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Molecular crowding creates an essential environment for the formation of stable G-quadruplexes in long double-stranded DNA
Large numbers of guanine-rich sequences with potential to form G-quadruplexes have been identified in genomes of various organisms. Such sequences are constrained at both ends by long DNA duplex with a complementary strand in close proximity to compete for duplex formation. G-quadruplex/duplex compe...
Autores principales: | , , , |
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Formato: | Texto |
Lenguaje: | English |
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Oxford University Press
2010
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2800236/ https://www.ncbi.nlm.nih.gov/pubmed/19858105 http://dx.doi.org/10.1093/nar/gkp898 |
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author | Zheng, Ke-wei Chen, Zhao Hao, Yu-hua Tan, Zheng |
author_facet | Zheng, Ke-wei Chen, Zhao Hao, Yu-hua Tan, Zheng |
author_sort | Zheng, Ke-wei |
collection | PubMed |
description | Large numbers of guanine-rich sequences with potential to form G-quadruplexes have been identified in genomes of various organisms. Such sequences are constrained at both ends by long DNA duplex with a complementary strand in close proximity to compete for duplex formation. G-quadruplex/duplex competition in long double-stranded DNA has rarely been studied. In this work, we used DMS footprinting and gel electrophoresis to study G-quadruplex formation in long double-stranded DNA derived from human genome under both dilute and molecular crowding condition created by PEG. G-quadruplex formation was observed in the process of RNA transcription and after heat denaturation/renaturation under molecular crowding condition. Our results showed that the heat denaturation/renaturation treatment followed by gel electrophoresis could provide a simple method to quantitatively access the ability of G-quadruplex formation in long double-stranded DNA. The effect of K(+) and PEG concentration was investigated and we found that stable G-quadruplexes could only form under the crowding condition with PEG at concentrations near the physiological concentration of biomass in living cells. This observation reveals a physical basis for the formation of stable G-quadruplexes in genome and supports its presence under the in vivo molecular crowding condition. |
format | Text |
id | pubmed-2800236 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2010 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-28002362009-12-31 Molecular crowding creates an essential environment for the formation of stable G-quadruplexes in long double-stranded DNA Zheng, Ke-wei Chen, Zhao Hao, Yu-hua Tan, Zheng Nucleic Acids Res Structural Biology Large numbers of guanine-rich sequences with potential to form G-quadruplexes have been identified in genomes of various organisms. Such sequences are constrained at both ends by long DNA duplex with a complementary strand in close proximity to compete for duplex formation. G-quadruplex/duplex competition in long double-stranded DNA has rarely been studied. In this work, we used DMS footprinting and gel electrophoresis to study G-quadruplex formation in long double-stranded DNA derived from human genome under both dilute and molecular crowding condition created by PEG. G-quadruplex formation was observed in the process of RNA transcription and after heat denaturation/renaturation under molecular crowding condition. Our results showed that the heat denaturation/renaturation treatment followed by gel electrophoresis could provide a simple method to quantitatively access the ability of G-quadruplex formation in long double-stranded DNA. The effect of K(+) and PEG concentration was investigated and we found that stable G-quadruplexes could only form under the crowding condition with PEG at concentrations near the physiological concentration of biomass in living cells. This observation reveals a physical basis for the formation of stable G-quadruplexes in genome and supports its presence under the in vivo molecular crowding condition. Oxford University Press 2010-01 2009-10-25 /pmc/articles/PMC2800236/ /pubmed/19858105 http://dx.doi.org/10.1093/nar/gkp898 Text en © The Author(s) 2009. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/2.5/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/2.5/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Structural Biology Zheng, Ke-wei Chen, Zhao Hao, Yu-hua Tan, Zheng Molecular crowding creates an essential environment for the formation of stable G-quadruplexes in long double-stranded DNA |
title | Molecular crowding creates an essential environment for the formation of stable G-quadruplexes in long double-stranded DNA |
title_full | Molecular crowding creates an essential environment for the formation of stable G-quadruplexes in long double-stranded DNA |
title_fullStr | Molecular crowding creates an essential environment for the formation of stable G-quadruplexes in long double-stranded DNA |
title_full_unstemmed | Molecular crowding creates an essential environment for the formation of stable G-quadruplexes in long double-stranded DNA |
title_short | Molecular crowding creates an essential environment for the formation of stable G-quadruplexes in long double-stranded DNA |
title_sort | molecular crowding creates an essential environment for the formation of stable g-quadruplexes in long double-stranded dna |
topic | Structural Biology |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2800236/ https://www.ncbi.nlm.nih.gov/pubmed/19858105 http://dx.doi.org/10.1093/nar/gkp898 |
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