Insights into structure, dynamics and hydration of locked nucleic acid (LNA) strand-based duplexes from molecular dynamics simulations.

Nucleic Acids Research
Vineet Pande, L Nilsson

Abstract

Locked nucleic acid (LNA) is a chemically modified nucleic acid with its sugar ring locked in an RNA-like (C3'-endo) conformation. LNAs show extraordinary thermal stabilities when hybridized with DNA, RNA or LNA itself. We performed molecular dynamics simulations on five isosequential duplexes (LNA-DNA, LNA-LNA, LNA-RNA, RNA-DNA and RNA-RNA) in order to characterize their structure, dynamics and hydration. Structurally, the LNA-DNA and LNA-RNA duplexes are found to be similar to regular RNA-DNA and RNA-RNA duplexes, whereas the LNA-LNA duplex is found to have its helix partly unwound and does not resemble RNA-RNA duplex in a number of properties. Duplexes with an LNA strand have on average longer interstrand phosphate distances compared to RNA-DNA and RNA-RNA duplexes. Furthermore, intrastrand phosphate distances in LNA strands are found to be shorter than in DNA and slightly shorter than in RNA. In case of induced sugar puckering, LNA is found to tune the sugar puckers in partner DNA strand toward C3'-endo conformations more efficiently than RNA. The LNA-LNA duplex has lesser backbone flexibility compared to the RNA-RNA duplex. Finally, LNA is less hydrated compared to DNA or RNA but is found to have a well-organized water str...Continue Reading

References

Jan 1, 1988·Annual Review of Biophysics and Biophysical Chemistry·E Westhof
Aug 1, 1988·Journal of Biomolecular Structure & Dynamics·R Lavery, H Sklenar
Feb 19, 2000·Journal of Molecular Recognition : JMR·M PetersenJ P Jacobsen
Jul 25, 2000·Journal of Molecular Biology·P Auffinger, E Westhof
Sep 2, 2000·Biophysical Journal·J Norberg, L Nilsson
Sep 14, 2000·Chemistry : a European Journal·K BondensgaardJ P Jacobsen
Feb 22, 2001·Chemistry & Biology·D A Braasch, D R Corey
May 23, 2002·Journal of the American Chemical Society·Michael PetersenJens Peter Jacobsen
May 30, 2002·Nucleic Acids Research·Rita CrinelliMauro Magnani
Jun 19, 2002·Accounts of Chemical Research·Jan Norberg, Lennart Nilsson
Nov 15, 2002·Journal of the American Chemical Society·Birte VesterJesper Wengel
Jan 30, 2004·Annual Review of Medicine·Stanley T Crooke
Nov 20, 2004·Nucleic Acids Research·Jesper J SørensenMichael Petersen
Jan 18, 2005·Nucleic Acids Research·Joacim ElménClaes Wahlestedt
Mar 31, 2005·Journal of the American Chemical Society·Agnes NoyModesto Orozco
Nov 10, 2005·Journal of the American Chemical Society·Lin WangWeihong Tan
Dec 22, 2005·Nature Methods·Wigard P KloostermanRonald H A Plasterk
Jul 21, 2006·The Journal of Physical Chemistry. B·Nicolas Foloppe, Lennart Nilsson

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Citations

Mar 30, 2012·Journal of Computer-aided Molecular Design·Amit Kumar ChaubeyRajendra Prasad Ojha
Jun 10, 2010·Nucleic Acids Research·André EichertCharlotte Förster
Aug 10, 2015·Journal of Molecular Graphics & Modelling·Gorle Suresh, U Deva Priyakumar
Dec 17, 2010·Journal of Molecular Graphics & Modelling·Taejin KimBruce A Shapiro
Jan 1, 2014·The Journal of Physical Chemistry. B·David E CondonDouglas H Turner
Jun 6, 2012·Journal of Nucleic Acids·Charlotte FörsterJens P Fürste
Oct 16, 2012·Wiley Interdisciplinary Reviews. Computational Molecular Science·Xiao ZhuAlexander D Mackerell
Apr 7, 2011·Journal of Computational Chemistry·Elizabeth J DenningAlexander D Mackerell
Nov 2, 2012·Molecular BioSystems·Teena GoelSouvik Maiti
Jun 28, 2016·Biochimica Et Biophysica Acta·Paulo MatosPeter Jordan
Aug 26, 2010·Journal of the American Chemical Society·Mahesh HariharanFrederick D Lewis
Feb 9, 2012·Langmuir : the ACS Journal of Surfaces and Colloids·Sourav MishraRupa Mukhopadhyay
Aug 12, 2014·Langmuir : the ACS Journal of Surfaces and Colloids·Sourav MishraRupa Mukhopadhyay
Dec 28, 2012·Analytical Chemistry·Sourav MishraRupa Mukhopadhyay
Nov 24, 2016·Diagnostics·Mílton CordeiroPedro Viana Baptista
Jan 20, 2017·Journal of Computational Chemistry·You XuLennart Nilsson
Jul 25, 2018·Expert Review of Molecular Diagnostics·Pedro V Baptista
Oct 5, 2018·Journal of Biomolecular Structure & Dynamics·Mallikarjunachari V N UppuladinneRajendra R Joshi
Sep 10, 2017·Scientific Reports·Y Vladimir Pabon-MartinezRula Zain
Dec 11, 2020·Nucleic Acids Research·Asem AlenaizanAnton S Petrov
Jul 13, 2021·Journal of Chemical Information and Modeling·Izabela FerreiraGerald Weber
Sep 26, 2019·Journal of Chemical Theory and Computation·Zhifeng JingPengyu Ren
Nov 7, 2018·Langmuir : the ACS Journal of Surfaces and Colloids·Hiya LahiriRupa Mukhopadhyay
Mar 15, 2018·Journal of Chemical Information and Modeling·Yossa Dwi HartonoAlessandra Villa
Aug 30, 2019··Vishnudatt PandeyRajendra Prasad Ojha

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Methods Mentioned

BETA
NMR
X-ray

Software Mentioned

CHARMM27
CURVES
Insight
CHARMM

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