Cargando…
‘Z-DNA like’ fragments in RNA: a recurring structural motif with implications for folding, RNA/protein recognition and immune response
Since the work of Alexander Rich, who solved the first Z-DNA crystal structure, we have known that d(CpG) steps can adopt a particular structure that leads to forming left-handed helices. However, it is still largely unrecognized that other sequences can adopt ‘left-handed’ conformations in DNA and...
Autores principales: | , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2016
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4937326/ https://www.ncbi.nlm.nih.gov/pubmed/27151194 http://dx.doi.org/10.1093/nar/gkw388 |
_version_ | 1782441692177104896 |
---|---|
author | D'Ascenzo, Luigi Leonarski, Filip Vicens, Quentin Auffinger, Pascal |
author_facet | D'Ascenzo, Luigi Leonarski, Filip Vicens, Quentin Auffinger, Pascal |
author_sort | D'Ascenzo, Luigi |
collection | PubMed |
description | Since the work of Alexander Rich, who solved the first Z-DNA crystal structure, we have known that d(CpG) steps can adopt a particular structure that leads to forming left-handed helices. However, it is still largely unrecognized that other sequences can adopt ‘left-handed’ conformations in DNA and RNA, in double as well as single stranded contexts. These ‘Z-like’ steps involve the coexistence of several rare structural features: a C2’-endo puckering, a syn nucleotide and a lone pair–π stacking between a ribose O4’ atom and a nucleobase. This particular arrangement induces a conformational stress in the RNA backbone, which limits the occurrence of Z-like steps to ≈0.1% of all dinucleotide steps in the PDB. Here, we report over 600 instances of Z-like steps, which are located within r(UNCG) tetraloops but also in small and large RNAs including riboswitches, ribozymes and ribosomes. Given their complexity, Z-like steps are probably associated with slow folding kinetics and once formed could lock a fold through the formation of unique long-range contacts. Proteins involved in immunologic response also specifically recognize/induce these peculiar folds. Thus, characterizing the conformational features of these motifs could be a key to understanding the immune response at a structural level. |
format | Online Article Text |
id | pubmed-4937326 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-49373262016-07-11 ‘Z-DNA like’ fragments in RNA: a recurring structural motif with implications for folding, RNA/protein recognition and immune response D'Ascenzo, Luigi Leonarski, Filip Vicens, Quentin Auffinger, Pascal Nucleic Acids Res Structural Biology Since the work of Alexander Rich, who solved the first Z-DNA crystal structure, we have known that d(CpG) steps can adopt a particular structure that leads to forming left-handed helices. However, it is still largely unrecognized that other sequences can adopt ‘left-handed’ conformations in DNA and RNA, in double as well as single stranded contexts. These ‘Z-like’ steps involve the coexistence of several rare structural features: a C2’-endo puckering, a syn nucleotide and a lone pair–π stacking between a ribose O4’ atom and a nucleobase. This particular arrangement induces a conformational stress in the RNA backbone, which limits the occurrence of Z-like steps to ≈0.1% of all dinucleotide steps in the PDB. Here, we report over 600 instances of Z-like steps, which are located within r(UNCG) tetraloops but also in small and large RNAs including riboswitches, ribozymes and ribosomes. Given their complexity, Z-like steps are probably associated with slow folding kinetics and once formed could lock a fold through the formation of unique long-range contacts. Proteins involved in immunologic response also specifically recognize/induce these peculiar folds. Thus, characterizing the conformational features of these motifs could be a key to understanding the immune response at a structural level. Oxford University Press 2016-07-08 2016-05-05 /pmc/articles/PMC4937326/ /pubmed/27151194 http://dx.doi.org/10.1093/nar/gkw388 Text en © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com |
spellingShingle | Structural Biology D'Ascenzo, Luigi Leonarski, Filip Vicens, Quentin Auffinger, Pascal ‘Z-DNA like’ fragments in RNA: a recurring structural motif with implications for folding, RNA/protein recognition and immune response |
title | ‘Z-DNA like’ fragments in RNA: a recurring structural motif with implications for folding, RNA/protein recognition and immune response |
title_full | ‘Z-DNA like’ fragments in RNA: a recurring structural motif with implications for folding, RNA/protein recognition and immune response |
title_fullStr | ‘Z-DNA like’ fragments in RNA: a recurring structural motif with implications for folding, RNA/protein recognition and immune response |
title_full_unstemmed | ‘Z-DNA like’ fragments in RNA: a recurring structural motif with implications for folding, RNA/protein recognition and immune response |
title_short | ‘Z-DNA like’ fragments in RNA: a recurring structural motif with implications for folding, RNA/protein recognition and immune response |
title_sort | ‘z-dna like’ fragments in rna: a recurring structural motif with implications for folding, rna/protein recognition and immune response |
topic | Structural Biology |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4937326/ https://www.ncbi.nlm.nih.gov/pubmed/27151194 http://dx.doi.org/10.1093/nar/gkw388 |
work_keys_str_mv | AT dascenzoluigi zdnalikefragmentsinrnaarecurringstructuralmotifwithimplicationsforfoldingrnaproteinrecognitionandimmuneresponse AT leonarskifilip zdnalikefragmentsinrnaarecurringstructuralmotifwithimplicationsforfoldingrnaproteinrecognitionandimmuneresponse AT vicensquentin zdnalikefragmentsinrnaarecurringstructuralmotifwithimplicationsforfoldingrnaproteinrecognitionandimmuneresponse AT auffingerpascal zdnalikefragmentsinrnaarecurringstructuralmotifwithimplicationsforfoldingrnaproteinrecognitionandimmuneresponse |