Cargando…

Mechanical properties of symmetric and asymmetric DNA A-tracts: implications for looping and nucleosome positioning

A-tracts are functionally important DNA sequences which induce helix bending and have peculiar structural properties. While A-tract structure has been qualitatively well characterized, their mechanical properties remain controversial. A-tracts appear structurally rigid and resist nucleosome formatio...

Descripción completa

Detalles Bibliográficos
Autores principales:	Dršata, Tomáš, Špačková, Naďa, Jurečka, Petr, Zgarbová, Marie, Šponer, Jiří, Lankaš, Filip
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Oxford University Press 2014
Materias:	Structural Biology
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4066768/ https://www.ncbi.nlm.nih.gov/pubmed/24829460 http://dx.doi.org/10.1093/nar/gku338

Ejemplares similares

A measure of bending in nucleic acids structures applied to A-tract DNA
por: Lankaš, F., et al.
Publicado: (2010)

Interstrand cross-linking implies contrasting structural consequences for DNA: insights from molecular dynamics
por: Bignon, Emmanuelle, et al.
Publicado: (2017)

The temperature dependence of the helical twist of DNA
por: Kriegel, Franziska, et al.
Publicado: (2018)

A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA
por: Lavery, Richard, et al.
Publicado: (2010)

μABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA
por: Pasi, Marco, et al.
Publicado: (2014)

Revisiting the planarity of nucleic acid bases: Pyramidilization at glycosidic nitrogen in purine bases is modulated by orientation of glycosidic torsion
por: Sychrovsky, Vladimir, et al.
Publicado: (2009)

Multivalency of nucleosome recognition by LEDGF
por: Koutná, Eliška, et al.
Publicado: (2023)

Explaining the varied glycosidic conformational, G-tract length and sequence preferences for anti-parallel G-quadruplexes
por: Cang, Xiaohui, et al.
Publicado: (2011)

Explaining the striking difference in twist-stretch coupling between DNA and RNA: A comparative molecular dynamics analysis
por: Liebl, Korbinian, et al.
Publicado: (2015)

Cooperation between intrinsically disordered and ordered regions of Spt6 regulates nucleosome and Pol II CTD binding, and nucleosome assembly
por: Kasiliauskaite, Aiste, et al.
Publicado: (2022)

Structure and dynamics of DNA loops on nucleosomes studied with atomistic, microsecond-scale molecular dynamics
por: Pasi, Marco, et al.
Publicado: (2016)

Towards a molecular dynamics consensus view of B-DNA flexibility
por: Pérez, Alberto, et al.
Publicado: (2008)

Structural dynamics of possible late-stage intermediates in folding of quadruplex DNA studied by molecular simulations
por: Stadlbauer, Petr, et al.
Publicado: (2013)

Dynamic curvature regulation accounts for the symmetric and asymmetric beats of Chlamydomonas flagella
por: Sartori, Pablo, et al.
Publicado: (2016)

Assessing the Current State of Amber Force Field Modifications for DNA—2023 Edition
por: Love, Olivia, et al.
Publicado: (2023)

How does hydroxyl introduction influence the double helical structure: the stabilization of an altritol nucleic acid:ribonucleic acid duplex
por: Ovaere, Margriet, et al.
Publicado: (2012)

Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles
por: Zgarbová, Marie, et al.
Publicado: (2011)

On the structure and dynamics of the complex of the nucleosome and the linker histone
por: Pachov, Georgi V., et al.
Publicado: (2011)

Revealing transient structures of nucleosomes as DNA unwinds
por: Chen, Yujie, et al.
Publicado: (2014)

Assessing the Current State of Amber Force Field Modifications for DNA
por: Galindo-Murillo, Rodrigo, et al.
Publicado: (2016)

Structure and mechanical properties of the ribosomal L1 stalk three-way junction
por: Réblová, Kamila, et al.
Publicado: (2012)

Synergy between NMR measurements and MD simulations of protein/RNA complexes: application to the RRMs, the most common RNA recognition motifs
por: Krepl, Miroslav, et al.
Publicado: (2016)

Perturbations in nucleosome structure from heavy metal association
por: Mohideen, Kareem, et al.
Publicado: (2010)

The mechanics behind DNA sequence-dependent properties of the nucleosome
por: Chua, Eugene Y. D., et al.
Publicado: (2012)

Molecular dynamics simulations and their application to four-stranded DNA
por: Šponer, Jiří, et al.
Publicado: (2007)

Molecular dynamics simulations of sarcin–ricin rRNA motif
por: Špačková, Nad'a, et al.
Publicado: (2006)

Recognition of asymmetrically dimethylated arginine by TDRD3
por: Sikorsky, Tomas, et al.
Publicado: (2012)

DNA stretching in the nucleosome facilitates alkylation by an intercalating antitumour agent
por: Davey, Gabriela E., et al.
Publicado: (2010)

Insight into formation propensity of pseudocircular DNA G-hairpins
por: Živković, Martina Lenarčič, et al.
Publicado: (2021)

Conformational dynamics of the human propeller telomeric DNA quadruplex on a microsecond time scale
por: Islam, Barira, et al.
Publicado: (2013)

Structural study of the Fox-1 RRM protein hydration reveals a role for key water molecules in RRM-RNA recognition
por: Krepl, Miroslav, et al.
Publicado: (2017)

Structure of Actin-related protein 8 and its contribution to nucleosome binding
por: Gerhold, Christian B., et al.
Publicado: (2012)

The beginning and the end: flanking nucleotides induce a parallel G-quadruplex topology
por: Chen, Jielin, et al.
Publicado: (2021)

Cryo-EM structure of the nucleosome core particle containing Giardia lamblia histones
por: Sato, Shoko, et al.
Publicado: (2021)

Nucleosome composition regulates the histone H3 tail conformational ensemble and accessibility
por: Morrison, Emma A, et al.
Publicado: (2021)

Bivalent interaction of the PZP domain of BRPF1 with the nucleosome impacts chromatin dynamics and acetylation
por: Klein, Brianna J., et al.
Publicado: (2016)

Structure of the primed state of the ATPase domain of chromatin remodeling factor ISWI bound to the nucleosome
por: Chittori, Sagar, et al.
Publicado: (2019)

Nucleosome conformational variability in solution and in interphase nuclei evidenced by cryo-electron microscopy of vitreous sections
por: Eltsov, Mikhail, et al.
Publicado: (2018)

Asymmetric recognition of HIV-1 Envelope trimer by V1V2 loop-targeting antibodies
por: Wang, Haoqing, et al.
Publicado: (2017)

Cation binding to 15-TBA quadruplex DNA is a multiple-pathway cation-dependent process
por: Reshetnikov, Roman V., et al.
Publicado: (2011)

Cannot write session to /tmp/vufind_sessions/sess_3hr6osteo9vlrg9l9fvu04gcik