Results 21 to 30 of about 20,403 (100)

A Mathematical Model for RNA 3D Structures

Mathematics
The computational prediction of RNA three-dimensional (3D) structures remains a significant challenge, largely due to the limited understanding of RNA folding pathways.
Sixiang Zhang, Liming Cai
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The Thermodynamic and Kinetic Properties of the dA-rU DNA-RNA Hybrid Base Pair Investigated via Molecular Dynamics Simulations

Molecules
DNA-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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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, Alessandra Villa, Berk Hess   +2 more
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Insights into the Structures of DNA Damaged by Hydroxyl Radical: Crystal Structures of DNA Duplexes Containing 5-Formyluracil

Journal of Nucleic Acids, 2010
Hydroxyl radicals are potent mutagens that attack DNA to form various base and ribose derivatives. One of the major damaged thymine derivatives is 5-formyluracil (fU), which induces pyrimidine transition during replication.
Masaru Tsunoda, Takeshi Sakaue, Satoko Naito, Tomoko Sunami, Naoko Abe, Yoshihito Ueno, Akira Matsuda, Akio Takénaka   +7 more
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Detection of genetic variation and base modifications at base-pair resolution on both DNA and RNA

Communications Biology, 2021
Wang et al. show how genetic sequence and base modifications can be detected simultaneously on single molecules of both DNA and RNA using magnetic tweezers.
Zhen Wang, Jérôme Maluenda, Laurène Giraut, Thibault Vieille, Andréas Lefevre, David Salthouse, Gaël Radou, Rémi Moulinas, Sandra Astete, Pol D’Avezac, Geoff Smith, Charles André, Jean-François Allemand, David Bensimon, Vincent Croquette, Jimmy Ouellet, Gordon Hamilton   +16 more
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Base-pair ambiguity and the kinetics of RNA folding

BMC Bioinformatics, 2019
Background A folding RNA molecule encounters multiple opportunities to form non-native yet energetically favorable pairings of nucleotide sequences. Given this forbidding free-energy landscape, mechanisms have evolved that contribute to a directed and ...
Guangyao Zhou, Jackson Loper, Stuart Geman   +2 more
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Shedding light on the base-pair opening dynamics of nucleic acids in living human cells

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, Takashi Nagata, Keiko Kondo, Tomoki Sakamoto, Shohei Takami, Masato Katahira   +5 more
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Biomechanics of DNA: rotational oscillations of bases [PDF]

Компьютерные исследования и моделирование, 2011
In this paper we study the rotational oscillations of the nitrous bases forming a central pair in a short DNA fragment consisting of three base pairs.
L. V. Yakushevich
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Reversibly locked thionucleobase pairs in DNA to study base flipping enzymes

Beilstein Journal of Organic Chemistry, 2014
Covalently interstrand cross-linked DNA is an interesting tool to study DNA binding proteins that locally open up the DNA duplex by flipping single bases out of the DNA helix or melting whole stretches of base pairs to perform their function.
Christine Beuck, Elmar Weinhold
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Study of Genetic Diversity of Some Persian walnut Genotypes in Mashhad Commercial Orchards by using ISSR Marker

Majallah-i ̒Ulum-i Bāghbānī, 2018
Introduction: Persian walnut (Juglans regia L.), belonging to the Juglandaceae family, has its natural origin in the mountainous regions of central Asia and especially northern forests of Iran.
Shadi Attar, Gholamhossein Davarynejad, Leila Samiee, Mohammad Moghadam   +3 more
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