding of strands by repair helicases, and annealing of homologous strands by strand-exchange enzymes.

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8

Domljanovic, Ivana, Alessandro Ianiro, Curzio Rüegg, Michael Mayer, and Maria Taskova. "Natural and Modified Oligonucleotide Sequences Show Distinct Strand Displacement Kinetics and These Are Affected Further by Molecular Crowders." Biomolecules 12, no. 9 (2022): 1249. http://dx.doi.org/10.3390/biom12091249.

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DNA and RNA strand exchange is a process of fundamental importance in biology. Herein, we used a FRET-based assay to investigate, for the first time, the stand exchange kinetics of natural DNA, natural RNA, and locked nucleic acid (LNA)-modified DNA sequences in vitro in PBS in the absence or presence of molecular additives and macromolecular crowders such as diethylene glycol dimethyl ether (deg), polyethylene glycol (peg), and polyvinylpyrrolidone (pvp). The results show that the kinetics of strand exchange mediated by DNA, RNA, and LNA-DNA oligonucleotide sequences are different. Different

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9

Cronan, Glen E., Elena A. Kouzminova, and Andrei Kuzminov. "Near-continuously synthesized leading strands inEscherichia coliare broken by ribonucleotide excision." Proceedings of the National Academy of Sciences 116, no. 4 (2019): 1251–60. http://dx.doi.org/10.1073/pnas.1814512116.

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In vitro, purified replisomes drive model replication forks to synthesize continuous leading strands, even without ligase, supporting the semidiscontinuous model of DNA replication. However, nascent replication intermediates isolated from ligase-deficientEscherichia colicomprise only short (on average 1.2-kb) Okazaki fragments. It was long suspected that cells replicate their chromosomal DNA by the semidiscontinuous mode observed in vitro but that, in vivo, the nascent leading strand was artifactually fragmented postsynthesis by excision repair. Here, using high-resolution separation of pulse-

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Delagoutte, Emmanuelle, and Giuseppe Baldacci. "5′CAG and 5′CTG Repeats Create Differential Impediment to the Progression of a Minimal Reconstituted T4 Replisome Depending on the Concentration of dNTPs." Molecular Biology International 2011 (August 10, 2011): 1–14. http://dx.doi.org/10.4061/2011/213824.

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Instability of repetitive sequences originates from strand misalignment during repair or replicative DNA synthesis. To investigate the activity of reconstituted T4 replisomes across trinucleotide repeats (TNRs) during leading strand DNA synthesis, we developed a method to build replication miniforks containing a TNR unit of defined sequence and length. Each minifork consists of three strands, primer, leading strand template, and lagging strand template with a 5′ single-stranded (ss) tail. Each strand is prepared independently, and the minifork is assembled by hybridization of the three strands

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11

Hernandez, Alfredo J., Seung-Joo Lee, and Charles C. Richardson. "Primer release is the rate-limiting event in lagging-strand synthesis mediated by the T7 replisome." Proceedings of the National Academy of Sciences 113, no. 21 (2016): 5916–21. http://dx.doi.org/10.1073/pnas.1604894113.

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DNA replication occurs semidiscontinuously due to the antiparallel DNA strands and polarity of enzymatic DNA synthesis. Although the leading strand is synthesized continuously, the lagging strand is synthesized in small segments designated Okazaki fragments. Lagging-strand synthesis is a complex event requiring repeated cycles of RNA primer synthesis, transfer to the lagging-strand polymerase, and extension effected by cooperation between DNA primase and the lagging-strand polymerase. We examined events controlling Okazaki fragment initiation using the bacteriophage T7 replication system. Prim

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12

Bielawski, Joseph P., and John R. Gold. "Mutation Patterns of Mitochondrial H- and L-Strand DNA in Closely Related Cyprinid Fishes." Genetics 161, no. 4 (2002): 1589–97. http://dx.doi.org/10.1093/genetics/161.4.1589.

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Abstract Mitochondrial genome replication is asymmetric. Replication starts from the origin of heavy (H)-strand replication, displacing the parental H-strand as it proceeds along the molecule. The H-strand remains single stranded until light (L)-strand replication is initiated from a second origin of replication. It has been suggested that single-stranded H-strand DNA is more sensitive to mutational damage, giving rise to substitutional rate differences between the two strands and among genes in mammalian mitochondrial DNA. In this study, we analyzed sequences of the cytochrome b, ND4, ND4L, a

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Prévost, Chantal, and Masayuki Takahashi. "Geometry of the DNA strands within the RecA nucleofilament: role in homologous recombination." Quarterly Reviews of Biophysics 36, no. 4 (2003): 429–53. http://dx.doi.org/10.1017/s0033583504003956.

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1. Introduction 4302. Transformations of the RecA filament 4312.1 The different forms of the RecA filament 4312.2 Orientation and position of the RecA monomers in the active filament 4332.3 Transmission of structural information along the filament 4333. RecA-induced DNA deformations 4353.1 Characteristics of RecA-bound DNA 4353.2 Stretching properties of double-stranded DNA 4363.3 DNA bound to architectural proteins 4373.4 Implications for RecA-induced DNA deformations 4383.5 Axial distribution of the DNA stretching deformation 4384. Contacts between RecA and the DNA strands 4404.1 The DNA-bin

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14

Loeb, Daniel D., and Ru Tian. "Mutations That Increase In Situ Priming Also Decrease Circularization for Duck Hepatitis B Virus." Journal of Virology 75, no. 14 (2001): 6492–97. http://dx.doi.org/10.1128/jvi.75.14.6492-6497.2001.

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ABSTRACT The process of hepadnavirus reverse transcription involves two template switches during the synthesis of plus-strand DNA. The first involves translocation of the plus-strand primer from its site of generation, the 3′ end of minus-strand DNA, to the complementary sequence DR2, located near the 5′ end of the minus-strand DNA. Plus strands initiated from DR2 are extended to the 5′ end of the minus-strand DNA. At this point, the 3′ end of the minus strand becomes the template via the second template switch, a process called circularization. Elongation of circularized plus-strand DNA gener

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15

Vaitsiankova, Alina, Kamila Burdova, Margarita Sobol, et al. "PARP inhibition impedes the maturation of nascent DNA strands during DNA replication." Nature Structural & Molecular Biology 29, no. 4 (2022): 329–38. http://dx.doi.org/10.1038/s41594-022-00747-1.

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AbstractPoly(ADP-ribose) polymerase 1 (PARP1) is implicated in the detection and processing of unligated Okazaki fragments and other DNA replication intermediates, highlighting such structures as potential sources of genome breakage induced by PARP inhibition. Here, we show that PARP1 activity is greatly elevated in chicken and human S phase cells in which FEN1 nuclease is genetically deleted and is highest behind DNA replication forks. PARP inhibitor reduces the integrity of nascent DNA strands in both wild-type chicken and human cells during DNA replication, and does so in FEN1−/− cells to a

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16

Moore, John D., and Jocelyn E. Krebs. "Histone modifications and DNA double-strand break repair." Biochemistry and Cell Biology 82, no. 4 (2004): 446–52. http://dx.doi.org/10.1139/o04-034.

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The roles of different histone modifications have been explored extensively in a number of nuclear processes, particularly in transcriptional regulation. Only recently has the role of histone modification in signaling or facilitating DNA repair begun to be elucidated. DNA broken along both strands in the same region, a double-strand break, is damaged in the most severe way possible and can be the most difficult type of damage to repair accurately. To successfully repair the double-strand break, the cell must gain access to the damaged ends of the DNA and recruit repair factors, and in the case

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17

Hahn, Jaeseung, and William M. Shih. "Thermal cycling of DNA devices via associative strand displacement." Nucleic Acids Research 47, no. 20 (2019): 10968–75. http://dx.doi.org/10.1093/nar/gkz844.

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Abstract DNA-based devices often operate through a series of toehold-mediated strand-displacement reactions. To achieve cycling, fluidic mixing can be used to introduce ‘recovery’ strands to reset the system. However, such mixing can be cumbersome, non-robust, and wasteful of materials. Here we demonstrate mixing-free thermal cycling of DNA devices that operate through associative strand-displacement cascades. These cascades are favored at low temperatures due to the primacy of a net increase in base pairing, whereas rebinding of ‘recovery’ strands is favored at higher temperatures due to the

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18

Yu, Man, and Warren Masker. "T7 Single Strand DNA Binding Protein but Not T7 Helicase Is Required for DNA Double Strand Break Repair." Journal of Bacteriology 183, no. 6 (2001): 1862–69. http://dx.doi.org/10.1128/jb.183.6.1862-1869.2001.

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ABSTRACT An in vitro system based on Escherichia coliinfected with bacteriophage T7 was used to test for involvement of host and phage recombination proteins in the repair of double strand breaks in the T7 genome. Double strand breaks were placed in a uniqueXhoI site located approximately 17% from the left end of the T7 genome. In one assay, repair of these breaks was followed by packaging DNA recovered from repair reactions and determining the yield of infective phage. In a second assay, the product of the reactions was visualized after electrophoresis to estimate the extent to which the doub

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19

Weiser, Martin, and Hans-Achim Wagenknecht. "Dynamic DNA architectures: spontaneous DNA strand exchange and self-sorting driven by perylene bisimide interactions." Chemical Communications 51, no. 92 (2015): 16530–33. http://dx.doi.org/10.1039/c5cc06491k.

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Three differently bay-substituted perylene bisimides together with the conventional unsubstituted chromophore were synthetically incorporated as homodimers in DNA double strands and undergo spontaneous strand exchange if mixed together.

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20

Thomas, David C., Yegor A. Voronin, Galina N. Nikolenko, Jianbo Chen, Wei-Shau Hu, and Vinay K. Pathak. "Determination of the Ex Vivo Rates of Human Immunodeficiency Virus Type 1 Reverse Transcription by Using Novel Strand-Specific Amplification Analysis." Journal of Virology 81, no. 9 (2007): 4798–807. http://dx.doi.org/10.1128/jvi.02471-06.

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ABSTRACT Replication of human immunodeficiency virus type 1 (HIV-1), like all organisms, involves synthesis of a minus-strand and a plus-strand of nucleic acid. Currently available PCR methods cannot distinguish between the two strands of nucleic acids. To carry out detailed analysis of HIV-1 reverse transcription from infected cells, we have developed a novel strand-specific amplification (SSA) assay using single-stranded padlock probes that are specifically hybridized to a target strand, ligated, and quantified for sensitive analysis of the kinetics of HIV-1 reverse transcription in cells. U

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21

Hentosh, P., and P. Grippo. "2-Chloro-2′-deoxyadenosine monophosphate residues in DNA enhance susceptibility to 3′ → 5′ exonucleases." Biochemical Journal 302, no. 2 (1994): 567–71. http://dx.doi.org/10.1042/bj3020567.

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2-Chloro-2′-deoxyadenosine triphosphate, a purine nucleotide analogue and potent antileukaemic agent, was incorporated into double-stranded 36-mers in place of dATP to investigate the effects of 2-chloroadenine (ClAde) on DNA polymerase-associated 3′-->5′ exonuclease activity. ClAde residues within one strand of duplex DNA did not inhibit exonuclease activity; on the contrary, ClAde-containing minus strands were digested to a greater extent than was control DNA in the absence of deoxyribonucleoside triphosphates by Escherichia coli Klenow fragment, yeast DNA polymerase II and T4 DNA polymer

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22

Griffith, Jack D., Lorelei D. Harris, and Stephen L. Brenner. "Dna Strand Exchange." Critical Reviews in Biochemistry 23, sup1 (1988): S43—S86. http://dx.doi.org/10.3109/10409238809083375.

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23

Scalise, Dominic, Nisita Dutta, and Rebecca Schulman. "DNA Strand Buffers." Journal of the American Chemical Society 140, no. 38 (2018): 12069–76. http://dx.doi.org/10.1021/jacs.8b05373.

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Wu, CHUNG-I. "DNA strand asymmetry." Nature 352, no. 6331 (1991): 114. http://dx.doi.org/10.1038/352114b0.

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Boyer, Benjamin, Claudia Danilowicz, Mara Prentiss, and Chantal Prévost. "Weaving DNA strands: structural insight on ATP hydrolysis in RecA-induced homologous recombination." Nucleic Acids Research 47, no. 15 (2019): 7798–808. http://dx.doi.org/10.1093/nar/gkz667.

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Abstract Homologous recombination is a fundamental process in all living organisms that allows the faithful repair of DNA double strand breaks, through the exchange of DNA strands between homologous regions of the genome. Results of three decades of investigation and recent fruitful observations have unveiled key elements of the reaction mechanism, which proceeds along nucleofilaments of recombinase proteins of the RecA family. Yet, one essential aspect of homologous recombination has largely been overlooked when deciphering the mechanism: while ATP is hydrolyzed in large quantity during the p

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26

Gao, Yang, Yanxiang Cui, Tara Fox, et al. "Structures and operating principles of the replisome." Science 363, no. 6429 (2019): eaav7003. http://dx.doi.org/10.1126/science.aav7003.

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Visualization in atomic detail of the replisome that performs concerted leading– and lagging–DNA strand synthesis at a replication fork has not been reported. Using bacteriophage T7 as a model system, we determined cryo–electron microscopy structures up to 3.2-angstroms resolution of helicase translocating along DNA and of helicase-polymerase-primase complexes engaging in synthesis of both DNA strands. Each domain of the spiral-shaped hexameric helicase translocates sequentially hand-over-hand along a single-stranded DNA coil, akin to the way AAA+ ATPases (adenosine triphosphatases) unfold pep

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Lin, D. C., B. Yurke, and N. A. Langrana. "Inducing Reversible Stiffness Changes in DNA-crosslinked Gels." Journal of Materials Research 20, no. 6 (2005): 1456–64. http://dx.doi.org/10.1557/jmr.2005.0186.

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Researchers have constructed a number of DNA-based nanodevices that undergo stepped configuration changes through the application of single-stranded DNA oligomers. Such devices can be incorporated into gel networks to create new classes of active materials with controllable bulk mechanical properties. This concept was demonstrated in a DNA-crosslinked gel, the stiffness of which was modulated through the application of DNA strands. Each crosslink incorporated a single-stranded region to which a DNA strand with a complementary base sequence (called the fuel strand) bound, thereby changing the n

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Lukac, David, Zuzana Machacova, and Pavel Moudry. "Emetine blocks DNA replication via proteosynthesis inhibition not by targeting Okazaki fragments." Life Science Alliance 5, no. 12 (2022): e202201560. http://dx.doi.org/10.26508/lsa.202201560.

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DNA synthesis of the leading and lagging strands works independently and cells tolerate single-stranded DNA generated during strand uncoupling if it is protected by RPA molecules. Natural alkaloid emetine is used as a specific inhibitor of lagging strand synthesis, uncoupling leading and lagging strand replication. Here, by analysis of lagging strand synthesis inhibitors, we show that despite emetine completely inhibiting DNA replication: it does not induce the generation of single-stranded DNA and chromatin-bound RPA32 (CB-RPA32). In line with this, emetine does not activate the replication c

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Masai, Hisao, Naoko Kakusho, Rino Fukatsu, et al. "Molecular architecture of G-quadruplex structures generated on duplex Rif1-binding sequences." Journal of Biological Chemistry 293, no. 44 (2018): 17033–49. http://dx.doi.org/10.1074/jbc.ra118.005240.

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G-quadruplexes (G4s) are four-stranded DNA structures comprising stacks of four guanines, are prevalent in genomes, and have diverse biological functions in various chromosomal structures. A conserved protein, Rap1-interacting factor 1 (Rif1) from fission yeast (Schizosaccharomyces pombe), binds to Rif1-binding sequence (Rif1BS) and regulates DNA replication timing. Rif1BS is characterized by the presence of multiple G-tracts, often on both strands, and their unusual spacing. Although previous studies have suggested generation of G4-like structures on duplex Rif1BS, its precise molecular archi

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Kapadia, Jay Bhakti, Nawwaf Kharma, Alen Nellikulam Davis, Nicolas Kamel, and Jonathan Perreault. "Toehold-mediated strand displacement to measure released product from self-cleaving ribozymes." RNA 28, no. 2 (2021): 263–73. http://dx.doi.org/10.1261/rna.078823.121.

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This paper presents a probe comprising a fluorophore and a quencher, enabling measurement of released product from self-cleaving hammerhead ribozyme, without labeled RNA molecules, regular sampling or use of polyacrylamide gels. The probe is made of two DNA strands; one strand is labeled with a fluorophore at its 5′-end, while the other strand is labeled with a quencher at its 3′-end. These two DNA strands are perfectly complementary, but with a 3′-overhang of the fluorophore strand. These unpaired nucleotides act as a toehold, which is utilized by a detached cleaved fragment (coming from a se

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Lestienne, Patrick P. "Priming DNA Replication from Triple Helix Oligonucleotides: Possible Threestranded DNA in DNA Polymerases." Molecular Biology International 2011 (September 14, 2011): 1–9. http://dx.doi.org/10.4061/2011/562849.

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Triplex associate with a duplex DNA presenting the same polypurine or polypyrimidine-rich sequence in an antiparallel orientation. So far, triplex forming oligonucleotides (TFOs) are known to inhibit transcription, replication, and to induce mutations. A new property of TFO is reviewed here upon analysis of DNA breakpoint yielding DNA rearrangements; the synthesized sequence of the first direct repeat displays a skewed polypurine- rich sequence. This synthesized sequence can bind the second homologous duplex sequence through the formation of a triple helix, which is able to prime further DNA r

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Lin, Maoxuan, and Jun-tao Guo. "New insights into protein–DNA binding specificity from hydrogen bond based comparative study." Nucleic Acids Research 47, no. 21 (2019): 11103–13. http://dx.doi.org/10.1093/nar/gkz963.

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Abstract Knowledge of protein–DNA binding specificity has important implications in understanding DNA metabolism, transcriptional regulation and developing therapeutic drugs. Previous studies demonstrated hydrogen bonds between amino acid side chains and DNA bases play major roles in specific protein–DNA interactions. In this paper, we investigated the roles of individual DNA strands and protein secondary structure types in specific protein–DNA recognition based on side chain-base hydrogen bonds. By comparing the contribution of each DNA strand to the overall binding specificity between DNA-bi

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Lo, Chen-Yu, and Yang Gao. "DNA Helicase–Polymerase Coupling in Bacteriophage DNA Replication." Viruses 13, no. 9 (2021): 1739. http://dx.doi.org/10.3390/v13091739.

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Bacteriophages have long been model systems to study the molecular mechanisms of DNA replication. During DNA replication, a DNA helicase and a DNA polymerase cooperatively unwind the parental DNA. By surveying recent data from three bacteriophage replication systems, we summarized the mechanistic basis of DNA replication by helicases and polymerases. Kinetic data have suggested that a polymerase or a helicase alone is a passive motor that is sensitive to the base-pairing energy of the DNA. When coupled together, the helicase–polymerase complex is able to unwind DNA actively. In bacteriophage T

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Aldag, Pierre, Fabian Welzel, Leonhard Jakob, et al. "Probing the stability of the SpCas9–DNA complex after cleavage." Nucleic Acids Research 49, no. 21 (2021): 12411–21. http://dx.doi.org/10.1093/nar/gkab1072.

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Abstract CRISPR–Cas9 is a ribonucleoprotein complex that sequence-specifically binds and cleaves double-stranded DNA. Wildtype Cas9 and its nickase and cleavage-incompetent mutants have been used in various biological techniques due to their versatility and programmable specificity. Cas9 has been shown to bind very stably to DNA even after cleavage of the individual DNA strands, inhibiting further turnovers and considerably slowing down in-vivo repair processes. This poses an obstacle in genome editing applications. Here, we employed single-molecule magnetic tweezers to investigate the binding

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35

Mohamadi, Maryam, Ali Mostafavi, and Masoud Torkzadeh-Mahani. "Design of a Sensitive and Selective Electrochemical Aptasensor for the Determination of the Complementary cDNA of miRNA-145 Based on the Intercalation and Electrochemical Reduction of Doxorubicin." Journal of AOAC INTERNATIONAL 100, no. 6 (2017): 1754–60. http://dx.doi.org/10.5740/jaoacint.16-0302.

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Abstract The aim of this research was the determination of a microRNA (miRNA) using a DNA electrochemical aptasensor. In this biosensor, the complementary complementary DNA (cDNA) of miRNA-145 (a sense RNA transcript) was the target strand and the cDNA of miRNA-145 was the probe strand. Both cDNAs can be the product of the reverse transcriptase-polymerase chain reaction of miRNA. The proposed aptasensor’s function was based on the hybridization of target strands with probes immobilized on the surface of a working electrode and the subsequent intercalation of doxorubicin (DOX) molecules functio

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Meagher, Martin, Alexander Myasnikov, and Eric J. Enemark. "Two Distinct Modes of DNA Binding by an MCM Helicase Enable DNA Translocation." International Journal of Molecular Sciences 23, no. 23 (2022): 14678. http://dx.doi.org/10.3390/ijms232314678.

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A six-subunit ATPase ring forms the central hub of the replication forks in all domains of life. This ring performs a helicase function to separate the two complementary DNA strands to be replicated and drives the replication machinery along the DNA. Disruption of this helicase/ATPase ring is associated with genetic instability and diseases such as cancer. The helicase/ATPase rings of eukaryotes and archaea consist of six minichromosome maintenance (MCM) proteins. Prior structural studies have shown that MCM rings bind one encircled strand of DNA in a spiral staircase, suggesting that the ring

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Nelson, W. G., and M. B. Kastan. "DNA strand breaks: the DNA template alterations that trigger p53-dependent DNA damage response pathways." Molecular and Cellular Biology 14, no. 3 (1994): 1815–23. http://dx.doi.org/10.1128/mcb.14.3.1815-1823.1994.

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The tumor suppressor protein p53 serves as a critical regulator of a G1 cell cycle checkpoint and of apoptosis following exposure of cells to DNA-damaging agents. The mechanism by which DNA-damaging agents elevate p53 protein levels to trigger G1/S arrest or cell death remains to be elucidated. In fact, whether damage to the DNA template itself participates in transducing the signal leading to p53 induction has not yet been demonstrated. We exposed human cell lines containing wild-type p53 alleles to several different DNA-damaging agents and found that agents which rapidly induce DNA strand br

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Nelson, W. G., and M. B. Kastan. "DNA strand breaks: the DNA template alterations that trigger p53-dependent DNA damage response pathways." Molecular and Cellular Biology 14, no. 3 (1994): 1815–23. http://dx.doi.org/10.1128/mcb.14.3.1815.

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The tumor suppressor protein p53 serves as a critical regulator of a G1 cell cycle checkpoint and of apoptosis following exposure of cells to DNA-damaging agents. The mechanism by which DNA-damaging agents elevate p53 protein levels to trigger G1/S arrest or cell death remains to be elucidated. In fact, whether damage to the DNA template itself participates in transducing the signal leading to p53 induction has not yet been demonstrated. We exposed human cell lines containing wild-type p53 alleles to several different DNA-damaging agents and found that agents which rapidly induce DNA strand br

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Szambowska, Anna, Ingrid Tessmer, Petri Kursula, et al. "DNA binding properties of human Cdc45 suggest a function as molecular wedge for DNA unwinding." Nucleic Acids Research 42, no. 4 (2013): 2308–19. http://dx.doi.org/10.1093/nar/gkt1217.

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Abstract The cell division cycle protein 45 (Cdc45) represents an essential replication factor that, together with the Mcm2-7 complex and the four subunits of GINS, forms the replicative DNA helicase in eukaryotes. Recombinant human Cdc45 (hCdc45) was structurally characterized and its DNA-binding properties were determined. Synchrotron radiation circular dichroism spectroscopy, dynamic light scattering, small-angle X-ray scattering and atomic force microscopy revealed that hCdc45 exists as an alpha-helical monomer and possesses a structure similar to its bacterial homolog RecJ. hCdc45 bound l

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Yu, Chuanhe, Haiyun Gan, Albert Serra-Cardona, et al. "A mechanism for preventing asymmetric histone segregation onto replicating DNA strands." Science 361, no. 6409 (2018): 1386–89. http://dx.doi.org/10.1126/science.aat8849.

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How parental histone (H3-H4)2 tetramers, the primary carriers of epigenetic modifications, are transferred onto leading and lagging strands of DNA replication forks for epigenetic inheritance remains elusive. Here we show that parental (H3-H4)2 tetramers are assembled into nucleosomes onto both leading and lagging strands, with a slight preference for lagging strands. The lagging-strand preference increases markedly in budding yeast cells lacking Dpb3 and Dpb4, two subunits of the leading strand DNA polymerase, Pol ε, owing to the impairment of parental (H3-H4)2 transfer to leading strands. Dp

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Zhang, Zi-Mou, Peng-Cheng Gao, Zhi-Fei Wang, Bai-Wang Sun, and Yong Jiang. "DNA-caged gold nanoparticles for controlled release of doxorubicin triggered by a DNA enzyme and pH." Chemical Communications 51, no. 65 (2015): 12996–99. http://dx.doi.org/10.1039/c5cc05164a.

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DNA polyhedron-caged AuNPs were self-assembled using four-point-star DNAs, with three strands hybridizing to each other and the fourth strand attaching to the AuNPs. The caged AuNPs can act as doxorubicin nanocarriers; a DNA enzyme and pH can trigger controlled release.

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Thompson, Shannon J., Aoife Rooney, Kevin M. Prise, and Stephen J. McMahon. "Evaluating Iodine-125 DNA Damage Benchmarks of Monte Carlo DNA Damage Models." Cancers 14, no. 3 (2022): 463. http://dx.doi.org/10.3390/cancers14030463.

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A wide range of Monte Carlo models have been applied to predict yields of DNA damage based on nanoscale track structure calculations. While often similar on the macroscopic scale, these models frequently employ different assumptions which lead to significant differences in nanoscale dose deposition. However, the impact of these differences on key biological readouts remains unclear. A major challenge in this area is the lack of robust datasets which can be used to benchmark models, due to a lack of resolution at the base pair level required to deeply test nanoscale dose deposition. Studies inv

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Zhang, Jiahui, Ashkan Fakharzadeh, Feng Pan, Christopher Roland, and Celeste Sagui. "Atypical structures of GAA/TTC trinucleotide repeats underlying Friedreich’s ataxia: DNA triplexes and RNA/DNA hybrids." Nucleic Acids Research 48, no. 17 (2020): 9899–917. http://dx.doi.org/10.1093/nar/gkaa665.

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Abstract Expansion of the GAA/TTC repeats in the first intron of the FXN gene causes Friedreich’s ataxia. Non-canonical structures are linked to this expansion. DNA triplexes and R-loops are believed to arrest transcription, which results in frataxin deficiency and eventual neurodegeneration. We present a systematic in silico characterization of the possible DNA triplexes that could be assembled with GAA and TTC strands; the two hybrid duplexes [r(GAA):d(TTC) and d(GAA):r(UUC)] in an R-loop; and three hybrid triplexes that could form during bidirectional transcription when the non-template DNA

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Gao, Rui, Zhuang Cai, Jianbang Wang, and Huajie Liu. "Condensed DNA Nanosphere for DNA Origami Cryptography." Chemistry 5, no. 4 (2023): 2406–17. http://dx.doi.org/10.3390/chemistry5040159.

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Maintaining the confidentiality and integrity of the messages during a transmission is one of the most important aims of encrypted communication systems. Many achievements were made using biomolecules to improve the quality of the messages in communication. At the same time, it is still a challenge to construct cooperative communications based on the interactions between biomolecules to achieve the confidentiality and integrity of the transmitted messages. DNA-based encrypted communications have been developed, and in particular, DNA-origami-based message encryption can combine steganography a

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Pavco, P. A., and G. C. Van Tuyle. "Purification and general properties of the DNA-binding protein (P16) from rat liver mitochondria." Journal of Cell Biology 100, no. 1 (1985): 258–64. http://dx.doi.org/10.1083/jcb.100.1.258.

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The mitochondrial DNA-binding protein P16 was isolated from rat liver mitochondrial lysates by affinity chromatography on single strand DNA agarose and separated from DNA in the preparation by alkaline CsCl isopycnic gradients. The top fraction of the gradients contained a single polypeptide species (Mr approximately equal to 15,200) based upon SDS PAGE. Digestion of single strand DNA-bound P16 with proteinase K produced a protease-insensitive, DNA-binding fragment (Mr approximately equal to 6,000) that has been purified by essentially the same procedures used for intact P16. The partial amino

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Shen, Hong Ming, Sarayu Ratnam, and Ursula Storb. "Targeting of the Activation-Induced Cytosine Deaminase Is Strongly Influenced by the Sequence and Structure of the Targeted DNA." Molecular and Cellular Biology 25, no. 24 (2005): 10815–21. http://dx.doi.org/10.1128/mcb.25.24.10815-10821.2005.

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ABSTRACT Activation-induced deaminase (AID) initiates immunoglobulin somatic hypermutation (SHM). Since in vitro AID was shown to deaminate cytosines on single-stranded DNA or the nontranscribed strand, it remained a puzzle how in vivo AID targets both DNA strands equally. Here we investigate the roles of transcription and DNA sequence in cytosine deamination. Strikingly different results are found with different substrates. Depending on the target sequence, the transcribed DNA strand is targeted as well as or better than the nontranscribed strand. The preferential targeting is not related to

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Balak, O. K., S. O. Balak, and O. Yu Lymanska. "Identification of intramolecular conserved G-quadruplex motifs in the genome of the bovine foamy virus." Journal for Veterinary Medicine, Biotechnology and Biosafety 10, no. 2 (2024): 13–19. http://dx.doi.org/10.36016/jvmbbs-2024-10-2-3.

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G-quadruplexes (G4s) are guanine-rich DNA structures, which play an essential regulatory role in key steps of the viral life cycle (replication, transcription regulation, translation). Currently, there is no relevant information about putative G4s in the bovine foamy virus (BFV) genome. The goal of the present study was the determination of such conservative non-B-DNA structures as conservative G-quadruplexes, which can be formed by two and three G-quartets in the mRNA, sense, and antisense strands of the bovine foamy virus proviral DNA. Bioinformatic analysis was used to search motifs of intr

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Di Paola, Vincenza, Martina Morrone, Valentina Poli, Andrea Fuso, Esterina Pascale, and Walter Adriani. "How Can CpG Methylations, and Pair-to-Pair Correlations between the Main (Gene) and the Opposite Strands, Suggest a Bending DNA Loop: Insights into the 5′-UTR of DAT1." Genes 14, no. 1 (2023): 190. http://dx.doi.org/10.3390/genes14010190.

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A working hypothesis issues from patterns of methylation in the 5′-UTR of the DAT1 gene. We considered relationships between pairs of CpGs, of which one on the main-gene strand and another on the complementary opposite strand (COS). We elaborated on data from ADHD children: we calculated all possible combinations of probabilities (estimated by multiplying two raw values of methylation) in pairs of CpGs from either strand. We analyzed all correlations between any given pair and all other pairs. For pairs correlating with M6-M6COS, some pairs had cytosines positioning to the reciprocal right (e.

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Beecham, E. J., J. F. Mushinski, E. Shacter, M. Potter, and V. A. Bohr. "DNA repair in the c-myc proto-oncogene locus: possible involvement in susceptibility or resistance to plasmacytoma induction in BALB/c mice." Molecular and Cellular Biology 11, no. 6 (1991): 3095–104. http://dx.doi.org/10.1128/mcb.11.6.3095-3104.1991.

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This report describes an unexpected difference in the efficiency of removal of UV-induced DNA damage in the c-myc locus in splenic B lymphoblasts from two inbred strains of mice. In cells from plasmacytoma-resistant DBA/2N mice, 35% of UV-induced damage in the regulatory and 5' flank of c-myc is removed by 12 h. However, in cells from plasmacytoma-susceptible BALB/cAn mice, damage is not removed from this region. In the protein-encoding region and 3' flank of c-myc as well as in two dihydrofolate reductase gene fragments, UV damage is repaired with similar efficiency in B lymphoblasts from bot

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Beecham, E. J., J. F. Mushinski, E. Shacter, M. Potter, and V. A. Bohr. "DNA repair in the c-myc proto-oncogene locus: possible involvement in susceptibility or resistance to plasmacytoma induction in BALB/c mice." Molecular and Cellular Biology 11, no. 6 (1991): 3095–104. http://dx.doi.org/10.1128/mcb.11.6.3095.

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This report describes an unexpected difference in the efficiency of removal of UV-induced DNA damage in the c-myc locus in splenic B lymphoblasts from two inbred strains of mice. In cells from plasmacytoma-resistant DBA/2N mice, 35% of UV-induced damage in the regulatory and 5' flank of c-myc is removed by 12 h. However, in cells from plasmacytoma-susceptible BALB/cAn mice, damage is not removed from this region. In the protein-encoding region and 3' flank of c-myc as well as in two dihydrofolate reductase gene fragments, UV damage is repaired with similar efficiency in B lymphoblasts from bot

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