Relevant bibliographies by topics / DNA strand

Contents

  1. Journal articles
  2. Dissertations / Theses
  3. Books
  4. Book chapters
  5. Conference papers
  6. Reports

Academic literature on the topic 'DNA strand'

Author: Grafiati
Published: 7 July 2024
Last updated: 31 July 2025

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Journal articles on the topic "DNA strand"

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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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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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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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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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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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Dissertations / Theses on the topic "DNA strand"

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Lo, Allen Tak Yiu. "Protein dynamics on the lagging strand during DNA synthesis." Thesis, School of Chemistry, 2012. https://ro.uow.edu.au/theses/3684.

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DNA replication is one of the vital processes in the cell; it duplicates chromosomal DNA before a cell divides. In all organisms, DNA synthesis on the leading-strand template occurs continuously, whereas on the lagging strand a different mechanism is required. Due to the anti-parallel structure of double-stranded DNA, lagging-strand synthesis requires repeated RNA priming by a specialist primase and synthesis of short Okazaki fragments. How proteins carry out this dynamic process is still unknown. For Escherichia coli DNA replication, a lagging-strand three-point switch was proposed in 1999 to
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Tingey, Andrew Philip. "Strand passage in DNA gyrase." Thesis, University of Leicester, 1996. http://hdl.handle.net/2381/35173.

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DNA gyrase, a type II topoisomerase, catalyses the introduction of negative supercoils into closed-circular DNA, using the energy from ATP hydrolysis. The reaction mechanism involves the breakage of one DNA double strand (the DNA gate) and the passing of another DNA strand (the passage helix) through that break and finally the re-sealing of the DNA gate. The strand-passage reaction was studied by the use of novel DNA substrates and by site-directed mutagenesis of one of the gyrase proteins. The DNA substrates were used to attempt to define the DNA segments used by the enzyme as the DNA gate an
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Ho, F. M. "Strand exchange for duplex DNA detection." Thesis, University of Cambridge, 2004. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.604106.

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The phenomenon of strand exchange between an unlabelled double-stranded target oligonucleotide and a single-stranded, fluorophore labelled probe oliognucleotide was investigated. This behaviour was characterised using fluorescence resonance energy transfer (FRET). The individual fluorescence characteristics of the fluorophores the minor-groove binder Hoechst 33258 and the dye Oregon Green 488 were studied, as well as their properties in combination as a FRET pair. These dyes allowed the use of FRET for the study of duplex DNA without the need for covalently attaching two labels on the componen
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Washbrook, Elinor. "Alternate strand DNA triple helix formation." Thesis, University of Southampton, 1996. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.242223.

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Lansita, Janice A. (Janice Ann) 1975. "Physicochemical characterization of immortal strand DNA." Thesis, Massachusetts Institute of Technology, 2004. http://hdl.handle.net/1721.1/18038.

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Thesis (Ph. D.)--Massachusetts Institute of Technology, Biological Engineering Division, 2004.<br>Includes bibliographical references.<br>Adult tissue differentiation involves the generation of distinct cell types from adult stem cells (ASCs). Current understanding of tissue differentiation mechanisms is based on studies of protein and RNAs that asymmetrically segregate between daughter cells during embryogenesis. Whether or not other types of biomolecules segregate asymmetrically has not been widely studied. In 1975, John Cairns proposed that ASCs preferentially segregate the oldest parental
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Absalon, Michael Joseph. "DNA double-strand cleavage mediated by bleomycin." Thesis, Massachusetts Institute of Technology, 1994. http://hdl.handle.net/1721.1/11927.

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Morant, Nick. "Novel thermostable DNA polymerases for isothermal DNA amplification." Thesis, University of Bath, 2015. https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.667735.

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DNA polymerases play a fundamental role in the transmission and maintenance of genetic information and have become an important in vitro diagnostic and analytical tool. The Loop-mediated isothermal DNA amplification (LAMP) method has major applications for disease and pathogen detection and utilises the unique strand-displacement activity of a small group of thermostable DNA polymerases. The Large (Klenow-like) Fragment of Geobacillus stearothermophilus DNA polymerase I (B.st LF Pol I) currently serves as the enzyme of choice for the majority of these isothermal reactions, with few alternative
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Tatavarthi, Haritha. "Action of Tyrosyl DNA Phosphodiesterase on 3'-Phosphoglycolate Terminated DNA Strand Breaks." VCU Scholars Compass, 2006. http://hdl.handle.net/10156/1799.

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Razavy, Haide. "Single-strand DNA ends in recombination in vivo." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1997. http://www.collectionscanada.ca/obj/s4/f2/dsk3/ftp04/mq22661.pdf.

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Fan, Saijun. "DNA strand breaks induced by gamma-ray irradiation." Thesis, University of Leicester, 1992. http://hdl.handle.net/2381/33667.

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Part I: Plasmid DNA System The effects of a range of buffers and additives on the radiation damage in frozen aqueous plasmid DNA have been studied. In studies of various buffers, the results show that phosphate buffer system sensitise radiation DNA damage, EDTA and Tris present protections against DNA damage, in comparison with pure water system. In studies of other additives, radioprotection by NaI and LiCl increase with increasing concentrations, whilst radiosensitivity of DNA with Na2SO4 and NaClO4 increase with increasing their concentrations. DMSO shows a radioprotection. A range concentr
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Books on the topic "DNA strand"

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Mills, Kevin D. Silencing, Heterochromatin and DNA Double Strand Break Repair. Springer US, 2001. http://dx.doi.org/10.1007/978-1-4615-4361-9.

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Al-Zain, Amr M. Mutagenic Repair Outcomes of DNA Double-Strand Breaks. [publisher not identified], 2021.

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Caroll, Robin. Strand of deception. B & H Books, 2013.

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Schrank, Benjamin Robin. Nuclear Arp2/3 drives DNA double-strand break clustering for homology-directed repair. [publisher not identified], 2019.

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Lee, So Jung. Mre11-Rad50-Xrs2 Complex in Coordinated Repair of DNA Double-Strand Break Ends from I-SceI, TALEN, and CRISPR-Cas9. [publisher not identified], 2022.

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Sinsheimer, Robert. The strands of a life: The science of DNA and the art of education. University of California Press, 1994.

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Keim, Celia D. Post Translational Regulation of AID Targeting to Both Strands of a Transcribed DNA Substrate. [publisher not identified], 2012.

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Affaitati, Marco. Dia logos: Lungo le strade della bellezza. Artemide, 2012.

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Sitohang, Japanton. Masalah perbatasan wilayah laut Indonesia dengan Malaysia dan Singapura. Edited by Lembaga Ilmu Pengetahuan Indonesia. Lembaga Ilmu Pengetahuan Indonesia, 2013.

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producer, Neuenfeldt Karl author, Pegrum Roger producer, and Dan Seaman 1929-, eds. Steady steady: The life and music of Seaman Dan. Aboriginal Studies Press, 2013.

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Book chapters on the topic "DNA strand"

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Wang, Zhiyu, Yingxin Hu, Zhekun Chen, Sulin Liao, and Yabing Huang. "Performing DNA Strand Displacement with DNA Polymerase." In Communications in Computer and Information Science. Springer Singapore, 2020. http://dx.doi.org/10.1007/978-981-15-3415-7_16.

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Olive, P. L. "Discussion: Cellular DNA Strand Breakage." In The Early Effects of Radiation on DNA. Springer Berlin Heidelberg, 1991. http://dx.doi.org/10.1007/978-3-642-75148-6_11.

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Cardelli, Luca. "Strand Algebras for DNA Computing." In Lecture Notes in Computer Science. Springer Berlin Heidelberg, 2009. http://dx.doi.org/10.1007/978-3-642-10604-0_2.

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Thachuk, Chris, Erik Winfree, and David Soloveichik. "Leakless DNA Strand Displacement Systems." In Lecture Notes in Computer Science. Springer International Publishing, 2015. http://dx.doi.org/10.1007/978-3-319-21999-8_9.

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Gloor, Gregory B., Tammy Dray, and Kathy Keeler. "Analyzing Double-Strand Repair Events in Drosophila." In DNA Repair Protocols. Humana Press, 1999. http://dx.doi.org/10.1007/978-1-4612-1608-7_34.

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Falk, Martin, Emilie Lukasova, and Stanislav Kozubek. "Repair of DNA Double-Strand Breaks." In Radiation Damage in Biomolecular Systems. Springer Netherlands, 2011. http://dx.doi.org/10.1007/978-94-007-2564-5_20.

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Liang, Feng, and Maria Jasin. "Extrachromosomal Assay for DNA Double-Strand Break Repair." In DNA Repair Protocols. Humana Press, 1999. http://dx.doi.org/10.1007/978-1-4612-1608-7_40.

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Kameda, Atsushi, Masahito Yamamoto, Hiroki Uejima, Masami Hagiya, Kensaku Sakamoto, and Azuma Ohuchi. "Conformational Addressing Using the Hairpin Structure of Single-Strand DNA." In DNA Computing. Springer Berlin Heidelberg, 2004. http://dx.doi.org/10.1007/978-3-540-24628-2_22.

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Lindahl, Tomas, Masahiko S. Satoh, and Grigory Dianov. "Enzymes acting at strand interruptions in DNA." In DNA Repair and Recombination. Springer Netherlands, 1995. http://dx.doi.org/10.1007/978-94-011-0537-8_8.

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Madzac, Catherine, and Alain Sarasin. "Single-Strand DNA Shuttle Vectors for Analyzing DNA-Damage Processing." In Anticarcinogenesis and Radiation Protection 2. Springer US, 1991. http://dx.doi.org/10.1007/978-1-4615-3850-9_11.

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Conference papers on the topic "DNA strand"

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Zhu, Yixuan, Shilin Tan, and Xuedong Zheng. "DNA cascading circuits based on combinatorial strand displacement." In 2024 Fourth International Conference on Biomedicine and Bioinformatics Engineering (ICBBE 2024), edited by Pier Paolo Piccaluga, Ahmed El-Hashash, and Xiangqian Guo. SPIE, 2024. http://dx.doi.org/10.1117/12.3044476.

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Walter, Frederik, Omer Sabary, Antonia Wachter-Zeh, and Eitan Yaakobi. "Coding for Composite DNA to Correct Substitutions, Strand Losses, and Deletions." In 2024 IEEE International Symposium on Information Theory (ISIT). IEEE, 2024. http://dx.doi.org/10.1109/isit57864.2024.10619202.

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Mindek, Peter, Tobias Klein, and Alfredo De Biasio. "DNA replication of the lagging strand." In SIGGRAPH '23 Electronic Theater: Special Interest Group on Computer Graphics and Interactive Techniques Conference: Electronic Theater. ACM, 2023. http://dx.doi.org/10.1145/3577024.3588981.

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Xie, Wenzhang, Junli Li, Chunyan Li, Rui Qiu, Congchong Yan, and Zhi Zeng. "Comparison of DNA strand-break simulated with different DNA models." In SNA + MC 2013 - Joint International Conference on Supercomputing in Nuclear Applications + Monte Carlo, edited by D. Caruge, C. Calvin, C. M. Diop, F. Malvagi, and J. C. Trama. EDP Sciences, 2014. http://dx.doi.org/10.1051/snamc/201405126.

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Zheng, Xuedong, and Yang Ru. "Autonomous DNA Neuron Learning Algorithm Based on DNA Strand Displacement." In BIC 2022: 2022 2nd International Conference on Bioinformatics and Intelligent Computing. ACM, 2022. http://dx.doi.org/10.1145/3523286.3524540.

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Shi, Lanlan, Changjun Zhou, and Qiang Zhang. "The neuronal perceptron with DNA strand displacement." In 2018 Tenth International Conference on Advanced Computational Intelligence (ICACI ). IEEE, 2018. http://dx.doi.org/10.1109/icaci.2018.8377534.

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Spencer, Frankie, Usman Sanwal, and Eugen Czeizler. "Distributed Simulations of DNA Multi-strand Dynamics." In 12th International Conference on Simulation and Modeling Methodologies, Technologies and Applications. SCITEPRESS - Science and Technology Publications, 2022. http://dx.doi.org/10.5220/0011266400003274.

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Hossain, Roksana, Robinson Mittmann, Ebrahim Ghafar-Zadeh, Geoffery G. Messier, and Sebastian Magierowski. "GPU base calling for DNA strand sequencing." In 2017 IEEE 60th International Midwest Symposium on Circuits and Systems (MWSCAS). IEEE, 2017. http://dx.doi.org/10.1109/mwscas.2017.8052869.

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Zheng, Xuedong, Zixin Qiu, Renjie Ma, and Shilin Tan. "Construction of DNA Circuits Based on Cooperative Hairpin DNA Strand Displacement." In ICBIT 2024: 2024 International Conference on Biomedicine and Intelligent Technology. ACM, 2024. https://doi.org/10.1145/3700486.3700497.

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Adi, Wibowo, and Kosuke Sekiyama. "One double-stranded DNA probes as classifier of multi targeting strand." In 2014 International Symposium on Micro-NanoMechatronics and Human Science (MHS). IEEE, 2014. http://dx.doi.org/10.1109/mhs.2014.7006166.

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Reports on the topic "DNA strand"

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Chen, Phang-Lang. BRCA2 and the DNA Double-Strand Break Repair Machinery. Defense Technical Information Center, 2000. http://dx.doi.org/10.21236/ada392755.

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Shih, William. DNA Strand Displacement Driven Molecular Additive Manufacturing (DSD-MAM). Office of Scientific and Technical Information (OSTI), 2025. https://doi.org/10.2172/2520465.

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Abratt, V., J. Santangelo, D. Woods, M. Peak, and J. Peak. Induction and repair of DNA strand-breaks in Bacteroides fragilis. Office of Scientific and Technical Information (OSTI), 1989. http://dx.doi.org/10.2172/5365674.

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Beal, P. A., and P. B. Dervan. Recognition of Double Helical DNA by Alternate Strand Triple Helix Formation. Defense Technical Information Center, 1992. http://dx.doi.org/10.21236/ada251499.

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Anderson, Carl W., and Mangala Tawde. Differential Expression of DNA Double-Strand Break Repair Proteins in Breast Cells. Defense Technical Information Center, 2001. http://dx.doi.org/10.21236/ada396787.

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Anderson, Carl W., and Mangale Tawde. Differential Expression of DNA Double-Strand Break Repair Proteins in Breast Cells. Defense Technical Information Center, 2002. http://dx.doi.org/10.21236/ada408738.

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Anderson, Carl W. Differential Expression of DNA Double-Strand Break Repair Proteins in Breast Cells. Defense Technical Information Center, 2003. http://dx.doi.org/10.21236/ada419972.

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Chen, D. J., and R. B. Cary. Identification and Characterization of a Human DNA Double-Strand Break Repair Complex. Office of Scientific and Technical Information (OSTI), 1999. http://dx.doi.org/10.2172/759194.

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Deininger, Prescott L. The Human L1 Element Causes DNA Double-Strand Breaks in Breast Cancer. Defense Technical Information Center, 2006. http://dx.doi.org/10.21236/ada474882.

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Dickman, Rebekah. Thermodynamic Effects of 5' and 3' Single Strand Dangling Ends on Short Duplex DNA. Portland State University Library, 2000. http://dx.doi.org/10.15760/etd.94.

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