A comparison of the solution structures of an LNA:DNA duplex and the unmodified DNA:DNA duplex

Modified oligonucleotides, containing restricted nucleotides with a 2'-O,4'-C-methylene bridge (LNA), hybridized toward either DNA or RNA display an unprecedented increase in melting temperatures. In order to understand the structural basis for this high stability we have used H-1 NMR spectroscopy to determine the high resolution solution structures of an LNA-modified oligonucleotide, as well as the structure of the corresponding unmodified duplex. The modified duplex is an LNA:DNA duplex containing three thymidine LNA modifications (T-L), d(C(1)T(2)(L)G(3)A(4)T(5)(L)A(6)T(7)(L)G(8)C(9)):d(G(10)C(11)A(12)T(13)A(14)T(15)C(16)A(17)G(18)). A full relaxation matrix approach by the program RANDMARDI was used to obtain interproton distance bounds from NOESY cross peak intensities. These distance bounds were used as restraints in molecular dynamics (rMD) calculations. Both duplexes have right-handed helix conformations with all bases in the anti conformation forming normal Watson-Crick base pairs. The LNA strand in the modified duplex has predominantly N-type sugar conformations compared to the S-type conformations of the complementary strand. The unmodified DNA:DNA strand has almost exclusively S-type sugar conformations. The structural strain introduced by the conformational changes of the ribose rings in the LNA:DNA duplex is released by unwinding the helix and widening the minor groove, but as a whole the structure of the duplex is surprisingly unaffected by introducing the modified LNA nucleotides.