The Thermodynamic and Kinetic Properties of the dA-rU DNA-RNA Hybrid Base Pair Investigated via Molecular Dynamics Simulations [PDF]
MoleculesDNA-RNA hybrid duplexes play essential roles during the reverse transcription of RNA viruses and DNA replication. The opening and conformation changes of individual base pairs are critical to their biological functions.
Taigang Liu, Lei Bao, Yujie Wang
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Metal-mediated DNA strand displacement and molecular device operations based on base-pair switching of 5-hydroxyuracil nucleobases [PDF]
Nature Communications, 2023 Rational design of self-assembled DNA nanostructures has become one of the fastest-growing research areas in molecular science. Particular attention is focused on the development of dynamic DNA nanodevices whose configuration and function are regulated ...
Yusuke Takezawa +6 more
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DNA calorimetric force spectroscopy at single base pair resolution [PDF]
Nature CommunicationsDNA hybridization is a fundamental molecular reaction with wide-ranging applications in biotechnology. The knowledge of the temperature dependence of the thermodynamic parameters of duplex formation is crucial for quantitative predictions throughout the ...
P. Rissone +3 more
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Deep generalizable prediction of RNA secondary structure via base pair motif energy [PDF]
Nature CommunicationsDeep learning methods have demonstrated great performance for RNA secondary structure prediction. However, generalizability is a common unsolved issue on unseen out-of-distribution RNA families, which hinders further improvement of the accuracy and ...
Heqin Zhu +5 more
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Joint disease-specificity at the regulatory base-pair level [PDF]
Nature Communications, 2021 While many genetic loci have been found to be associated with disease, not many have had their causal variants and mechanisms investigated. Here, the authors experimentally dissect two loci near GDF5 which are associated with two different joint ...
Pushpanathan Muthuirulan +18 more
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Recognition and Sequencing of Mutagenic DNA Adduct at Single‐Base Resolution Through Unnatural Base Pair [PDF]
Advanced ScienceDNA lesions are linked to cancer, aging, and various diseases. The recognition and sequencing of special DNA lesions are of great interest but highly challenging.
Honglei Wang +8 more
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Shedding light on the base-pair opening dynamics of nucleic acids in living human cells [PDF]
Nature Communications, 2022 Base-pair opening is important for nucleic acids to exert biological functions, but studying its dynamics inside living cells is challenging. Here, the authors determine the base-pair opening kinetics of hairpin and G-quadruplex structures inside living ...
Yudai Yamaoki +5 more
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Dynamic Structure and Stability of DNA Duplexes Bearing a Dinuclear Hg(II)-Mediated Base Pair [PDF]
Molecules, 2020 Quantum mechanical (QM) and hybrid quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulations of a recently reported dinuclear mercury(II)-mediated base pair were performed aiming to analyse its intramolecular bonding pattern, its ...
Jim Bachmann +3 more
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DFT study on metal-mediated uracil base pair complexes
Journal of Saudi Chemical Society, 2017 The most stable of metal-mediated uracil base pair complexes were determined. Method was used density functional theory, B3LYP. The calculations of systems containing C, H, N, O were described by 6-311++G(d,p) and cc-PVTZ basis sets and LANL2DZ and SDD ...
Ayhan Üngördü, Nurten Tezer
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Cooperativity and Interdependency between RNA Structure and RNA–RNA Interactions
Non-Coding RNA, 2021 Complex RNA–RNA interactions are increasingly known to play key roles in numerous biological processes from gene expression control to ribonucleoprotein granule formation.
Ilias Skeparnias, Jinwei Zhang
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