Interplay of LNA and 2'-O-methyl RNA in the structure and thermodynamics of RNA hybrid systems: a molecular dynamics study using the revised AMBER force field and comparison with experimental results.

摘要: When used in nucleic acid duplexes, locked (LNA) and 2′-O-methyl RNA residues enhance the duplex stabilities, this makes it possible to create much better aptamers target specific molecules cells. Thus, LNA are finding increasingly widespread use RNA-based therapeutics. Herein, we utilize molecular dynamics (MD) simulations UV melting experiments investigate structural thermodynamic properties of 13 including full DNA, RNA, LNA, duplexes as well hybrid systems such LNA:RNA, RNA:RNA, LNA/2′-O-methyl RNA/2′-O-methyl RNA:RNA duplexes. The MD based on a version Amber force field revised specifically for residues. Our results indicate that have two different hybridization mechanisms when included with wherein former underwinds while latter overwinds Thes...