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Journal articles on the topic 'Watson-Crick'

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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, Watson-Crick linear grammars and Watson-Crick context-free grammars. In this research, a new variant of Watson-Crick grammar called a static Watson-Crick context-free grammar, which is a grammar counterpart of sticker systems that generates the double-stranded strings and uses rule as in context-free grammar, is introduced. The static Watson-Crick context-free grammar differs from a dynamic Watson-Crick context-free grammar in generating double-stranded strings, as well as for regular and linear grammars. The main result of the paper is to determine the generative powers of static Watson-Crick context-free grammars. Besides, the relationship of the families of languages generated by Chomsky grammars, sticker systems and Watson-Crick grammars are presented in terms of their hierarchy.

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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 proposed DNA computing models make use of this concept, including the Watson-Crick grammars and sticker systems. Watson-Crick grammars and their variants can be explored using formal language theory which allows the development of new concepts of Watson-Crick grammars. In this research, a new variant of Watson-Crick grammar called a static Watson-Crick regular grammar is introduced as an analytical counterpart of sticker systems. The computation of a sticker system starts from a given set of incomplete double stranded sequence to form a complete double stranded sequence. Here, a static Watson-Crick regular grammar differs from a dynamic Watson-Crick regular grammar in generating double stranded strings: the latter grammar produces each strand string “independently” and only check for the Watson-Crick complementarity of a generated complete double stranded string at the end, while the former grammar generates both strand strings “dependently”, i.e., checking for the Watson-Crick complementarity for each complete substring. In this paper, computational properties of static Watson-Crick regular grammars are investigated to correlate with the Chomsky hierarchy and hierarchy of the families of dynamic Watson-Crick regular languages. The relationship between families of languages generated by static Watson-Crick regular grammars with several variants of sticker systems, Watson-Crick regular grammars and Chomsky grammars are presented by showing the hierarchy.

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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-free grammar. The research finding on the computational power of these grammar shows that the family of context-free languages is strictly included in the family of static Watson-Crick context-free languages; the static Watson-Crick context-free grammars can generate non context-free languages; the family of Watson-Crick context-free languages is included in the family of static Watson-Crick context-free languages which are presented in terms of their hierarchy.

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4

Rangadurai, Atul, Eric S. Szymanski, Isaac Kimsey, Honglue Shi, and 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, no. 8-9 (August 12, 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 molecular dynamics simulations, we show that wobble G·T mismatches adopt sugar-backbone conformations that deviate from the canonical Watson–Crick conformation and that transitions toward tautomeric and anionic Watson–Crick-like G·T mismatches restore the canonical Watson–Crick sugar-backbone. These measurements also reveal kinetic isotope effects for tautomerization in D2O versus H2O, which provide experimental evidence in support of a transition state involving proton transfer. The results provide additional evidence in support of mutagenic Watson–Crick-like G·T mismatches, help rule out alternative inverted wobble conformations in the case of anionic G·T−, and also establish sugar carbons as new non-exchangeable probes of this exchange process.

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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 bind to itself forming a hairpin-like structure. This paper studies a mathematical formalization of a particular case of hairpins, the Watson-Crick bordered words. A Watson-Crick bordered word is a word with the property that it has a prefix that is Watson-Crick complementary to its suffix. We namely study algebraic properties of Watson-Crick bordered and unbordered words. We also give a complete characterization of the syntactic monoid of the language consisting of all Watson-Crick bordered words over a given alphabet. Our results hold for the more general case where the Watson-Crick complement function is replaced by an arbitrary antimorphic involution.

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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 investigate some closure properties. We also try to place the duplication closure of a word in Watson–Crick jumping finite automata family. We have discussed the closure property of Watson–Crick jumping finite automata family under duplication operations.

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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 pairs that expose the Watson–Crick faces of purine nucleobases to solvent. Whether this can influence the damage susceptibility of dsDNA remains unknown. Using dot-blot and primer extension assays, we measured the susceptibility of adenine-N1 to methylation by dimethyl sulfate (DMS) when in an A-T Watson–Crick versus Hoogsteen conformation. Relative to unpaired adenines in a bulge, Watson–Crick A-T base pairs in dsDNA only conferred ∼130-fold protection against adenine-N1 methylation, and this protection was reduced to ∼40-fold for A(syn)-T Hoogsteen base pairs embedded in a DNA-drug complex. Our results indicate that Watson–Crick faces of nucleobases are accessible to alkylating agents in canonical dsDNA and that Hoogsteen base pairs increase this accessibility. Given the higher abundance of dsDNA relative to ssDNA, these results suggest that dsDNA could be a substantial source of cytotoxic damage. The work establishes DMS probing as a method for characterizing A(syn)-T Hoogsteen base pairs in vitro and also lays the foundation for a sequencing approach to map A(syn)-T Hoogsteen and unpaired adenines genome-wide in vivo.

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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 BASES 4467. DEFINING A LIBRARY OF ISOSTERIC PAIRINGS 4468. CONCLUSIONS 4519. ACKNOWLEDGEMENTS 45210. REFERENCES 452RNA molecules fold into a bewildering variety of complex 3D structures. Almost every new RNA structure obtained at high resolution reveals new, unanticipated structural motifs, which we are rarely able to predict at the current stage of our theoretical understanding. Even at the most basic level of specific RNA interactions – base-to-base pairing – new interactions continue to be uncovered as new structures appear. Compilations of possible non-canonical base-pairing geometries have been presented in previous reviews and monographs (Saenger, 1984; Tinoco, 1993). In these compilations, the guiding principle applied was the optimization of hydrogen-bonding. All possible pairs with two standard H-bonds were presented and these were organized according to symmetry or base type. However, many of the features of RNA base-pairing interactions that have been revealed by high-resolution crystallographic analysis could not have been anticipated and, therefore were not incorporated into these compilations. These will be described and classified in the present review. A recently presented approach for inferring basepair geometry from patterns of sequence variation (Gautheret & Gutell, 1997) relied on the 1984 compilation of basepairs (Saenger, 1984), and was extended to include all possible single H-bond combinations not subject to steric clashes. Another recent review may be consulted for a discussion of the NMR spectroscopy and thermodynamic effects of non-canonical (‘mismatched’) RNA basepairs on duplex stability (Limmer, 1997).

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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 single-nucleotide addition to a class of self-assembling DNA 13-mers leads to a significantly different overall structure under identical crystallization conditions. The DNA 13-mers self-assemble in the presence of Mg2+through a combination of Watson–Crick and noncanonical base-pairing interactions. The crystal structures described here show that all of the predicted Watson–Crick base pairs are present, with the major difference being a significant rearrangement of noncanonical base pairs. This includes the formation of a sheared A–G base pair, a junction of strands formed from base-triple interactions, and tertiary interactions that generate structural features similar to tandem sheared G–A base pairs. The adoption of this alternate noncanonical structure is dependent in part on the sequence in the Watson–Crick duplex region. These results provide important new insights into the sequence–structure relationship of short DNA oligonucleotides and demonstrate a unique interplay between Watson–Crick and noncanonical base pairs that is responsible for crystallization fate.

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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 interactions, is the hairpin: If some subsequences of a DNA single string are complementary to each other, the string will bind to itself forming a hairpin-like structure. This paper studies a mathematical formalization of a particular case of hairpins, the Watson-Crick bordered words. A Watson-Crick bordered word is a word with the property that it has a prefix that is Watson-Crick complementary to its suffix. More generally, we investigate the notion of θ-bordered words, where θ is a morphic or antimorphic involution. We show that the set of all θ-bordered words is regular, when θ is an antimorphic involution and the set of all θ-bordered words is context-sensitive when θ is a morphic involution. We study the properties of θ-bordered and θ-unbordered words and also the relation between θ-bordered and θ-unbordered words and certain type of involution codes.

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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, and Seongmin Lee. "Insights into the effect of minor groove interactions and metal cofactors on mutagenic replication by human DNA polymerase β." Biochemical Journal 475, no. 3 (February 9, 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 complex with incoming dTTP and templating dG or O6-methyl-dG. The crystal structure of the Asn279Ala polβ-G:T complex showed a wobble dG:dTTP base pair, indicating that the previously observed Watson–Crick-like dG:dTTP conformation was induced by the minor groove contact. In contrast, O6-methyl-dG, an analog of the enol tautomer of guanine, formed a Watson–Crick-like base pair with dTTP in the absence of the minor groove contact. These results suggest that the Watson–Crick-like G:T base pair at the insertion site is formed by the rare enol tautomers of G or T, whose population is increased by the minor groove hydrogen bond with Asn279. Kinetic studies showed that Asn279Ala mutation decreased dG:dTTP misincorporation rate six-fold in the presence of Mg2+ but increased the rate three-fold in the presence of Mn2+, highlighting the effect of minor groove interactions and metal ions on promutagenic replication by polβ.

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30

Zhang, Yanbin, Fenghua Yuan, Xiaohua Wu, and Zhigang Wang. "Preferential Incorporation of G Opposite Template T by the Low-Fidelity Human DNA Polymerase ι." Molecular and Cellular Biology 20, no. 19 (October 1, 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, leading to G incorporation opposite template T. The resulting T-G base pair was less efficiently extended by human Polι compared to the Watson-Crick base pairs. Consequently, DNA synthesis frequently aborted opposite template T, a property we designated the T stop. This T stop restricted human Polι to a very short stretch of DNA synthesis. Furthermore, kinetic analyses show that human Polι copies template C with extraordinarily low fidelity, misincorporating T, A, and C with unprecedented frequencies of 1/9, 1/10, and 1/11, respectively. Human Polι incorporated one nucleotide opposite a template abasic site more efficiently than opposite a template T, suggesting a role for human Polι in DNA lesion bypass. The unique features of preferential G incorporation opposite template T and T stop suggest that DNA Polι may additionally play a specialized function in human biology.

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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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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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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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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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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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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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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 in Watson Crick base pairs is not exceptionally strong and (ii) the N–H⋯N is the most favorable hydrogen bond in both unnatural and natural base pairs while O–H⋯N/O bonds are the less favorable in unnatural base pairs and not found at all in natural base pairs. In addition, the important role of non-classical C–H⋯N/O bonds for the stabilization of base pairs was revealed, especially the role of C–H⋯O bonds in Watson Crick base pairs. Hydrogen bonding in Watson Crick base pairs modeled in the DNA via a QM/MM approach showed that the DNA environment increases the strength of the central N–H⋯N bond and the C–H⋯O bonds, and at the same time decreases the strength of the N–H⋯O bond. However, the general trends observed in the gas phase calculations remain unchanged. The new methodology presented and tested in this work provides the bioengineering community with an efficient design tool to assess and predict the type and strength of hydrogen bonding in artificial base pairs.

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

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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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