6i1v: Difference between revisions
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The | ==Structure of the RNA duplex containing pseudouridine residue (5'-Cp(PSU)pG-3' sequence context)== | ||
<StructureSection load='6i1v' size='340' side='right'caption='[[6i1v]], [[NMR_Ensembles_of_Models | 10 NMR models]]' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[6i1v]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6I1V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6I1V FirstGlance]. <br> | |||
</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene></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=6i1v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6i1v OCA], [http://pdbe.org/6i1v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6i1v RCSB], [http://www.ebi.ac.uk/pdbsum/6i1v PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6i1v ProSAT]</span></td></tr> | |||
</table> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Pseudouridine (Psi) is the most common chemical modification present in RNA. In general, Psi increases the thermodynamic stability of RNA. However, the degree of stabilization depends on the sequence and structural context. To explain experimentally observed sequence dependence of the effect of Psi on the thermodynamic stability of RNA duplexes, we investigated the structure, dynamics and hydration of RNA duplexes with an internal Psi-A base pair in different nearest-neighbor sequence contexts. The structures of two RNA duplexes containing 5'-GPsiC/3'-CAG and 5'-CPsiG/3'-GAC motifs were determined using NMR spectroscopy. To gain insight into the effect of Psi on duplex dynamics and hydration, we performed molecular dynamics (MD) simulations of RNA duplexes with 5'-GPsiC/3'-CAG, 5'-CPsiG/3'-GAC, 5'-APsiU/3'-UAA and 5'-UPsiA/3'-AAU motifs and their unmodified counterparts. Our results showed a subtle impact from Psi modification on the structure and dynamics of the RNA duplexes studied. The MD simulations confirmed the change in hydration pattern when U is replaced with Psi. Quantum chemical calculations showed that the replacement of U with Psi affected the intrinsic stacking energies at the base pair steps depending on the sequence context. The calculated intrinsic stacking energies help to explain the experimentally observed sequence dependent changes in the duplex stability from Psi modification. | |||
Computational and NMR studies of RNA duplexes with an internal pseudouridine-adenosine base pair.,Deb I, Popenda L, Sarzynska J, Malgowska M, Lahiri A, Gdaniec Z, Kierzek R Sci Rep. 2019 Nov 7;9(1):16278. doi: 10.1038/s41598-019-52637-0. PMID:31700156<ref>PMID:31700156</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
<div class="pdbe-citations 6i1v" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Deb, I]] | [[Category: Deb, I]] | ||
[[Category: Gdaniec, Z]] | |||
[[Category: Popenda, L]] | [[Category: Popenda, L]] | ||
[[Category: | [[Category: Sarzynska, J]] | ||
[[Category: Duplex]] | |||
[[Category: Pseudouridine]] | |||
[[Category: Rna]] | |||
Latest revision as of 18:17, 20 November 2019
Structure of the RNA duplex containing pseudouridine residue (5'-Cp(PSU)pG-3' sequence context)Structure of the RNA duplex containing pseudouridine residue (5'-Cp(PSU)pG-3' sequence context)
Structural highlights
Publication Abstract from PubMedPseudouridine (Psi) is the most common chemical modification present in RNA. In general, Psi increases the thermodynamic stability of RNA. However, the degree of stabilization depends on the sequence and structural context. To explain experimentally observed sequence dependence of the effect of Psi on the thermodynamic stability of RNA duplexes, we investigated the structure, dynamics and hydration of RNA duplexes with an internal Psi-A base pair in different nearest-neighbor sequence contexts. The structures of two RNA duplexes containing 5'-GPsiC/3'-CAG and 5'-CPsiG/3'-GAC motifs were determined using NMR spectroscopy. To gain insight into the effect of Psi on duplex dynamics and hydration, we performed molecular dynamics (MD) simulations of RNA duplexes with 5'-GPsiC/3'-CAG, 5'-CPsiG/3'-GAC, 5'-APsiU/3'-UAA and 5'-UPsiA/3'-AAU motifs and their unmodified counterparts. Our results showed a subtle impact from Psi modification on the structure and dynamics of the RNA duplexes studied. The MD simulations confirmed the change in hydration pattern when U is replaced with Psi. Quantum chemical calculations showed that the replacement of U with Psi affected the intrinsic stacking energies at the base pair steps depending on the sequence context. The calculated intrinsic stacking energies help to explain the experimentally observed sequence dependent changes in the duplex stability from Psi modification. Computational and NMR studies of RNA duplexes with an internal pseudouridine-adenosine base pair.,Deb I, Popenda L, Sarzynska J, Malgowska M, Lahiri A, Gdaniec Z, Kierzek R Sci Rep. 2019 Nov 7;9(1):16278. doi: 10.1038/s41598-019-52637-0. PMID:31700156[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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