Influence of BII Backbone Substates on DNA Twist: A Unified View and Comparison of Simulation and Experiment for All 136 Distinct Tetranucleotide Sequences

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61989592%3A15310%2F17%3A73583955" target="_blank" >RIV/61989592:15310/17:73583955 - isvavai.cz</a>

Alternative codes found

RIV/68081707:_____/17:00477377 RIV/60461373:22310/17:43914586

Result on the web

<a href="http://pubs.acs.org/doi/10.1021/acs.jcim.6b00621" target="_blank" >http://pubs.acs.org/doi/10.1021/acs.jcim.6b00621</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1021/acs.jcim.6b00621" target="_blank" >10.1021/acs.jcim.6b00621</a>

Result language

angličtina

Original language name

Influence of BII Backbone Substates on DNA Twist: A Unified View and Comparison of Simulation and Experiment for All 136 Distinct Tetranucleotide Sequences

Original language description

Reliable representation of the B-DNA base-pair step twist is one of the crucial requirements for theoretical modeling of DNA supercoiling and other biologically relevant phenomena in B-DNA. It has long been suspected that the twist is inaccurately described by current empirical force fields. Unfortunately, comparison of simulation results with experiments is not straightforward because of the presence of BII backbone substates, whose populations may differ in experimental and simulation ensembles. In this work, we provide a comprehensive view of the effect of BII substates on the overall B-DNA helix twist and show how to reliably compare twist values from experiment and simulation in two scenarios. First, for longer DNA segments freely moving in solution, we show that sequence averaged twists of different BI/BII ensembles can be compared directly because of approximate cancellation of the opposing BII effects. Second, for sequence-specific data, such as a particular base-pair step or tetranucleotide twist, can be compared only for a clearly defined BI/BII backbone conformation. For the purpose of force field testing, we designed a compact set of fourteen 22-base-pair B-DNA duplexes (Set 14) containing all 136 distinct tetranucleotide sequences and carried out a total of 84 mu s of molecular dynamics simulations, primarily with the OL15 force field. Our results show that the ff99bsc0 epsilon zeta(OL1 chi OL4), parmbscl, and OL15 force fields model the B-DNA helical twist in good agreement with X-ray and minicircle ligation experiments. The comprehensive understanding obtained regarding the effect of BEE substates on the base-pair step geometry should aid meaningful comparisons of various conformational ensembles in future research.

Czech name

—

Czech description

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Type

J_imp - Article in a specialist periodical, which is included in the Web of Science database

CEP classification

—

OECD FORD branch

10403 - Physical chemistry

Project

Result was created during the realization of more than one project. More information in the Projects tab.

Continuities

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Publication year

2017

Confidentiality

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Name of the periodical

Journal of Chemical Information and Modeling

ISSN

1549-9596

e-ISSN

—

Volume of the periodical

57

Issue of the periodical within the volume

2

Country of publishing house

US - UNITED STATES

Number of pages

13

Pages from-to

275-287

UT code for WoS article

000395226100018

EID of the result in the Scopus database

2-s2.0-85014205547