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The electrostatic characteristics of G·U wobble base pairs
G·U wobble base pairs are the most common and highly conserved non-Watson–Crick base pairs in RNA. Previous surface maps imply uniformly negative electrostatic potential at the major groove of G·U wobble base pairs embedded in RNA helices, suitable for entrapment of cationic ligands. In this work, w...
Autores principales: | , , , |
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Formato: | Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2007
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1920249/ https://www.ncbi.nlm.nih.gov/pubmed/17526525 http://dx.doi.org/10.1093/nar/gkm274 |
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author | Xu, Darui Landon, Theresa Greenbaum, Nancy L. Fenley, Marcia O. |
author_facet | Xu, Darui Landon, Theresa Greenbaum, Nancy L. Fenley, Marcia O. |
author_sort | Xu, Darui |
collection | PubMed |
description | G·U wobble base pairs are the most common and highly conserved non-Watson–Crick base pairs in RNA. Previous surface maps imply uniformly negative electrostatic potential at the major groove of G·U wobble base pairs embedded in RNA helices, suitable for entrapment of cationic ligands. In this work, we have used a Poisson–Boltzmann approach to gain a more detailed and accurate characterization of the electrostatic profile. We found that the major groove edge of an isolated G·U wobble displays distinctly enhanced negativity compared with standard GC or AU base pairs; however, in the context of different helical motifs, the electrostatic pattern varies. G·U wobbles with distinct widening have similar major groove electrostatic potentials to their canonical counterparts, whereas those with minimal widening exhibit significantly enhanced electronegativity, ranging from 0.8 to 2.5 kT/e, depending upon structural features. We propose that the negativity at the major groove of G·U wobble base pairs is determined by the combined effect of the base atoms and the sugar-phosphate backbone, which is impacted by stacking pattern and groove width as a result of base sequence. These findings are significant in that they provide predictive power with respect to which G·U sites in RNA are most likely to bind cationic ligands. |
format | Text |
id | pubmed-1920249 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2007 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-19202492007-07-19 The electrostatic characteristics of G·U wobble base pairs Xu, Darui Landon, Theresa Greenbaum, Nancy L. Fenley, Marcia O. Nucleic Acids Res RNA G·U wobble base pairs are the most common and highly conserved non-Watson–Crick base pairs in RNA. Previous surface maps imply uniformly negative electrostatic potential at the major groove of G·U wobble base pairs embedded in RNA helices, suitable for entrapment of cationic ligands. In this work, we have used a Poisson–Boltzmann approach to gain a more detailed and accurate characterization of the electrostatic profile. We found that the major groove edge of an isolated G·U wobble displays distinctly enhanced negativity compared with standard GC or AU base pairs; however, in the context of different helical motifs, the electrostatic pattern varies. G·U wobbles with distinct widening have similar major groove electrostatic potentials to their canonical counterparts, whereas those with minimal widening exhibit significantly enhanced electronegativity, ranging from 0.8 to 2.5 kT/e, depending upon structural features. We propose that the negativity at the major groove of G·U wobble base pairs is determined by the combined effect of the base atoms and the sugar-phosphate backbone, which is impacted by stacking pattern and groove width as a result of base sequence. These findings are significant in that they provide predictive power with respect to which G·U sites in RNA are most likely to bind cationic ligands. Oxford University Press 2007-06 2007-05-25 /pmc/articles/PMC1920249/ /pubmed/17526525 http://dx.doi.org/10.1093/nar/gkm274 Text en © 2007 The Author(s) http://creativecommons.org/licenses/by-nc/2.0/uk/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | RNA Xu, Darui Landon, Theresa Greenbaum, Nancy L. Fenley, Marcia O. The electrostatic characteristics of G·U wobble base pairs |
title | The electrostatic characteristics of G·U wobble base pairs |
title_full | The electrostatic characteristics of G·U wobble base pairs |
title_fullStr | The electrostatic characteristics of G·U wobble base pairs |
title_full_unstemmed | The electrostatic characteristics of G·U wobble base pairs |
title_short | The electrostatic characteristics of G·U wobble base pairs |
title_sort | electrostatic characteristics of g·u wobble base pairs |
topic | RNA |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1920249/ https://www.ncbi.nlm.nih.gov/pubmed/17526525 http://dx.doi.org/10.1093/nar/gkm274 |
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