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| | ==Solution structure of 2'F-ANA and ANA self-complementary duplex== | | ==Solution structure of 2'F-ANA and ANA self-complementary duplex== |
| - | <StructureSection load='2lsc' size='340' side='right' caption='[[2lsc]], [[NMR_Ensembles_of_Models | 20 NMR models]]' scene=''> | + | <StructureSection load='2lsc' size='340' side='right'caption='[[2lsc]]' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2lsc]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LSC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2LSC FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2lsc]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LSC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2LSC FirstGlance]. <br> |
| - | </td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=A5O:ADENINE+ARABINOSE-5-PHOSPHATE'>A5O</scene>, <scene name='pdbligand=CFL:4-AMINO-1-(2-DEOXY-2-FLUORO-5-O-PHOSPHONO-BETA-D-ARABINOFURANOSYL)PYRIMIDIN-2(1H)-ONE'>CFL</scene>, <scene name='pdbligand=GFL:2-AMINO-9-(2-DEOXY-2-FLUORO-5-O-PHOSPHONO-BETA-D-ARABINOFURANOSYL)-1,9-DIHYDRO-6H-PURIN-6-ONE'>GFL</scene>, <scene name='pdbligand=UAR:URACIL+ARABINOSE-5-PHOSPHATE'>UAR</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2lsc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lsc OCA], [http://pdbe.org/2lsc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2lsc RCSB], [http://www.ebi.ac.uk/pdbsum/2lsc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2lsc ProSAT]</span></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=A5O:ADENINE+ARABINOSE-5-PHOSPHATE'>A5O</scene>, <scene name='pdbligand=CFL:4-AMINO-1-(2-DEOXY-2-FLUORO-5-O-PHOSPHONO-BETA-D-ARABINOFURANOSYL)PYRIMIDIN-2(1H)-ONE'>CFL</scene>, <scene name='pdbligand=GFL:2-AMINO-9-(2-DEOXY-2-FLUORO-5-O-PHOSPHONO-BETA-D-ARABINOFURANOSYL)-1,9-DIHYDRO-6H-PURIN-6-ONE'>GFL</scene>, <scene name='pdbligand=UAR:URACIL+ARABINOSE-5-PHOSPHATE'>UAR</scene></td></tr> |
| | + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2lsc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lsc OCA], [https://pdbe.org/2lsc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2lsc RCSB], [https://www.ebi.ac.uk/pdbsum/2lsc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2lsc ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Campos, R]] | + | [[Category: Large Structures]] |
| - | [[Category: Damha, M]] | + | [[Category: Campos R]] |
| - | [[Category: Gonzalez, C]] | + | [[Category: Damha M]] |
| - | [[Category: Martin-Pintado, N]] | + | [[Category: Gonzalez C]] |
| - | [[Category: Noronha, A]] | + | [[Category: Martin-Pintado N]] |
| - | [[Category: Wilds, C]] | + | [[Category: Noronha A]] |
| - | [[Category: Yahyaee, M]] | + | [[Category: Wilds C]] |
| - | [[Category: Dickerson drew dodecamer]]
| + | [[Category: Yahyaee M]] |
| - | [[Category: Dna]]
| + | |
| Structural highlights
Publication Abstract from PubMed
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.
The solution structure of double helical arabino nucleic acids (ANA and 2'F-ANA): effect of arabinoses in duplex-hairpin interconversion.,Martin-Pintado N, Yahyaee-Anzahaee M, Campos-Olivas R, Noronha AM, Wilds CJ, Damha MJ, Gonzalez C Nucleic Acids Res. 2012 Oct 1;40(18):9329-39. doi: 10.1093/nar/gks672. Epub 2012 , Jul 14. PMID:22798499[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Martin-Pintado N, Yahyaee-Anzahaee M, Campos-Olivas R, Noronha AM, Wilds CJ, Damha MJ, 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. 2012 Oct 1;40(18):9329-39. doi: 10.1093/nar/gks672. Epub 2012 , Jul 14. PMID:22798499 doi:http://dx.doi.org/10.1093/nar/gks672
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