2LSC: Solution Structure Of 2'f-Ana And Ana Self-Complementary Duplex

Citation:
Abstract
We report here the first structure of double helical arabino nucleic acid (ANA), the C2'-stereoisomer of RNA, and the 2'-fluoro-ANA analogue (2'F-ANA). A chimeric dodecamer based on the Dickerson sequence, containing a contiguous central segment of arabino nucleotides, flanked by two 2'-deoxy-2'F-ANA wings was studied. Our data show that this chimeric oligonucleotide can adopt two different structures of comparable thermal stabilities. One structure is a monomeric hairpin in which the stem is formed by base paired 2'F-ANA nucleotides and the loop by unpaired ANA nucleotides. The second structure is a bimolecular duplex, with all the nucleotides (2'F-ANA and ANA) forming Watson-Crick base pairs. The duplex structure is canonical B-form, with all arabinoses adopting a pure C2'-endo conformation. In the ANA:ANA segment, steric interactions involving the 2'-OH substituent provoke slight changes in the glycosidic angles and, therefore, in the ANA:ANA base pair geometry. These distortions are not present in the 2'F-ANA:2'F-ANA regions of the duplex, where the -OH substituent is replaced by a smaller fluorine atom. 2'F-ANA nucleotides adopt the C2'-endo sugar pucker and fit very well into the geometry of B-form duplex, allowing for favourable 2'F...H8 interactions. This interaction shares many features of pseudo-hydrogen bonds previously observed in 2'F-ANA:RNA hybrids and in single 2'F-ANA nucleotides.
PDB ID: 2LSCDownload
MMDB ID: 101281
PDB Deposition Date: 2012/4/26
Updated in MMDB: 2012/10
Experimental Method:
solution nmr
Biological Unit for 2LSC: dimeric; determined by author
Molecular Components in 2LSC
Label Count Molecule
Nucleotide(1 molecule)
2
DNA (5'-d(*(cfl)p*(gfl)p*(cfl)p*(gfl)p*(a5o)p*(a5o)p*(uar) P*(uar)p*(cfl)p*(gfl)p*(cfl)p*(gfl))-3')
Molecule annotation
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