2‐Methoxypyridine as a Thymidine Mimic in Watson–Crick Base Pairs of DNA and PNA: Synthesis, Thermal Stability, and NMR Structural Studies
Sign Up to like & getrecommendations! Published in 2017 at "ChemBioChem"
DOI: 10.1002/cbic.201700400
Abstract: The development of nucleic acid base‐pair analogues that use new modes of molecular recognition is important both for fundamental research and practical applications. The goal of this study was to evaluate 2‐methoxypyridine as a cationic… read more here.
Keywords: watson crick; dna; thymidine mimic; base ... See more keywords
On deterministic sensing $$5'\rightarrow 3'$$5′→3′ Watson–Crick finite automata: a full hierarchy in 2detLIN
Sign Up to like & getrecommendations! Published in 2021 at "Acta Informatica"
DOI: 10.1007/s00236-019-00362-6
Abstract: Watson–Crick (abbreviated as WK) finite automata are working on double stranded DNA molecule that is also called Watson–Crick tape. Subsequently, these automata have two reading heads, one for each strand. While in traditional WK automata… read more here.
Keywords: sensing rightarrow; watson crick; finite automata; watson ... See more keywords
Probing conformational transitions towards mutagenic Watson–Crick-like G·T mismatches using off-resonance sugar carbon R1ρ relaxation dispersion
Sign Up to like & getrecommendations! Published in 2020 at "Journal of Biomolecular Nmr"
DOI: 10.1007/s10858-020-00337-7
Abstract: NMR off-resonance R 1ρ 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.… read more here.
Keywords: watson crick; crick like; sugar; like mismatches ... See more keywords
Electrostatics affects formation of Watson-Crick complex between DNA bases in monolayers of nucleolipids deposited at a gold electrode surface
Sign Up to like & getrecommendations! Published in 2021 at "Electrochimica Acta"
DOI: 10.1016/j.electacta.2021.138816
Abstract: Abstract Chronocoulometry was applied to determine charge in a monolayer of nucleolipid (1,2-dipalmitoyl-sn‑glycero-3-(cytidine diphosphate)) deposited at a gold electrode surface. The immersion method was used to measure the potential of zero charge of the interface… read more here.
Keywords: surface; electrode surface; watson crick; electrostatics ... See more keywords
Activatable Self-Dissociation of Watson-Crick Structures with Fluorescent Nucleotides for Sensing Multiple Human Glycosylases at Single-Cell Level.
Sign Up to like & getrecommendations! Published in 2022 at "Analytical chemistry"
DOI: 10.1021/acs.analchem.2c04624
Abstract: Nucleobase oxidation and alkylation can destroy Watson-Crick base-pairing to challenge the genomic integrity. Human 8-oxoguanine glycosylase 1 (hOGG1) and alkyladenine glycosylase (hAAG) are evolved to counter these two cytotoxic lesions through base-excision repair, and their… read more here.
Keywords: cell; crick structures; self dissociation; watson crick ... See more keywords
Alchemical Free-Energy Calculations of Watson–Crick and Hoogsteen Base Pairing Interconversion in DNA
Sign Up to like & getrecommendations! Published in 2022 at "Journal of Chemical Theory and Computation"
DOI: 10.1021/acs.jctc.2c00848
Abstract: Hoogsteen (HG) base pairs have a transient nature and can be structurally similar to Watson–Crick (WC) base pairs, making their occurrence and thermodynamic stability difficult to determine experimentally. Herein, we employed the restrain–free-energy perturbation–release (R-FEP-R)… read more here.
Keywords: base pairing; free energy; watson crick; hoogsteen base ... See more keywords
Expanded Genetic Alphabets: Managing Nucleotides That Lack Tautomeric, Protonated, or Deprotonated Versions Complementary to Natural Nucleotides.
Sign Up to like & getrecommendations! Published in 2017 at "ACS synthetic biology"
DOI: 10.1021/acssynbio.6b00193
Abstract: 2,4-Diaminopyrimidine (trivially K) and imidazo[1,2-a]-1,3,5-triazine-2(8H)-4(3H)-dione (trivially X) form a nucleobase pair with Watson-Crick geometry as part of an artificially expanded genetic information system (AEGIS). Neither K nor X can form a Watson-Crick pair with any… read more here.
Keywords: watson crick; pair; expanded genetic; nucleobase ... See more keywords
Cooperative vibrational properties of hydrogen bonds in Watson–Crick DNA base pairs
Sign Up to like & getrecommendations! Published in 2017 at "New Journal of Chemistry"
DOI: 10.1039/c7nj03088f
Abstract: A detailed analysis of hydrogen bonding (H-bonding) nuclear motions is presented for adenine–thymine (AT) and guanine–cytosine (GC) Watson–Crick DNA base pairs. Using first-principles calculations, we investigated the infrared (IR) spectroscopy and nuclear vibrating patterns of… read more here.
Keywords: watson crick; crick dna; base pairs; dna base ... See more keywords
Probing Watson-Crick and Hoogsteen base pairing in duplex DNA using dynamic nuclear polarization solid-state NMR spectroscopy
Sign Up to like & getrecommendations! Published in 2022 at "Proceedings of the National Academy of Sciences of the United States of America"
DOI: 10.1073/pnas.2200681119
Abstract: Significance Hoogsteen base pairs, which are thermodynamically less stable than the canonical Watson-Crick base pairs, often feature in complexes of DNA with proteins and small molecules, where they play key roles in DNA recognition, repair,… read more here.
Keywords: watson crick; spectroscopy; hoogsteen base; base ... See more keywords
Complexes of DNA bases and Watson–Crick base pairs interaction with neutral silver Agn (n = 8, 10, 12) clusters: a DFT and TDDFT study
Sign Up to like & getrecommendations! Published in 2018 at "Journal of Biomolecular Structure and Dynamics"
DOI: 10.1080/07391102.2017.1310059
Abstract: We study the binding of the neutral Agn (n = 8, 10, 12) to the DNA base-adenine (A), guanine (G) and Watson–Crick –adenine-thymine, guanine-cytosine pairs. Geometries of complexes were optimized at the DFT level using… read more here.
Keywords: watson crick; dna; study; silver ... See more keywords
Insights into Watson–Crick/Hoogsteen breathing dynamics and damage repair from the solution structure and dynamic ensemble of DNA duplexes containing m1A
Sign Up to like & getrecommendations! Published in 2017 at "Nucleic Acids Research"
DOI: 10.1093/nar/gkx186
Abstract: Abstract In the canonical DNA double helix, Watson–Crick (WC) base pairs (bps) exist in dynamic equilibrium with sparsely populated (∼0.02–0.4%) and short-lived (lifetimes ∼0.2–2.5 ms) Hoogsteen (HG) bps. To gain insights into transient HG bps,… read more here.
Keywords: watson crick; dna; structure dynamic; solution structure ... See more keywords