Theoretical insights into the effect of size and substitution patterns of azobenzene derivatives on the DNA G-quadruplex

Physical Chemistry Chemical Physics : PCCP
Kiana Gholamjani MoghaddamShirin Faraji

Abstract

Introducing photoswitches into the DNA G-quadruplex provides excellent opportunities to control folding and unfolding of these assemblies, demonstrating their potential in the development of novel nanodevices with medical and nanotechnology applications. Using a quantum mechanics/molecular mechanics (QM/MM) scheme, we carried out a series of simulations to identify the effect of the size and substitution patterns of three azobenzene derivatives (AZ1, AZ2 and AZ3) on the excitation energies of the two lowest excited states of the smallest photoswitchable G-quadruplex reported to date. We demonstrated that the size and the substitution pattern do not affect the ultrafast cis-trans photoiomerization mechanism of the azobenzene derivatives significantly, in agreement with the experiment. However, molecular dynamics simulations revealed that while AZ2 and AZ3 G-quadruplexes are structurally stable during the simulations, the AZ1 G-quadruplex undergoes larger structural changes and shows two ground state populations that differ in the azobenzene backbone adopting two different conformations. AZ1, with para-para substitution pattern, provides more flexibility to the whole G-quadruplex structure compared to AZ2 and AZ3, and can thus fa...Continue Reading

References

May 15, 2003·Nucleosides, Nucleotides & Nucleic Acids·Daisuke MiyoshiNaoki Sugimoto
Jul 3, 2003·Journal of the American Chemical Society·Thomas SchultzAlbert Stolow
Aug 9, 2003·Journal of the American Chemical Society·Heike FlieglReinhart Ahlrichs
Mar 12, 2004·Journal of the American Chemical Society·Alessandro CembranGiorgio Orlandi
Apr 28, 2004·Chemistry : a European Journal·Cosimo CiminelliMaurizio Persico
Apr 30, 2004·Journal of Computational Chemistry·Junmei WangDavid A Case
Sep 7, 2006·Journal of Computational Chemistry·Stefan Grimme
Oct 3, 2006·Nucleic Acids Research·Sarah BurgeStephen Neidle
Oct 13, 2006·Organic & Biomolecular Chemistry·Diana P N GonçalvesJeremy K M Sanders
Nov 17, 2006·Chemical Communications : Chem Comm·Diana P N GonçalvesJeremy K M Sanders
Jan 11, 2007·The Journal of Chemical Physics·Giovanni BussiMichele Parrinello
Jun 15, 2007·Angewandte Chemie·Raphaël RodriguezShankar Balasubramanian
Jul 3, 2008·The Journal of Physical Chemistry. B·In Suk Joung, Thomas E Cheatham
Nov 8, 2008·Physical Chemistry Chemical Physics : PCCP·Jeng-Da Chai, Martin Head-Gordon
Jan 29, 2009·Angewandte Chemie·Hans Martin Senn, Walter Thiel
Jun 3, 2009·Current Opinion in Structural Biology·Stephen Neidle
Jul 11, 2009·Trends in Cell Biology·Hans J Lipps, Daniela Rhodes
Jul 29, 2009·Angewandte Chemie·Shinzi Ogasawara, Mizuo Maeda
Nov 26, 2009·The Journal of Physical Chemistry. a·Marcus BöckmannDominik Marx
Apr 15, 2010·Angewandte Chemie·Stefano LenaGian Piero Spada
Jun 24, 2010·Angewandte Chemie·Xiaolin WangXiang Zhou
Feb 24, 2011·Journal of the American Chemical Society·Martin McCullaghGeorge C Schatz
Mar 16, 2011·Journal of the American Chemical Society·Teresa CusatiMaurizio Persico
Jun 22, 2011·The Journal of Physical Chemistry. a·Marek PederzoliHans Lischka
Oct 20, 2011·Chemical Society Reviews·H M Dhammika Bandara, Shawn C Burdette
Oct 4, 2012·Nature Reviews. Genetics·Matthew L BochmanVirginia A Zakian
Apr 26, 2013·Chemical Reviews·Wiktor SzymańskiBen L Feringa
Apr 10, 2014·The Journal of Chemical Physics·Kristina D ClosserMartin Head-Gordon
Jun 24, 2014·The Journal of Physical Chemistry. B·Dominique RastädterIrene Burghardt
Aug 21, 2014·Biophysical Journal·Mithun Biswas, Irene Burghardt
Dec 19, 2014·Angewandte Chemie·Fuan WangItamar Willner
Jul 10, 2012·Journal of Chemical Theory and Computation·José A GámezWalter Thiel
May 11, 2010·Journal of Chemical Theory and Computation·Satoshi MaedaKeiji Morokuma
Mar 1, 2008·Journal of Chemical Theory and Computation·Berk HessErik Lindahl
Sep 1, 2007·Journal of Chemical Theory and Computation·Marcus BöckmannDominik Marx
Jan 26, 2016·Angewandte Chemie·Julie ThevarpadamAlexander Heckel
Jul 12, 2016·Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry·Josep CasellasMar Reguero
Sep 27, 2016·Frontiers in Chemistry·Debmalya BhattacharyyaSoumitra Basu
Jan 28, 2017·Chemical Society Reviews·Anouk S LubbeBen L Feringa
Feb 23, 2017·Nature Reviews. Molecular Cell Biology·Robert Hänsel-HertschShankar Balasubramanian

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