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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...

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Autores principales: Zheng, Ke-wei, Chen, Zhao, Hao, Yu-hua, Tan, Zheng
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2010
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.
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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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