Literature DB >> 26396657

A computational study of dsDNA pairs and vibrational resonance in separating water.

Richard J Calloway1, Michael D Proctor2, Victor M Boyer2, Samantha Napier2.   

Abstract

This article investigates the relationship between molecular sequence and dependent interacting behavior of molecular segment pairs and secondly, sequence dependent, vibrational resonance in surrounding normal saline, protein-free water. The development of a molecular model to explore these systems phenomena, the results of several nanoscale molecular dynamics simulations, and analysis of behavior of interacting ΦX174 double-stranded DNA segment pair models in various configurations are presented. Fourier analysis revealed intriguing vibration frequencies within the solvent plane between the segments, while subsequent frequency domain transformation of the time domain waveforms revealed statistically significant resonating harmonic signals in the THz range.

Entities:  

Keywords:  DNA; Homologous pairing; Molecular vibration; Resonance; Segregation

Year:  2014        PMID： 26396657      PMCID： PMC4571727          DOI： 10.1007/s11693-014-9157-3

Source DB:  PubMed          Journal:  Syst Synth Biol        ISSN： 1872-5325


  26 in total

Review 1.  What makes homologous chromosomes find each other in meiosis? A review and an hypothesis.

Authors:  J Sybenga
Journal:  Chromosoma       Date:  1999-08       Impact factor: 4.316

2.  Saccharomyces cerevisiae Dmc1 and Rad51 proteins preferentially function with Tid1 and Rad54 proteins, respectively, to promote DNA strand invasion during genetic recombination.

Authors:  Amitabh V Nimonkar; Christopher C Dombrowski; Joseph S Siino; Alicja Z Stasiak; Andrzej Stasiak; Stephen C Kowalczykowski
Journal:  J Biol Chem       Date:  2012-06-29       Impact factor: 5.157

3.  Picosecond fluctuating protein energy landscape mapped by pressure temperature molecular dynamics simulation.

Authors:  Lars Meinhold; Jeremy C Smith; Akio Kitao; Ahmed H Zewail
Journal:  Proc Natl Acad Sci U S A       Date:  2007-10-23       Impact factor: 11.205

4.  Single molecule nanometronome.

Authors:  Chittanon Buranachai; Sean A McKinney; Taekjip Ha
Journal:  Nano Lett       Date:  2006-03       Impact factor: 11.189

Review 5.  CHARMM: the biomolecular simulation program.

Authors:  B R Brooks; C L Brooks; A D Mackerell; L Nilsson; R J Petrella; B Roux; Y Won; G Archontis; C Bartels; S Boresch; A Caflisch; L Caves; Q Cui; A R Dinner; M Feig; S Fischer; J Gao; M Hodoscek; W Im; K Kuczera; T Lazaridis; J Ma; V Ovchinnikov; E Paci; R W Pastor; C B Post; J Z Pu; M Schaefer; B Tidor; R M Venable; H L Woodcock; X Wu; W Yang; D M York; M Karplus
Journal:  J Comput Chem       Date:  2009-07-30       Impact factor: 3.376

Review 6.  Comparison of protein force fields for molecular dynamics simulations.

Authors:  Olgun Guvench; Alexander D MacKerell
Journal:  Methods Mol Biol       Date:  2008

7.  The biological functions of low-frequency vibrations (phonons). 4. Resonance effects and allosteric transition.

Authors:  K C Chou
Journal:  Biophys Chem       Date:  1984-08       Impact factor: 2.352

8.  Sustained and rapid chromosome movements are critical for chromosome pairing and meiotic progression in budding yeast.

Authors:  Megan Sonntag Brown; Sarah Zanders; Eric Alani
Journal:  Genetics       Date:  2011-02-21       Impact factor: 4.562

9.  Intermolecular CH···O/N H-bonds in the biologically important pairs of natural nucleobases: a thorough quantum-chemical study.

Authors:  Ol'ha O Brovarets'; Yevgen P Yurenko; Dmytro M Hovorun
Journal:  J Biomol Struct Dyn       Date:  2013-06-03

10.  Evidence for the coincident initiation of homolog pairing and synapsis during the telomere-clustering (bouquet) stage of meiotic prophase.

Authors:  H W Bass; O Riera-Lizarazu; E V Ananiev; S J Bordoli; H W Rines; R L Phillips; J W Sedat; D A Agard; W Z Cande
Journal:  J Cell Sci       Date:  2000-03       Impact factor: 5.285
View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.