Results 51 to 60 of about 470,550 (372)
Rigid Base Biasing in Molecular Dynamics enables enhanced sampling of DNA conformations [PDF]
arXiv, 2022 All-atom simulations have become increasingly popular to study conformational and dynamical properties of nucleic acids as they are accurate and provide high spatial and time resolutions. This high resolution however comes at a heavy computational cost and within the time scales of simulations nucleic acids weakly fluctuate around their ideal structure
arxiv
Photonics, 2023 This review deals with modern approaches to systematic research on molecular-kinetic mechanisms of damage recognition and removal by pro- and eukaryotic enzymes of DNA base excision repair.
Nikita A. Kuznetsov
doaj +1 more source
Structure of d(TGCGCA)(2) and a comparison with other DNA Hexamers [PDF]
, 1998 The X-ray crystal structure of d(TGCGCA)(2) has been determined at 120 K to a resolution of 1.3 Angstrom. Hexamer duplexes, in the Z-DNA conformation, pack in an arrangement similar to the 'pure spermine form' [Egli et al. (1991). Biochemistry, 30, 11388-
Brannigan, J.A. +6 more
core +1 more source
A Chimeric DNA/RNA Antiparallel Quadruplex with Improved Stability
ChemistryOpen, 2022 Nucleic acid quadruplexes are proposed to play a role in the regulation of gene expression, are often present in aptamers selected for specific binding functions and have potential applications in medicine and biotechnology.
Elaina P. Boyle +3 more
doaj +1 more source
Ion-mediated RNA structural collapse: effect of spatial confinement [PDF]
, 2012 RNAs are negatively charged molecules residing in macromolecular crowding cellular environments. Macromolecular confinement can influence the ion effects in RNA folding.
Chen, Shi-Jie, Tan, Zhi-Jie
core +2 more sources
A nucleobase-centered coarse-grained representation for structure prediction of RNA motifs [PDF]
Nucleic Acids Res. 46, 1674 (2018), 2017 We introduce the SPlit-and-conQueR (SPQR) model, a coarse-grained representation of RNA designed for structure prediction and refinement. In our approach, the representation of a nucleotide consists of a point particle for the phosphate group and an anisotropic particle for the nucleoside.
arxiv +1 more source
Atypical response regulator ChxR from Chlamydia trachomatis is structurally poised for DNA binding. [PDF]
PLoS ONE, 2014 ChxR is an atypical two-component signal transduction response regulator (RR) of the OmpR/PhoB subfamily encoded by the obligate intracellular bacterial pathogen Chlamydia trachomatis. Despite structural homology within both receiver and effector domains
Michael L Barta +5 more
doaj +1 more source
Molecules, 2021 Specific RNA sequences regulate functions essential to life. The Trans-Activation Response element (TAR) is an RNA stem–bulge–loop structure involved in several steps of HIV-1 replication.
Alice Sosic +5 more
doaj +1 more source
Structural and mutagenic analysis of the RM controller protein C.Esp1396I [PDF]
, 2014 Bacterial restriction-modification (RM) systems are comprised of two complementary enzymatic activities that prevent the establishment of foreign DNA in a bacterial cell: DNA methylation and DNA restriction.
Kneale, Geoff +2 more
core +3 more sources
Multiple Lac-mediated loops revealed by Bayesian statistics and tethered particle motion [PDF]
Nucl. Acids Res. 42(16):10265-10277 (2014), 2014 The bacterial transcription factor LacI loops DNA by binding to two separate locations on the DNA simultaneously. Despite being one of the best-studied model systems for transcriptional regulation, the number and conformations of loop structures accessible to LacI remain unclear, though the importance of multiple co-existing loops has been implicated ...
arxiv +1 more source