Gel electrophoretic analysis of the geometry of a DNA four-way junction

Julia Promisel Cooper, Paul J Hagerman

Research output: Contribution to journalArticle

155 Citations (Scopus)

Abstract

Branched DNA molecules (Holliday structures) are believed to be key intermediates in the process of homologous genetic recombination. However, despite the importance of such structures, their transient nature makes it difficult to analyze their physical properties. In an effort to evaluate several models for the geometry of such branched molecules, a stable, synthetic DNA four-way junction has been constructed. The geometry of the synthetic junction has been probed by gel electrophoresis, utilizing the fact that bent DNA molecules demonstrate reduced mobilities on polyacrylamide gels to an extent that varies with the degree of the bend angle. From the synthetic four-way junction, we have produced a set of molecules in which all combinations of two junction arms have been extended by 105 base-pairs. The electrophoretic mobilities of the extended junctions differ in a manner which indicates that the junction is not a completely flexible structure; nor is it tetrahedral or planar-tetragonal. Instead, the four strands that comprise the DNA four-way junction are structurally non-equivalent. The significance of these observations with regard to previous models for four-way junction geometry is discussed.

Original languageEnglish (US)
Pages (from-to)711-719
Number of pages9
JournalJournal of Molecular Biology
Volume198
Issue number4
DOIs
StatePublished - Dec 20 1987
Externally publishedYes

Fingerprint

Gels
DNA
Homologous Recombination
Base Pairing
Genetic Recombination
Electrophoresis

ASJC Scopus subject areas

  • Virology

Cite this

Gel electrophoretic analysis of the geometry of a DNA four-way junction. / Cooper, Julia Promisel; Hagerman, Paul J.

In: Journal of Molecular Biology, Vol. 198, No. 4, 20.12.1987, p. 711-719.

Research output: Contribution to journalArticle

@article{e821b7c2f5264fd7b0b61e2786c31bc0,
title = "Gel electrophoretic analysis of the geometry of a DNA four-way junction",
abstract = "Branched DNA molecules (Holliday structures) are believed to be key intermediates in the process of homologous genetic recombination. However, despite the importance of such structures, their transient nature makes it difficult to analyze their physical properties. In an effort to evaluate several models for the geometry of such branched molecules, a stable, synthetic DNA four-way junction has been constructed. The geometry of the synthetic junction has been probed by gel electrophoresis, utilizing the fact that bent DNA molecules demonstrate reduced mobilities on polyacrylamide gels to an extent that varies with the degree of the bend angle. From the synthetic four-way junction, we have produced a set of molecules in which all combinations of two junction arms have been extended by 105 base-pairs. The electrophoretic mobilities of the extended junctions differ in a manner which indicates that the junction is not a completely flexible structure; nor is it tetrahedral or planar-tetragonal. Instead, the four strands that comprise the DNA four-way junction are structurally non-equivalent. The significance of these observations with regard to previous models for four-way junction geometry is discussed.",
author = "Cooper, {Julia Promisel} and Hagerman, {Paul J}",
year = "1987",
month = "12",
day = "20",
doi = "10.1016/0022-2836(87)90212-9",
language = "English (US)",
volume = "198",
pages = "711--719",
journal = "Journal of Molecular Biology",
issn = "0022-2836",
publisher = "Academic Press Inc.",
number = "4",

}

TY - JOUR

T1 - Gel electrophoretic analysis of the geometry of a DNA four-way junction

AU - Cooper, Julia Promisel

AU - Hagerman, Paul J

PY - 1987/12/20

Y1 - 1987/12/20

N2 - Branched DNA molecules (Holliday structures) are believed to be key intermediates in the process of homologous genetic recombination. However, despite the importance of such structures, their transient nature makes it difficult to analyze their physical properties. In an effort to evaluate several models for the geometry of such branched molecules, a stable, synthetic DNA four-way junction has been constructed. The geometry of the synthetic junction has been probed by gel electrophoresis, utilizing the fact that bent DNA molecules demonstrate reduced mobilities on polyacrylamide gels to an extent that varies with the degree of the bend angle. From the synthetic four-way junction, we have produced a set of molecules in which all combinations of two junction arms have been extended by 105 base-pairs. The electrophoretic mobilities of the extended junctions differ in a manner which indicates that the junction is not a completely flexible structure; nor is it tetrahedral or planar-tetragonal. Instead, the four strands that comprise the DNA four-way junction are structurally non-equivalent. The significance of these observations with regard to previous models for four-way junction geometry is discussed.

AB - Branched DNA molecules (Holliday structures) are believed to be key intermediates in the process of homologous genetic recombination. However, despite the importance of such structures, their transient nature makes it difficult to analyze their physical properties. In an effort to evaluate several models for the geometry of such branched molecules, a stable, synthetic DNA four-way junction has been constructed. The geometry of the synthetic junction has been probed by gel electrophoresis, utilizing the fact that bent DNA molecules demonstrate reduced mobilities on polyacrylamide gels to an extent that varies with the degree of the bend angle. From the synthetic four-way junction, we have produced a set of molecules in which all combinations of two junction arms have been extended by 105 base-pairs. The electrophoretic mobilities of the extended junctions differ in a manner which indicates that the junction is not a completely flexible structure; nor is it tetrahedral or planar-tetragonal. Instead, the four strands that comprise the DNA four-way junction are structurally non-equivalent. The significance of these observations with regard to previous models for four-way junction geometry is discussed.

UR - http://www.scopus.com/inward/record.url?scp=0023551842&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=0023551842&partnerID=8YFLogxK

U2 - 10.1016/0022-2836(87)90212-9

DO - 10.1016/0022-2836(87)90212-9

M3 - Article

C2 - 2828644

AN - SCOPUS:0023551842

VL - 198

SP - 711

EP - 719

JO - Journal of Molecular Biology

JF - Journal of Molecular Biology

SN - 0022-2836

IS - 4

ER -