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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Definitions, 2011 Two nitrogen-containing bases pair together between double-stranded DNA; only specific combinations of these bases (e.g., adenine with thymine; guanine with cytosine) are possible, a fact which facilitates accurate DNA replication; when quantified (e.g.,
J. Peretó
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DNA-Directed Base Pair Opening [PDF]
Molecules, 2012 Strand separation is a fundamental molecular process essential for the reading of the genetic information during DNA replication, transcription and recombination.
Youri Timsit
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Sequence dependency of canonical base pair opening in the DNA double helix. [PDF]
PLoS Computational Biology, 2017 The flipping-out of a DNA base from the double helical structure is a key step of many cellular processes, such as DNA replication, modification and repair.
Viveca Lindahl +2 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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Sequence-dependent base pair stepping dynamics in XPD helicase unwinding
eLife, 2013 Helicases couple the chemical energy of ATP hydrolysis to directional translocation along nucleic acids and transient duplex separation. Understanding helicase mechanism requires that the basic physicochemical process of base pair separation be ...
Zhi Qi +3 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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