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

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, intrast

SUBMITTER: Pande V 

PROVIDER: S-EPMC2275159 | biostudies-literature | 2008 Mar

REPOSITORIES: biostudies-literature