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Journal articles on the topic 'Watson-Crick'

Author: Grafiati

Published: 4 June 2021

Last updated: 20 February 2023

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1

Fong, Wan Heng, Aqilahfarhana Abdul Rahman, Nor Haniza Sarmin, and Sherzod Turaev. "Static Watson-Crick Context-Free Grammars." International Journal of Online and Biomedical Engineering (iJOE) 15, no. 10 (June 27, 2019): 65. http://dx.doi.org/10.3991/ijoe.v15i10.10878.

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Sticker systems and Watson-Crick automata are two modellings of DNA molecules in DNA computing. A sticker system is a computational model which is coded with single and double-stranded DNA molecules; while Watson-Crick automata is the automata counterpart of sticker system which represents the biological properties of DNA. Both of these models use the feature of Watson-Crick complementarity in DNA computing. Previously, the grammar counterpart of the Watson-Crick automata have been introduced, known as Watson-Crick grammars which are classified into three classes: Watson-Crick regular grammars

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2

Abdul Rahman, Aqilahfarhana, Wan Heng Fong, Nor Haniza Sarmin, Sherzod Turaev, and Nurul Liyana Mohamad Zulkufli. "Static Watson-Crick regular grammar." Malaysian Journal of Fundamental and Applied Sciences 14 (October 25, 2018): 457–62. http://dx.doi.org/10.11113/mjfas.v14n0.1282.

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DNA computing, or more generally, molecular computing, is a recent development at the interface of computer science and molecular biology. In DNA computing, many computational models have been proposed in the framework of formal language theory and automata such as Watson-Crick grammars and sticker systems. A Watson-Crick grammar is a grammar model that generates double stranded strings, whereas a sticker system is a DNA computing model of the ligation and annealing operations over DNA strands using the Watson-Crick complementarity to form a complete double stranded DNA sequence. Most of the p

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3

Fong, Wan Heng, Aqilahfarhana Abdul Rahman, Nor Haniza Sarmin, and Sherzod Turaev. "Computational Power of Static Watson-Crick Context-free Grammars." Science Proceedings Series 1, no. 2 (April 24, 2019): 82–85. http://dx.doi.org/10.31580/sps.v1i2.679.

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Sticker system is a computer model which is coded with single and double-stranded molecules of DNA; meanwhile, Watson-Crick automata is the automata counterpart of the sticker system representing the biological properties of DNA. Both are the modelings of DNA molecules in DNA computing which use the feature of Watson-Crick complementarity. Formerly, Watson-Crick grammars which are classified into three classes have been introduced [1]. In this research, a grammar counterpart of sticker systems that uses the rule as in context-free grammar is introduced, known as a static Watson-Crick context-f

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4

Rangadurai, Atul, Eric S. Szymanski, Isaac Kimsey, Honglue Shi та Hashim M. Al-Hashimi. "Probing conformational transitions towards mutagenic Watson–Crick-like G·T mismatches using off-resonance sugar carbon R1ρ relaxation dispersion". Journal of Biomolecular NMR 74, № 8-9 (12 серпня 2020): 457–71. http://dx.doi.org/10.1007/s10858-020-00337-7.

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Abstract NMR off-resonance R1ρ relaxation dispersion measurements on base carbon and nitrogen nuclei have revealed that wobble G·T/U mismatches in DNA and RNA duplexes exist in dynamic equilibrium with short-lived, low-abundance, and mutagenic Watson–Crick-like conformations. As Watson–Crick-like G·T mismatches have base pairing geometries similar to Watson–Crick base pairs, we hypothesized that they would mimic Watson–Crick base pairs with respect to the sugar-backbone conformation as well. Using off-resonance R1ρ measurements targeting the sugar C3′ and C4′ nuclei, a structure survey, and mo

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5

KARI, LILA, and KALPANA MAHALINGAM. "WATSON-CRICK BORDERED WORDS AND THEIR SYNTACTIC MONOID." International Journal of Foundations of Computer Science 19, no. 05 (October 2008): 1163–79. http://dx.doi.org/10.1142/s0129054108006200.

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DNA strands that, mathematically speaking, are finite strings over the alphabet {A, G, C, T} are used in DNA computing to encode information. Due to the fact that A is Watson-Crick complementary to T and G to C, DNA single strands that are Watson-Crick complementary can bind to each other or to themselves in either intended or unintended ways. One of the structures that is usually undesirable for biocomputation, since it makes the affected DNA string unavailable for future interactions, is the hairpin: If some subsequences of a DNA single string are complementary to each other, the string will

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6

Jemima, Samuel Mary, and Rajkumar Dare. "Watson-Crick Local Languages and Watson-Crick Two Dimensional Local Languages." International Journal of Mathematics and Soft Computing 5, no. 2 (July 10, 2015): 165. http://dx.doi.org/10.26708/ijmsc.2015.2.5.19.

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7

Mahalingam, Kalpana, Ujjwal Kumar Mishra, and Rama Raghavan. "Watson–Crick Jumping Finite Automata." International Journal of Foundations of Computer Science 31, no. 07 (November 2020): 891–913. http://dx.doi.org/10.1142/s0129054120500331.

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Watson–Crick jumping finite automata work on tapes which are double stranded sequences of symbols similar to that of Watson–Crick automata. The double stranded sequence is scanned in a discontinuous manner. That is, after reading a double stranded string, the automata can jump over some subsequence and continue scanning depending on the rule. Some variants of such automata are 1-limited, No state, All final and Simple Watson–Crick jumping finite automata. The comparison of the languages accepted by these variants with the language classes in Chomsky hierarchy has been carried out. We investiga

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8

Xu, Yu, Akanksha Manghrani, Bei Liu, Honglue Shi, Uyen Pham, Amy Liu, and Hashim M. Al-Hashimi. "Hoogsteen base pairs increase the susceptibility of double-stranded DNA to cytotoxic damage." Journal of Biological Chemistry 295, no. 47 (September 10, 2020): 15933–47. http://dx.doi.org/10.1074/jbc.ra120.014530.

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As the Watson–Crick faces of nucleobases are protected in dsDNA, it is commonly assumed that deleterious alkylation damage to the Watson–Crick faces of nucleobases predominantly occurs when DNA becomes single-stranded during replication and transcription. However, damage to the Watson–Crick faces of nucleobases has been reported in dsDNA in vitro through mechanisms that are not understood. In addition, the extent of protection from methylation damage conferred by dsDNA relative to ssDNA has not been quantified. Watson–Crick base pairs in dsDNA exist in dynamic equilibrium with Hoogsteen base p

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9

Chatterjee, Kingshuk, and Kumar Sankar Ray. "Reversible Watson–Crick automata." Acta Informatica 54, no. 5 (April 19, 2016): 487–99. http://dx.doi.org/10.1007/s00236-016-0267-0.

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10

Chatterjee, Kingshuk, and Kumar Sankar Ray. "Unary Watson-Crick automata." Theoretical Computer Science 782 (August 2019): 107–12. http://dx.doi.org/10.1016/j.tcs.2019.03.009.

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11

Honig, Barry, and Remo Rohs. "Flipping Watson and Crick." Nature 470, no. 7335 (February 2011): 472–73. http://dx.doi.org/10.1038/470472a.

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12

Ray, Kumar Sankar, Kingshuk Chatterjee, and Debayan Ganguly. "State complexity of deterministic Watson–Crick automata and time varying Watson–Crick automata." Natural Computing 14, no. 4 (February 20, 2015): 691–99. http://dx.doi.org/10.1007/s11047-015-9494-5.

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13

LEONTIS, NEOCLES B., and ERIC WESTHOF. "Conserved geometrical base-pairing patterns in RNA." Quarterly Reviews of Biophysics 31, no. 4 (November 1998): 399–455. http://dx.doi.org/10.1017/s0033583599003479.

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1. INTRODUCTION 3992. DEFINITIONS 4013. CIS BASEPAIRS 4103.1 Cis Watson–Crick/Watson–Crick 4103.2 Wobble pairings 4113.3 Cis Watson–Crick/Hoogsteen pairings 4163.4 Bifurcated pairings 4173.5 Cis open and water-inserted 4214. TRANS BASEPAIRS 4234.1 Trans Watson–Crick/Watson–Crick 4234.2 Trans wobble pairs 4244.3 Trans Watson–Crick/Hoogsteen pairs 4244.4 Trans Hoogsteen/Hoogsteen pairs 4304.5 Trans bifurcated pairings 4325. SHALLOW-GROOVE PAIRINGS 4325.1 Hoogsteen/Shallow-groove pairs 4335.2 Watson–Crick/Shallow-groove pairings 4385.3 Shallow-groove/Shallow-groove pairings 4406. SIDE-BY-SIDE BAS

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14

Honkala, Juha. "Discrete Watson–Crick dynamical systems." Theoretical Computer Science 701 (November 2017): 125–31. http://dx.doi.org/10.1016/j.tcs.2016.12.033.

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15

Slobodkin, L. B. "Just before Watson and Crick." Nature Genetics 33, no. 4 (April 2003): 451–52. http://dx.doi.org/10.1038/ng0403-451.

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16

MacMillan, A. M. "Fifty years of "Watson-Crick"." Pure and Applied Chemistry 76, no. 7-8 (January 1, 2004): 1521–24. http://dx.doi.org/10.1351/pac200476071521.

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Fifty years have passed since Watson and Crick proposed the molecular basis for the replication of nucleic acid and hence the transfer of genetic information. During this time, a model for the expression of this genetic information has been proposed and refined considerably. Coincident with these advances, the chemical synthesis of oligonucleotides combined with the power of molecular biology has facilitated dramatic advances in our understanding of the fundamental workings of the living cell.

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17

Chatterjee, Kingshuk, and Kumar Sankar Ray. "Multi-head Watson–Crick automata." International Journal of Computer Mathematics: Computer Systems Theory 1, no. 2 (April 2, 2016): 57–73. http://dx.doi.org/10.1080/23799927.2016.1246477.

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18

Wu, Wen-Jin, Mei-I. Su, Jian-Li Wu, Sandeep Kumar, Liang-hin Lim, Chun-Wei Eric Wang, Frank H. T. Nelissen, et al. "How a Low-Fidelity DNA Polymerase Chooses Non-Watson–Crick from Watson–Crick Incorporation." Journal of the American Chemical Society 136, no. 13 (March 21, 2014): 4927–37. http://dx.doi.org/10.1021/ja4102375.

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19

Saoji, Maithili, and Paul J. Paukstelis. "Sequence-dependent structural changes in a self-assembling DNA oligonucleotide." Acta Crystallographica Section D Biological Crystallography 71, no. 12 (November 26, 2015): 2471–78. http://dx.doi.org/10.1107/s1399004715019598.

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DNA has proved to be a remarkable molecule for the construction of sophisticated two-dimensional and three-dimensional architectures because of its programmability and structural predictability provided by complementary Watson–Crick base pairing. DNA oligonucleotides can, however, exhibit a great deal of local structural diversity. DNA conformation is strongly linked to both environmental conditions and the nucleobase identities inherent in the oligonucleotide sequence, but the exact relationship between sequence and local structure is not completely understood. This study examines how a singl

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20

KARI, LILA, and KALPANA MAHALINGAM. "INVOLUTIVELY BORDERED WORDS." International Journal of Foundations of Computer Science 18, no. 05 (October 2007): 1089–106. http://dx.doi.org/10.1142/s0129054107005145.

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In this paper we study a generalization of the classical notions of bordered and unbordered words, motivated by DNA computing. DNA strands can be viewed as finite strings over the alphabet {A, G, C, T}, and are used in DNA computing to encode information. Due to the fact that A is Watson-Crick complementary to T and G to C, DNA single strands that are Watson-Crick complementary can bind to each other or to themselves in either intended or unintended ways. One of the structures that is usually undesirable for biocomputation, since it makes the affected DNA string unavailable for future interact

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21

Vijayaraghavan, N., N. Jansirani, and V. R. Dare. "WATSON CRICK FUZZY AUTOMATA WITH OUTPUT." Advances in Mathematics: Scientific Journal 10, no. 3 (March 24, 2021): 1637–54. http://dx.doi.org/10.37418/amsj.10.3.47.

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22

Southgate, Christopher. "CRICK, WATSON, AND THE DOUBLE HELIX." Zygon® 42, no. 1 (February 27, 2007): 257–58. http://dx.doi.org/10.1111/j.1467-9744.2006.00820.x.

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23

Benner, Steven A., Nilesh B. Karalkar, Shuichi Hoshika, Roberto Laos, Ryan W. Shaw, Mariko Matsuura, Diego Fajardo, and Patricia Moussatche. "Alternative Watson–Crick Synthetic Genetic Systems." Cold Spring Harbor Perspectives in Biology 8, no. 11 (September 23, 2016): a023770. http://dx.doi.org/10.1101/cshperspect.a023770.

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24

Salomaa, Arto. "Uni-transitional Watson–Crick D0L systems." Theoretical Computer Science 281, no. 1-2 (June 2002): 537–53. http://dx.doi.org/10.1016/s0304-3975(02)00026-9.

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25

Westhof, Eric, and Valérie Fritsch. "RNA folding: beyond Watson–Crick pairs." Structure 8, no. 3 (March 2000): R55—R65. http://dx.doi.org/10.1016/s0969-2126(00)00112-x.

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26

Chen, Edward C. M., and Edward S. Chen. "Thermal electrons and Watson Crick AT(−)." Chemical Physics Letters 435, no. 4-6 (February 2007): 331–35. http://dx.doi.org/10.1016/j.cplett.2006.12.064.

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27

Nagy, Benedek. "5′→3′ Watson-Crick pushdown automata." Information Sciences 537 (October 2020): 452–66. http://dx.doi.org/10.1016/j.ins.2020.06.031.

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28

Kari, Lila, and Kalpana Mahalingam. "Watson–Crick palindromes in DNA computing." Natural Computing 9, no. 2 (May 20, 2009): 297–316. http://dx.doi.org/10.1007/s11047-009-9131-2.

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29

Koag, Myong-Chul, та Seongmin Lee. "Insights into the effect of minor groove interactions and metal cofactors on mutagenic replication by human DNA polymerase β". Biochemical Journal 475, № 3 (9 лютого 2018): 571–85. http://dx.doi.org/10.1042/bcj20170787.

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DNA polymerases accommodate various base-pair conformations in the event of incorrect insertions. In particular, Watson–Crick-like dG:dTTP base pair has been observed at the insertion site of human DNA polymerase β (pol β). A potential factor contributing to the diverse conformations of base-pair mismatches is minor groove interactions. To gain insights into the effect of minor groove interactions on base-pair conformations, we generated an Asn279Ala polβ mutant that cannot make minor groove contacts with an incoming nucleotide. We conducted structural and kinetic studies of Asn279Ala polβ in

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30

Zhang, Yanbin, Fenghua Yuan, Xiaohua Wu та Zhigang Wang. "Preferential Incorporation of G Opposite Template T by the Low-Fidelity Human DNA Polymerase ι". Molecular and Cellular Biology 20, № 19 (1 жовтня 2000): 7099–108. http://dx.doi.org/10.1128/mcb.20.19.7099-7108.2000.

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ABSTRACT DNA polymerase activity is essential for replication, recombination, repair, and mutagenesis. All DNA polymerases studied so far from any biological source synthesize DNA by the Watson-Crick base-pairing rule, incorporating A, G, C, and T opposite the templates T, C, G, and A, respectively. Non-Watson-Crick base pairs would lead to mutations. In this report, we describe the ninth human DNA polymerase, Polι, encoded by the RAD30B gene. We show that human Polι violates the Watson-Crick base-pairing rule opposite template T. During base selection, human Polι preferred T-G base pairing, l

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31

Sun, Yan, May Myat Moe, and Jianbo Liu. "Is non-statistical dissociation a general feature of guanine–cytosine base-pair ions? Collision-induced dissociation of a protonated 9-methylguanine–1-methylcytosine Watson–Crick base pair, and comparison with its deprotonated and radical cation analogues." Physical Chemistry Chemical Physics 22, no. 43 (2020): 24986–5000. http://dx.doi.org/10.1039/d0cp04243a.

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32

Mondal, Soma, Jyotsna Bhat, Jagannath Jana, Meghomukta Mukherjee, and Subhrangsu Chatterjee. "Reverse Watson–Crick G–G base pair in G-quadruplex formation." Molecular BioSystems 12, no. 1 (2016): 18–22. http://dx.doi.org/10.1039/c5mb00611b.

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33

Ding, Yuanqi, Lei Xie, Xinyi Yao, and Wei Xu. "Real-space evidence of Watson–Crick and Hoogsteen adenine–uracil base pairs on Au(111)." Chemical Communications 54, no. 30 (2018): 3715–18. http://dx.doi.org/10.1039/c8cc01134f.

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34

Leupold, Peter, and Benedek Nagy. "5′ → 3′ Watson-Crick AutomataWith Several Runs." Fundamenta Informaticae 104, no. 1-2 (2010): 71–91. http://dx.doi.org/10.3233/fi-2010-336.

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35

Pollack, Robert. "Darwin and Mendel versus Watson and Crick." FASEB Journal 12, no. 2 (February 1998): 149–50. http://dx.doi.org/10.1096/fasebj.12.2.149.

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36

Maddox, John. "Watson, Crick and the future of DNA." Nature 362, no. 6416 (March 1993): 105. http://dx.doi.org/10.1038/362105a0.

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37

Heuberger, Benjamin D., Dongwon Shin, and Christopher Switzer. "Two Watson−Crick-Like Metallo Base-Pairs." Organic Letters 10, no. 6 (March 2008): 1091–94. http://dx.doi.org/10.1021/ol703029d.

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38

Honkala, Juha, and Arto Salomaa. "Watson–Crick D0L systems with regular triggers." Theoretical Computer Science 259, no. 1-2 (May 2001): 689–98. http://dx.doi.org/10.1016/s0304-3975(01)00010-x.

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39

Sosı́k, Petr. "Universal computation with Watson-Crick D0L systems." Theoretical Computer Science 289, no. 1 (October 2002): 485–501. http://dx.doi.org/10.1016/s0304-3975(01)00328-0.

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40

Bottoni, Paolo, Anna Labella, Vincenzo Manca, and Victor Mitrana. "Superposition Based on Watson–Crick-Like Complementarity." Theory of Computing Systems 39, no. 4 (December 20, 2004): 503–24. http://dx.doi.org/10.1007/s00224-004-1175-1.

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41

Kaushik Rangadurai, Atul, Eric S. Szymanski, Honglue Shi, and Hashim M. Al-Hashimi. "Watson-Crick Like Mismatches in Replication Fidelity." Biophysical Journal 116, no. 3 (February 2019): 359a. http://dx.doi.org/10.1016/j.bpj.2018.11.1953.

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42

Qiao, Xiaoxin, and Yoshito Kishi. "Modelle für kovalent verknüpfte Watson-Crick-Basenpaare." Angewandte Chemie 111, no. 7 (April 1, 1999): 977–80. http://dx.doi.org/10.1002/(sici)1521-3757(19990401)111:7<977::aid-ange977>3.0.co;2-d.

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43

Sarkar, Sunipa, Priya Rajdev, and Prashant Chandra Singh. "Hydrogen bonding of ionic liquids in the groove region of DNA controls the extent of its stabilization: synthesis, spectroscopic and simulation studies." Physical Chemistry Chemical Physics 22, no. 27 (2020): 15582–91. http://dx.doi.org/10.1039/d0cp01548b.

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44

Karas, Lucas J., Chia-Hua Wu, Henrik Ottosson, and Judy I. Wu. "Electron-driven proton transfer relieves excited-state antiaromaticity in photoexcited DNA base pairs." Chemical Science 11, no. 37 (2020): 10071–77. http://dx.doi.org/10.1039/d0sc02294b.

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45

Beiranvand, Nassim, Marek Freindorf, and Elfi Kraka. "Hydrogen Bonding in Natural and Unnatural Base Pairs—A Local Vibrational Mode Study." Molecules 26, no. 8 (April 14, 2021): 2268. http://dx.doi.org/10.3390/molecules26082268.

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In this work hydrogen bonding in a diverse set of 36 unnatural and the three natural Watson Crick base pairs adenine (A)–thymine (T), adenine (A)–uracil (U) and guanine (G)–cytosine (C) was assessed utilizing local vibrational force constants derived from the local mode analysis, originally introduced by Konkoli and Cremer as a unique bond strength measure based on vibrational spectroscopy. The local mode analysis was complemented by the topological analysis of the electronic density and the natural bond orbital analysis. The most interesting findings of our study are that (i) hydrogen bonding

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46

Das, Shubhajit, Pralok K. Samanta, and Swapan K. Pati. "Watson–Crick base pairing, electronic and photophysical properties of triazole modified adenine analogues: a computational study." New Journal of Chemistry 39, no. 12 (2015): 9249–56. http://dx.doi.org/10.1039/c5nj01566a.

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47

Teive, Hélio A. G. "On the centenary of the birth of Francis H. C. Crick – from physics to genetics and neuroscience." Arquivos de Neuro-Psiquiatria 74, no. 4 (April 2016): 351–53. http://dx.doi.org/10.1590/0004-282x20160029.

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ABSTRACT The year 2016 marks the centenary of the birth of Francis Crick (1916–2004), who made outstanding contributions to genetics and neuroscience. In 1953, in a collaborative study, Francis Crick and James Watson discovered the DNA double helix, and in 1962 they and Maurice Wilkins were awarded the Noble Prize in Physiology or Medicine. Crick subsequently became very interested in neuroscience, particularly consciousness and its relationship to the claustrum, a small gray matter structure between the insula and putamen.

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48

Takahashi, Shuntaro, Hiromichi Okura, Pallavi Chilka, Saptarshi Ghosh, and Naoki Sugimoto. "Molecular crowding induces primer extension by RNA polymerase through base stacking beyond Watson–Crick rules." RSC Advances 10, no. 55 (2020): 33052–58. http://dx.doi.org/10.1039/d0ra06502a.

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49

Kosbar, Tamer R., Mamdouh A. Sofan, Laila Abou-Zeid та Erik B. Pedersen. "Thermal stability of G-rich anti-parallel DNA triplexes upon insertion of LNA and α-l-LNA". Organic & Biomolecular Chemistry 13, № 18 (2015): 5115–21. http://dx.doi.org/10.1039/c5ob00535c.

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50

Chen, Meijin, Shiduan Chen, Fukai Zhu, Fanfan Wang, Haina Tian, Zhongxiong Fan, Sunkui Ke, Zhenqing Hou, and Yang Li. "“Watson–Crick GC”-inspired supramolecular nanodrug of methotrexate and 5-fluorouracil for tumor microenvironment-activatable self-recognizing synergistic chemotherapy." Journal of Materials Chemistry B 8, no. 17 (2020): 3829–41. http://dx.doi.org/10.1039/d0tb00468e.

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