Unzipping and binding of small interfering RNA with single walled carbon nanotube: a platform for small interfering RNA delivery

The Journal of Chemical Physics
Mogurampelly SantoshPrabal K Maiti

Abstract

In an effort to design efficient platform for siRNA delivery, we combine all atom classical and quantum simulations to study the binding of small interfering RNA (siRNA) by pristine single wall carbon nanotube (SWCNT). Our results show that siRNA strongly binds to SWCNT surface via unzipping its base-pairs and the propensity of unzipping increases with the increase in the diameter of the SWCNTs. The unzipping and subsequent wrapping events are initiated and driven by van der Waals interactions between the aromatic rings of siRNA nucleobases and the SWCNT surface. However, molecular dynamics (MD) simulations of double strand DNA (dsDNA) of the same sequence show that the dsDNA undergoes much less unzipping and wrapping on the SWCNT in the simulation time scale of 70 ns. This interesting difference is due to smaller interaction energy of thymidine of dsDNA with the SWCNT compared to that of uridine of siRNA, as calculated by dispersion corrected density functional theory (DFT) methods. After the optimal binding of siRNA to SWCNT, the complex is very stable which serves as one of the major mechanisms of siRNA delivery for biomedical applications. Since siRNA has to undergo unwinding process with the effect of RNA-induced silencing...Continue Reading

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Citations

Jul 4, 2012·Journal of Biosciences·Bidisha NandyPrabal K Maiti
Jan 25, 2013·The Journal of Chemical Physics·Santosh Mogurampelly, Prabal K Maiti
Aug 17, 2012·The Journal of Chemical Physics·Santosh MogurampellyPrabal K Maiti
Jun 16, 2014·The Journal of Chemical Physics·Fernando J A L CruzJosé P B Mota
Apr 6, 2016·The Journal of Physical Chemistry. B·Soumadwip Ghosh, Rajarshi Chakrabarti
Mar 2, 2016·Biochimica Et Biophysica Acta·M RamezanpourD P Tieleman
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May 8, 2013·Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry·Deivasigamani Umadevi, G Narahari Sastry
Sep 12, 2020·Computational and Structural Biotechnology Journal·Xiaokang ZhangShihua Zhou
Mar 10, 2021·The European Physical Journal. E, Soft Matter·Maksym V KarachevtsevVictor A Karachevtsev
Jan 27, 2018·ACS Applied Materials & Interfaces·Anil Kumar SahooPrabal K Maiti
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Dec 29, 2020·Langmuir : the ACS Journal of Surfaces and Colloids·Ipsita Basu, Prabal K Maiti
Nov 3, 2021·Journal of Biomolecular Structure & Dynamics·Rakesh Kumar MishraDhananjay Bhattacharyya

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Methods Mentioned

BETA
transfecting

Software Mentioned

AMBER03
MOLDEN
GAUSSIAN09
NPT
AMBER
MD
AMBER9
parmbsc0

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