2LSC
Solution structure of 2'F-ANA and ANA self-complementary duplex
Summary for 2LSC
| Entry DOI | 10.2210/pdb2lsc/pdb |
| NMR Information | BMRB: 18427 |
| Descriptor | 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') (1 entity in total) |
| Functional Keywords | dna, dickerson drew dodecamer |
| Total number of polymer chains | 2 |
| Total formula weight | 7686.53 |
| Authors | Martin-Pintado, N.,Yahyaee, M.,Campos, R.,Noronha, A.,Wilds, C.,Damha, M.,Gonzalez, C. (deposition date: 2012-04-26, release date: 2012-07-18, Last modification date: 2024-05-15) |
| Primary citation | Martin-Pintado, N.,Yahyaee-Anzahaee, M.,Campos-Olivas, R.,Noronha, A.M.,Wilds, C.J.,Damha, M.J.,Gonzalez, C. The solution structure of double helical arabino nucleic acids (ANA and 2'F-ANA): effect of arabinoses in duplex-hairpin interconversion. Nucleic Acids Res., 40:9329-9339, 2012 Cited by PubMed 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. PubMed: 22798499DOI: 10.1093/nar/gks672 PDB entries with the same primary citation |
| Experimental method | SOLUTION NMR |
Structure validation
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