The RNA Base-Pairing Problem and Base-Pairing Solutions. [PDF]
Cold Spring Harb Perspect Biol, 2018 RNA molecules are folded into structures and complexes to perform a wide variety of functions. Determination of RNA structures and their interactions is a fundamental problem in RNA biology. Most RNA molecules in living cells are large and dynamic, posing unique challenges to structure analysis.
Lu Z, Chang HY.
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Journal of Experimental and Molecular Biology, 2022 In contrast to Watson-Crick (WC) base pairing, Hoogsteen (HG) base pairing involves flipping a purine base 180° between its anti and syn conformation.
Neelabh Datta
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Hydrogen Bonding (Base Pairing) in Antiviral Activity [PDF]
Viruses, 2023 Base pairing based on hydrogen bonding has, since its inception, been crucial in the antiviral activity of arabinosyladenine, 2′-deoxyuridines (i.e., IDU, TFT, BVDU), acyclic nucleoside analogues (i.e., acyclovir) and nucleoside reverse transcriptase ...
Erik De Clercq
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Constraint of Base Pairing on HDV Genome Evolution [PDF]
Viruses, 2021 The hepatitis delta virus is a single-stranded circular RNA virus, which is characterized by high self-complementarity. About 70% of the genome sequences can form base-pairs with internal nucleotides.
Saki Nagata +2 more
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CsrA regulation via binding to the base-pairing small RNA Spot 42. [PDF]
Mol Microbiol, 2022 The carbon storage regulator system and base‐pairing small RNAs (sRNAs) represent two predominant modes of bacterial post‐transcriptional regulation, which globally influence gene expression.
Lai YJ +5 more
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Stringent Nucleotide Recognition by the Ribosome at the Middle Codon Position [PDF]
Molecules, 2017 Accurate translation of the genetic code depends on mRNA:tRNA codon:anticodon base pairing. Here we exploit an emissive, isosteric adenosine surrogate that allows direct measurement of the kinetics of codon:anticodon University of California base ...
Wei Liu +5 more
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Watson‐Crick Base Pairing of N‐Methoxy‐1,3‐Oxazinane (MOANA) Nucleoside Analogues within Double‐Helical DNA [PDF]
ChemistryOpen, 2023 Hairpin oligodeoxynucleotides incorporating a (2R,3S)‐4‐(methoxyamino)butane‐1,2,3‐triol residue in the middle of the double‐helical stem and opposite to either one of the canonical nucleobases or an abasic 2‐(hydroxymethyl)tetrahydrofuran‐3‐ol spacer ...
Mark N. K. Afari +3 more
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The siRNA Off-Target Effect Is Determined by Base-Pairing Stabilities of Two Different Regions with Opposite Effects. [PDF]
Genes (Basel), 2022 In RNA interference (RNAi), small interfering RNA (siRNA) suppresses the expression of its target mRNA with a perfect complementary sequence. In addition, siRNA also suppresses the expression of unintended mRNAs with partially complementary sequences ...
Kobayashi Y, Tian S, Ui-Tei K.
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Watson-Crick Base-Pairing Requirements for ssDNA Recognition and Processing in Replication-Initiating HUH Endonucleases [PDF]
mBio, 2023 Replication-initiating HUH endonucleases (Reps) are sequence-specific nucleases that cleave and rejoin single-stranded DNA (ssDNA) during rolling-circle replication.
Adam T. Smiley +7 more
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Synthesis of 6-Alkynylated Purine-Containing DNA via On-Column Sonogashira Coupling and Investigation of Their Base-Pairing Properties [PDF]
Molecules, 2023 Synthetic unnatural base pairs have been proven to be attractive tools for the development of DNA-based biotechnology. Our group has very recently reported on alkynylated purine–pyridazine pairs, which exhibit selective and stable base-pairing via ...
Hidenori Okamura +4 more
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