“…We show that specificity of human Polη for PtGpG derives from an active site that is open to permit Watson-Crick geometry of the nascent PtGpG•dCTP base pair and to accommodate the lesion without steric hindrance. …”
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“…This has enabled the application of the methodology for an extended design of RNA devices with specified behavior, assuming different molecular interaction models based on Watson-Crick interaction. We designed several YES, NOT, AND, and OR logic gates, including the design of combinatorial riboregulators. …”
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“…We now report on the ligand-bound structure of the Thermotoga petrophila fluoride riboswitch, which adopts a higher-order RNA architecture stabilized by pseudoknot and long-range reversed Watson-Crick and Hoogsteen A•U pair formation. The bound fluoride ion is encapsulated within the junctional architecture, anchored in place through direct coordination to three Mg(2+) ions, which in turn are octahedrally coordinated to waters and five inwardly-pointing backbone phosphates. …”
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“…The T–Hg(II)–T base pairs whose chemical structure was determined with the (15)N NMR spectroscopy were well accommodated in a B-form double helix, mimicking normal Watson–Crick base pairs. The Hg atoms aligned along DNA helical axis were shielded from the bulk water. …”
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“…Controlling for phylogenetic dependencies, we find that the usage of these tRNA species is positively correlated with GC content and may derive directly from nucleotide bias or from preference of Watson–Crick codon–anticodon interactions. Our results highlight the highly dynamic nature of these tRNAs and their complicated balance with codon usage.…”
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“…A tutorial and further information are available at https://sourceforge.net/p/rpore/wiki/Home/ Contact: mick.watson@roslin.ed.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online.…”
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“…Removing the aromatic rings of either A or T has no effect on the Watson–Crick bond strength. Only when the smaller mimics become saturated, that is, when the hydrogen-bond acceptor and donor groups go from sp(2) to sp(3), does the stability of the resulting model complexes suddenly drop. …”
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“…Our GQ mapping indicates that the likelihood of GQ formation is substantially diminished in dsDNA, likely due to the competition from the Watson–Crick base pairing. Unlike GQ folding sequence in ssDNA which forms both parallel and antiparallel GQs, dsDNA displays only parallel folding. …”
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“…These reveal that APE1 molds the T:G mismatch into a unique Watson-Crick like geometry that distorts the active site reducing incision. …”
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“…Based on our findings, we suggest that DrOPS is a versatile tool that could be used to evolve any polymerase function, where optical detection can be achieved by Watson–Crick base pairing.…”
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“…The primary robust R (2) (2)(8) ring motif is formed in the Watson–Crick face via N—H⋯O and O—H⋯N hydrogen bonds (involving N1, N6—H and the carboxyl group of HBA). …”
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“…Though not described here, THA can also be done using the anterolateral approach (also known as the Watson Jones approach) as well as the two-incision approach. …”
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“…The C-, G-, and T-tailing activities were enhanced by guanine, cytosine, and adenine, respectively, and by derivatives thereof, suggesting a transient Watson-Click base pairing between an enhancer molecule and the nucleotide to be incorporated. …”
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“…We observe a stable alignment for the looped-out 6’N7’ bulge base, which stacks on the unpaired first base of the guide strand, with the looped-out alignment facilitated by weakened Watson–Crick and reversed non-canonical flanking pairs. …”
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“…Chemical reagents that modify the Watson–Crick (WC) face of unprotected nucleobases are particularly useful in structure elucidation. …”
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“…As uncharged nucleic acid analogs, PMO bind to complementary sequences of target mRNA by Watson–Crick base pairing to block protein translation through steric blockade. …”
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“…To potentiate the discovery of new DNA nanoscale assemblies, recently, silver cations have been introduced to pair DNA strands by base–Ag(+)–base bonding rather than by Watson–Crick pairing. In this work, we study the classical dynamics of a parallel silver-mediated homobase double helix and compare it to the dynamics of the antiparallel double helix. …”
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“…The Fanconi Anemia (FA) pathway is important for repairing interstrand crosslinks (ICLs) between the Watson-Crick strands of the DNA double helix. An initial and essential stage in the repair process is the detection of the ICL. …”
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“…Through rational design, here we report the synthesis of a novel bio-MOF featuring unobstructed Watson-Crick faces of adenine (Ade) pointing towards the MOF cavities. …”
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“…The five bases of the target strand are recognized meticulously by stacking contacts, van der Waals interactions and specific Watson–Crick polar hydrogen bonds to ensure high enzymatic specificity.…”
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