2n5o: Difference between revisions
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==Universal Base oligonucleotide structure== | ==Universal Base oligonucleotide structure== | ||
<StructureSection load='2n5o' size='340' side='right'caption='[[2n5o | <StructureSection load='2n5o' size='340' side='right'caption='[[2n5o]]' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[2n5o]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2N5O OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2N5O FirstGlance]. <br> | <table><tr><td colspan='2'>[[2n5o]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2N5O OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2N5O FirstGlance]. <br> | ||
</td></tr><tr id=' | </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=' | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=4EN:[(2R,3S,5R)-5-(4-AZANYLPYRAZOLO[3,4-D]PYRIMIDIN-2-YL)-3-OXIDANYL-OXOLAN-2-YL]METHYL+DIHYDROGEN+PHOSPHATE'>4EN</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=2n5o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2n5o OCA], [https://pdbe.org/2n5o PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2n5o RCSB], [https://www.ebi.ac.uk/pdbsum/2n5o PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2n5o ProSAT]</span></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=2n5o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2n5o OCA], [https://pdbe.org/2n5o PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2n5o RCSB], [https://www.ebi.ac.uk/pdbsum/2n5o PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2n5o ProSAT]</span></td></tr> | ||
</table> | </table> | ||
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</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Evich | [[Category: Synthetic construct]] | ||
[[Category: Germann | [[Category: Evich MG]] | ||
[[Category: Seela | [[Category: Germann MW]] | ||
[[Category: Spring-Connell | [[Category: Seela F]] | ||
[[Category: Spring-Connell AM]] | |||
Revision as of 15:44, 17 January 2024
Universal Base oligonucleotide structureUniversal Base oligonucleotide structure
Structural highlights
Publication Abstract from PubMedA truly universal nucleobase enables a host of novel applications such as simplified templates for PCR primers, randomized sequencing and DNA based devices. A universal base must pair indiscriminately to each of the canonical bases with little or preferably no destabilization of the overall duplex. In reality, many candidates either destabilize the duplex or do not base pair indiscriminatingly. The novel base 8-aza-7-deazaadenine (pyrazolo[3,4-d]pyrimidin- 4-amine) N8-(2'deoxyribonucleoside), a deoxyadenosine analog (UB), pairs with each of the natural DNA bases with little sequence preference. We have utilized NMR complemented with molecular dynamic calculations to characterize the structure and dynamics of a UB incorporated into a DNA duplex. The UB participates in base stacking with little to no perturbation of the local structure yet forms an unusual base pair that samples multiple conformations. These local dynamics result in the complete disappearance of a single UB proton resonance under native conditions. Accommodation of the UB is additionally stabilized via heightened backbone conformational sampling. NMR combined with various computational techniques has allowed for a comprehensive characterization of both structural and dynamic effects of the UB in a DNA duplex and underlines that the UB as a strong candidate for universal base applications. Using NMR and molecular dynamics to link structure and dynamics effects of the universal base 8-aza, 7-deaza, N8 linked adenosine analog.,Spring-Connell AM, Evich MG, Debelak H, Seela F, Germann MW Nucleic Acids Res. 2016 Aug 26. pii: gkw736. PMID:27566150[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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