Predictive modelling of topology and loop variations in dimeric DNA quadruplex structures.

Nucleic Acids Research
Pascale HazelStephen Neidle

Abstract

We have used a combination of simulated annealing (SA), molecular dynamics (MD) and locally enhanced sampling (LES) methods in order to predict the favourable topologies and loop conformations of dimeric DNA quadruplexes with T2 or T3 loops. This follows on from our previous MD simulation studies on the influence of loop lengths on the topology of intramolecular quadruplex structures [P. Hazel et al. (2004) J. Am. Chem. Soc., 126, 16 405-16 415], which provided results consistent with biophysical data. The recent crystal structures of d(G4T3G4)2 and d(G4BrUT2G4) (P. Hazel et al. (2006) J. Am. Chem. Soc., in press) and the NMR-determined topology of d(TG4T2G4T)2 [A.T. Phan et al. (2004) J. Mol. Biol., 338, 93-102] have been used in the present study for comparison with simulation results. These together with MM-PBSA free-energy calculations indicate that lateral T3 loops are favoured over diagonal loops, in accordance with the experimental structures; however, distinct loop conformations have been predicted to be favoured compared to those found experimentally. Several lateral and diagonal loop conformations have been found to be similar in energy. The simulations suggest an explanation for the distinct patterns of observed dime...Continue Reading

References

Aug 4, 1995·Journal of Molecular Biology·Y Wang, D J Patel
Oct 25, 1994·Proceedings of the National Academy of Sciences of the United States of America·F W SmithJ Feigon
Apr 15, 1993·Proceedings of the National Academy of Sciences of the United States of America·R F MacayaJ Feigon
Apr 4, 1998·Nucleic Acids Research·T SimonssonM Kubista
Apr 9, 1999·Biochemistry·V M Marathias, P H Bolton
Jun 29, 2001·Journal of Molecular Biology·M P Horvath, S C Schultz
Jun 7, 2002·Nature·Gary N ParkinsonStephen Neidle
Jun 25, 2002·Journal of Molecular Biology·Shozeb HaiderStephen Neidle
Jul 20, 2002·Journal of Molecular Biology·Martin CrnugeljJanez Plavec
Aug 27, 2002·Proceedings of the National Academy of Sciences of the United States of America·Adam Siddiqui-JainLaurence H Hurley
Jul 15, 2004·Journal of the American Chemical Society·Anh Tuân PhanDinshaw J Patel
Dec 17, 2004·Journal of the American Chemical Society·Pascale HazelStephen Neidle
May 26, 2005·Nucleic Acids Research·Alan K ToddStephen Neidle
May 26, 2005·Nucleic Acids Research·Julian L Huppert, Shankar Balasubramanian
Jun 30, 2005·Journal of the American Chemical Society·Evonne M RezlerLaurence H Hurley
Jul 28, 2005·Journal of the American Chemical Society·Sarah RankinStephen Neidle
Nov 25, 2005·Journal of the American Chemical Society·Michelle L GillJ Patrick Loria
Dec 8, 2005·Journal of the American Chemical Society·Na ZhangDinshaw J Patel

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Citations

Dec 15, 2012·Journal of Computer-aided Molecular Design·Jin-Qiang HouZhi-Shu Huang
Jun 7, 2011·Journal of Chemical Information and Modeling·Sìlvia G EstácioRita C Guedes
Oct 4, 2012·Nature Reviews. Genetics·Matthew L BochmanVirginia A Zakian
Aug 18, 2006·Nucleic Acids Research·Johanna Eddy, Nancy Maizels
Oct 3, 2006·Nucleic Acids Research·Sarah BurgeStephen Neidle
Jul 5, 2008·Nucleic Acids Research·Niti KumarSouvik Maiti
Dec 24, 2008·Nucleic Acids Research·Samir AmraneAnh Tuân Phan
Sep 24, 2010·Nucleic Acids Research·Melissa A MullenPhilip C Bevilacqua
Sep 7, 2011·Nucleic Acids Research·Roman V ReshetnikovAndrey V Golovin
Nov 16, 2010·Biochemistry. Biokhimii︠a︡·R V ReshetnikovA M Kopylov
Aug 21, 2010·Journal of Nucleic Acids·Joan CasalsCarlos González
Oct 3, 2013·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Anna ArteseStefano Alcaro
Nov 11, 2014·Inorganic Chemistry·Laureline LecarmeFabrice Thomas
Dec 9, 2009·European Journal of Medicinal Chemistry·Li AixiaoWang Ping
Jul 19, 2011·Journal of the American Chemical Society·Xiaohui CangThomas E Cheatham
Feb 1, 2008·ChemMedChem·Tian-miao OuLian-quan Gu
Nov 1, 2007·Chemistry : a European Journal·Mateus Webba da Silva
Oct 31, 2007·Methods : a Companion to Methods in Enzymology·Jirí Sponer, Nad'a Spacková
Apr 25, 2012·Methods : a Companion to Methods in Enzymology·Jiří SponerThomas E Cheatham
Dec 25, 2012·Biochemical and Biophysical Research Communications·Jing LinZhi-shu Huang
Jul 20, 2016·Chemistry : a European Journal·Madeleine LivendahlErik Chorell
Sep 27, 2016·Frontiers in Chemistry·Debmalya BhattacharyyaSoumitra Basu
Mar 30, 2017·Organic & Biomolecular Chemistry·M LivendahlE Chorell
Oct 18, 2018·Chemistry : a European Journal·Shu YangQianfan Yang
Jan 8, 2020·The Plant Journal : for Cell and Molecular Biology·Manohar ChakrabartiArthur G Hunt
Sep 8, 2009·Journal of Chemical Theory and Computation·Eva FadrnáJiří Šponer
Apr 10, 2009·Journal of Medicinal Chemistry·Jia-Heng TanLian-Quan Gu
Oct 7, 2008·Journal of the American Chemical Society·Peter PodbevsekJanez Plavec

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Methods Mentioned

BETA
X-ray
NMR

Software Mentioned

Insight SA
Insight
NMRCLUST
NMODE
Amber
PBSA
MM
Delphi II
Python

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