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DNA loops and semicatenated DNA junctions
BACKGROUND: Alternative DNA conformations are of particular interest as potential signals to mark important sites on the genome. The structural variability of CA microsatellites is particularly pronounced; these are repetitive poly(CA) · poly(TG) DNA sequences spread in all eukaryotic genomes as tra...
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Formato: | Texto |
Lenguaje: | English |
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BioMed Central
2000
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC29057/ https://www.ncbi.nlm.nih.gov/pubmed/11001588 http://dx.doi.org/10.1186/1471-2091-1-1 |
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author | Gaillard, Claire Strauss, François |
author_facet | Gaillard, Claire Strauss, François |
author_sort | Gaillard, Claire |
collection | PubMed |
description | BACKGROUND: Alternative DNA conformations are of particular interest as potential signals to mark important sites on the genome. The structural variability of CA microsatellites is particularly pronounced; these are repetitive poly(CA) · poly(TG) DNA sequences spread in all eukaryotic genomes as tracts of up to 60 base pairs long. Many in vitro studies have shown that the structure of poly(CA) · poly(TG) can vary markedly from the classical right handed DNA double helix and adopt diverse alternative conformations. Here we have studied the mechanism of formation and the structure of an alternative DNA structure, named Form X, which was observed previously by polyacrylamide gel electrophoresis of DNA fragments containing a tract of the CA microsatellite poly(CA) · poly(TG) but had not yet been characterized. RESULTS: Formation of Form X was found to occur upon reassociation of the strands of a DNA fragment containing a tract of poly(CA) · poly(TG), in a process strongly stimulated by the nuclear proteins HMG1 and HMG2. By inserting Form X into DNA minicircles, we show that the DNA strands do not run fully side by side but instead form a DNA knot. When present in a closed DNA molecule, Form X becomes resistant to heating to 100°C and to alkaline pH. CONCLUSIONS: Our data strongly support a model of Form X consisting in a DNA loop at the base of which the two DNA duplexes cross, with one of the strands of one duplex passing between the strands of the other duplex, and reciprocally, to form a semicatenated DNA junction also called a DNA hemicatenane. |
format | Text |
id | pubmed-29057 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2000 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-290572001-03-22 DNA loops and semicatenated DNA junctions Gaillard, Claire Strauss, François BMC Biochem Research Article BACKGROUND: Alternative DNA conformations are of particular interest as potential signals to mark important sites on the genome. The structural variability of CA microsatellites is particularly pronounced; these are repetitive poly(CA) · poly(TG) DNA sequences spread in all eukaryotic genomes as tracts of up to 60 base pairs long. Many in vitro studies have shown that the structure of poly(CA) · poly(TG) can vary markedly from the classical right handed DNA double helix and adopt diverse alternative conformations. Here we have studied the mechanism of formation and the structure of an alternative DNA structure, named Form X, which was observed previously by polyacrylamide gel electrophoresis of DNA fragments containing a tract of the CA microsatellite poly(CA) · poly(TG) but had not yet been characterized. RESULTS: Formation of Form X was found to occur upon reassociation of the strands of a DNA fragment containing a tract of poly(CA) · poly(TG), in a process strongly stimulated by the nuclear proteins HMG1 and HMG2. By inserting Form X into DNA minicircles, we show that the DNA strands do not run fully side by side but instead form a DNA knot. When present in a closed DNA molecule, Form X becomes resistant to heating to 100°C and to alkaline pH. CONCLUSIONS: Our data strongly support a model of Form X consisting in a DNA loop at the base of which the two DNA duplexes cross, with one of the strands of one duplex passing between the strands of the other duplex, and reciprocally, to form a semicatenated DNA junction also called a DNA hemicatenane. BioMed Central 2000-07-19 /pmc/articles/PMC29057/ /pubmed/11001588 http://dx.doi.org/10.1186/1471-2091-1-1 Text en Copyright © 2000 Gaillard and Strauss; licensee BioMed Central Ltd. This is an Open Access article: verbatim copying and redistribution of this article are permitted in all media for any purpose, provided this notice is preserved along with the article's original URL. |
spellingShingle | Research Article Gaillard, Claire Strauss, François DNA loops and semicatenated DNA junctions |
title | DNA loops and semicatenated DNA junctions |
title_full | DNA loops and semicatenated DNA junctions |
title_fullStr | DNA loops and semicatenated DNA junctions |
title_full_unstemmed | DNA loops and semicatenated DNA junctions |
title_short | DNA loops and semicatenated DNA junctions |
title_sort | dna loops and semicatenated dna junctions |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC29057/ https://www.ncbi.nlm.nih.gov/pubmed/11001588 http://dx.doi.org/10.1186/1471-2091-1-1 |
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