Cargando…

Molecular dynamics simulations and their application to four-stranded DNA

This review provides a critical assessment of the advantages and limitations of modeling methods available for guanine quadruplex (G-DNA) molecules. We characterize the relations of simulations to the experimental techniques and explain the actual meaning and significance of the results. The followi...

Descripción completa

Detalles Bibliográficos
Autores principales:	Šponer, Jiří, Špačková, Nad’a
Formato:	Texto
Lenguaje:	English
Publicado:	Academic Press 2007
Materias:	Article
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2431124/ https://www.ncbi.nlm.nih.gov/pubmed/17967698 http://dx.doi.org/10.1016/j.ymeth.2007.02.004

Ejemplares similares

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

Mechanical properties of symmetric and asymmetric DNA A-tracts: implications for looping and nucleosome positioning
por: Dršata, Tomáš, et al.
Publicado: (2014)

Effects of Restrained Sampling Space and Nonplanar Amino Groups on Free-Energy Predictions for RNA with Imino and Sheared Tandem GA Base Pairs Flanked by GC, CG, iGiC or iCiG Base Pairs
por: Yildirim, Ilyas, et al.
Publicado: (2009)

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

Atomistic Picture of Opening–Closing Dynamics of DNA Holliday Junction Obtained by Molecular Simulations
por: Zhang, Zhengyue, et al.
Publicado: (2023)

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

Dynamics of the base of ribosomal A-site finger revealed by molecular dynamics simulations and Cryo-EM
por: Réblová, Kamila, et al.
Publicado: (2010)

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)

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

Spontaneous binding of single-stranded RNAs to RRM proteins visualized by unbiased atomistic simulations with a rescaled RNA force field
por: Krepl, Miroslav, et al.
Publicado: (2022)

Sensitivity of the RNA Structure to Ion Conditions as Probed by Molecular Dynamics Simulations of Common Canonical RNA Duplexes
por: Kührová, Petra, et al.
Publicado: (2023)

Molecular dynamics simulations suggest that RNA three-way junctions can act as flexible RNA structural elements in the ribosome
por: Beššeová, Ivana, et al.
Publicado: (2010)

Molecular basis for the increased affinity of an RNA recognition motif with re-engineered specificity: A molecular dynamics and enhanced sampling simulations study
por: Bochicchio, Anna, et al.
Publicado: (2018)

MD simulations reveal the basis for dynamic assembly of Hfq–RNA complexes
por: Krepl, Miroslav, et al.
Publicado: (2021)

Interaction of single- and double-stranded DNA with multilayer MXene by fluorescence spectroscopy and molecular dynamics simulations
por: Manzanares-Palenzuela, C. Lorena, et al.
Publicado: (2019)

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)

Parallel G-triplexes and G-hairpins as potential transitory ensembles in the folding of parallel-stranded DNA G-Quadruplexes
por: Stadlbauer, Petr, et al.
Publicado: (2019)

Molecular Dynamics Simulations of Double-Stranded DNA in an Explicit Solvent Model with the Zero-Dipole Summation Method
por: Arakawa, Takamasa, et al.
Publicado: (2013)

FOUR-STRANDED DNA AS DETERMINED BY ELECTRON MICROSCOPY
por: Hall, Cecil E., et al.
Publicado: (1961)

Exploring the Dynamics of Propeller Loops in Human Telomeric DNA Quadruplexes Using Atomistic Simulations
por: Islam, Barira, et al.
Publicado: (2017)

RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview
por: Šponer, Jiří, et al.
Publicado: (2018)

Volumetric Properties of Four-Stranded DNA Structures
por: Chalikian, Tigran V., et al.
Publicado: (2021)

Four-Analog Computation Based on DNA Strand Displacement
por: Zou, Chengye, et al.
Publicado: (2017)

Molecular Dynamics and Quantum Mechanics of RNA: Conformational and Chemical Change We Can Believe In
por: Ditzler, Mark A., et al.
Publicado: (2009)

Elastic properties of ribosomal RNA building blocks: molecular dynamics of the GTPase-associated center rRNA
por: Rázga, Filip, et al.
Publicado: (2007)

Ab Initio Molecular Dynamics Study of Methanol-Water Mixtures under External Electric Fields
por: Cassone, Giuseppe, et al.
Publicado: (2020)

Extended molecular dynamics of a c-kit promoter quadruplex
por: Islam, Barira, et al.
Publicado: (2015)

Molecular dynamics simulation of four typical surfactants in aqueous solution
por: Shi, Peng, et al.
Publicado: (2019)

Temperature-induced melting of double-stranded DNA in the absence and presence of covalently bonded antitumour drugs: insight from molecular dynamics simulations
por: Bueren-Calabuig, Juan A., et al.
Publicado: (2011)

DNA-strand molecular beacon optical processor
por: Thabit, Qabeela Q., et al.
Publicado: (2019)

Probing the Nanosecond Dynamics of a Designed Three-Stranded Beta-Sheet with a Massively Parallel Molecular Dynamics Simulation
por: Voelz, Vincent A., et al.
Publicado: (2009)

Role of Inosine–Uracil Base Pairs in the Canonical RNA Duplexes
por: Špačková, Naďa, et al.
Publicado: (2018)

Cellular levels and molecular dynamics simulations of estragole DNA adducts point at inefficient repair resulting from limited distortion of the double-stranded DNA helix
por: Yang, Shuo, et al.
Publicado: (2020)

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)

Molecular Dynamics Simulations: Advances and Applications
por: Filipe, Hugo A. L., et al.
Publicado: (2022)

Idiopathic intracranial hypertension in pediatric patients
por: Jirásková, Nad’a, et al.
Publicado: (2008)

Design Improvement of Four-Strand Continuous-Casting Tundish Using Physical and Numerical Simulation
por: Li, Quanhui, et al.
Publicado: (2023)

A Computational Quantum-Based Perspective on the Molecular Origins of Life’s Building Blocks
por: Amante, Gabriele, et al.
Publicado: (2022)

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

Complexity of Guanine Quadruplex Unfolding Pathways Revealed by Atomistic Pulling Simulations
por: Stadlbauer, Petr, et al.
Publicado: (2023)

Cannot write session to /tmp/vufind_sessions/sess_6m3mr0ick2eahbjg4u4qn5h4b5