%0 Journal Article
%T Features of “All LNA” Duplexes Showing a New Type of Nucleic Acid Geometry
%A Charlotte F？rster
%A André Eichert
%A Dominik Oberthür
%A Christian Betzel
%A Reinhard Ge？ner
%A Andreas Nitsche
%A Jens P. Fürste
%J Journal of Nucleic Acids
%D 2012
%I Hindawi Publishing Corporation
%R 10.1155/2012/156035
%X “Locked nucleic acids” (LNAs) belong to the backbone-modified nucleic acid family. The 2′-O,4′-C-methylene-β-D-ribofuranose nucleotides are used for single or multiple substitutions in RNA molecules and thereby introduce enhanced bio- and thermostability. This renders LNAs powerful tools for diagnostic and therapeutic applications. RNA molecules maintain the overall canonical A-type conformation upon substitution of single or multiple residues/nucleotides by LNA monomers. The structures of “all” LNA homoduplexes, however, exhibit significant differences in their overall geometry, in particular a decreased twist, roll and propeller twist. This results in a widening of the major groove, a decrease in helical winding, and an enlarged helical pitch. Therefore, the LNA duplex structure can no longer be described as a canonical A-type RNA geometry but can rather be brought into proximity to other backbone-modified nucleic acids, like glycol nucleic acids or peptide nucleic acids. LNA-modified nucleic acids provide thus structural and functional features that may be successfully exploited for future application in biotechnology and drug discovery. 1. Introduction Modified nucleic acids have great potential for applications in oligonucleotide-based drug design. As natural RNA and DNA molecules are highly sensitive towards nuclease digestion and often possess low thermal stability, great effort has been made to design nucleic acid modifications that stabilize RNA or DNA while simultaneously maintaining the overall Watson-Crick base pairing ability. Modified nucleic acids are indispensable for future applications comprising diagnostic and clinical approaches like the use of aptamers or the siRNA technology. Extensive and challenging experiments and investigations have been undertaken to develop nucleotide analogues that maintain the overall A-RNA-type conformation and N-type sugar puckering, as such modifications are likely to allow the substitution of RNA without large changes in functionality. Considerable effort has been made in the synthesis and characterization of 2′-O-methyl-RNAs [1], 2′-F-RNAs [2], phosphoramidate-RNAs [3], and the “locked” nucleic acid family [4]. By using locked nucleotide building blocks containing the 2′-O,4′-C-methylene-β-D-ribofuranose (LNA) modification, a significant increase in thermostability can be observed in accordingly substituted RNAs. For example, the melting temperature of modified RNA helices can be increased by +2 to +10°C per LNA monomer substitution. To understand the stabilizing effects of LNA-substituted RNAs,
%U http://www.hindawi.com/journals/jna/2012/156035/