Holliday junction crossover topology

Tsu Ju Fu, Yuk Ching Tse-Dinh, Nadrian Seeman

Research output: Contribution to journalArticle

Abstract

The Holliday junction is a key intermediate in genetic recombination. It consists of four strands of DNA that associate to form four double-helical arms. Studies over the past decade with asymmetric analogs of Holliday junctions have shown that the four arms stack to generate two stacking domains. This arrangement of arms results in two strands with a roughly helical structure, and two that contain a crossover structure connecting the domains. Both parallel and antiparallel orientations of the helical strands are possible, although the antiparallel orientation is favored. In principle, there are two possible isomers of the Holliday junction, depending on which pairs of strands contain the crossover structure; isomerization between these two structures is key to many molecular models of recombination. Isomerization of parallel domain structures entails large end-to-end helical rotations if braiding of the crossover strands is to be avoided. We have examined the ability of the crossover strands to braid. This has been done by employing a double crossover molecule, whose termini are all hairpin loops. Such a molecule is a catenane of two single strands of DNA, whose linking number is a function of the sign of the node at the crossover. We have prepared linking standards by means of topological protection techniques, and have compared them to the catenane formed by the double crossover molecule. We find no evidence for braiding of the strands. Furthermore, no braided structures can be detected when the double crossover molecule is treated with Escherichia coli DNA topoisomerase I in the presence of varying amounts of Mg2+ cations.

Original languageEnglish (US)
Pages (from-to)91-105
Number of pages15
JournalJournal of Molecular Biology
Volume236
Issue number1
DOIs
StatePublished - 1994

Fingerprint

Cruciform DNA
Genetic Recombination
Type I DNA Topoisomerase
Molecular Models
DNA
Cations
Escherichia coli
catenane

Keywords

  • DNA catenanes
  • DNA topology
  • Holliday junctions
  • Recombination
  • Topological protection

ASJC Scopus subject areas

  • Virology

Cite this

Holliday junction crossover topology. / Fu, Tsu Ju; Tse-Dinh, Yuk Ching; Seeman, Nadrian.

In: Journal of Molecular Biology, Vol. 236, No. 1, 1994, p. 91-105.

Research output: Contribution to journalArticle

Fu, Tsu Ju ; Tse-Dinh, Yuk Ching ; Seeman, Nadrian. / Holliday junction crossover topology. In: Journal of Molecular Biology. 1994 ; Vol. 236, No. 1. pp. 91-105.
@article{79c309d056e64455a10a58820ecac99a,
title = "Holliday junction crossover topology",
abstract = "The Holliday junction is a key intermediate in genetic recombination. It consists of four strands of DNA that associate to form four double-helical arms. Studies over the past decade with asymmetric analogs of Holliday junctions have shown that the four arms stack to generate two stacking domains. This arrangement of arms results in two strands with a roughly helical structure, and two that contain a crossover structure connecting the domains. Both parallel and antiparallel orientations of the helical strands are possible, although the antiparallel orientation is favored. In principle, there are two possible isomers of the Holliday junction, depending on which pairs of strands contain the crossover structure; isomerization between these two structures is key to many molecular models of recombination. Isomerization of parallel domain structures entails large end-to-end helical rotations if braiding of the crossover strands is to be avoided. We have examined the ability of the crossover strands to braid. This has been done by employing a double crossover molecule, whose termini are all hairpin loops. Such a molecule is a catenane of two single strands of DNA, whose linking number is a function of the sign of the node at the crossover. We have prepared linking standards by means of topological protection techniques, and have compared them to the catenane formed by the double crossover molecule. We find no evidence for braiding of the strands. Furthermore, no braided structures can be detected when the double crossover molecule is treated with Escherichia coli DNA topoisomerase I in the presence of varying amounts of Mg2+ cations.",
keywords = "DNA catenanes, DNA topology, Holliday junctions, Recombination, Topological protection",
author = "Fu, {Tsu Ju} and Tse-Dinh, {Yuk Ching} and Nadrian Seeman",
year = "1994",
doi = "10.1006/jmbi.1994.1121",
language = "English (US)",
volume = "236",
pages = "91--105",
journal = "Journal of Molecular Biology",
issn = "0022-2836",
publisher = "Academic Press Inc.",
number = "1",

}

TY - JOUR

T1 - Holliday junction crossover topology

AU - Fu, Tsu Ju

AU - Tse-Dinh, Yuk Ching

AU - Seeman, Nadrian

PY - 1994

Y1 - 1994

N2 - The Holliday junction is a key intermediate in genetic recombination. It consists of four strands of DNA that associate to form four double-helical arms. Studies over the past decade with asymmetric analogs of Holliday junctions have shown that the four arms stack to generate two stacking domains. This arrangement of arms results in two strands with a roughly helical structure, and two that contain a crossover structure connecting the domains. Both parallel and antiparallel orientations of the helical strands are possible, although the antiparallel orientation is favored. In principle, there are two possible isomers of the Holliday junction, depending on which pairs of strands contain the crossover structure; isomerization between these two structures is key to many molecular models of recombination. Isomerization of parallel domain structures entails large end-to-end helical rotations if braiding of the crossover strands is to be avoided. We have examined the ability of the crossover strands to braid. This has been done by employing a double crossover molecule, whose termini are all hairpin loops. Such a molecule is a catenane of two single strands of DNA, whose linking number is a function of the sign of the node at the crossover. We have prepared linking standards by means of topological protection techniques, and have compared them to the catenane formed by the double crossover molecule. We find no evidence for braiding of the strands. Furthermore, no braided structures can be detected when the double crossover molecule is treated with Escherichia coli DNA topoisomerase I in the presence of varying amounts of Mg2+ cations.

AB - The Holliday junction is a key intermediate in genetic recombination. It consists of four strands of DNA that associate to form four double-helical arms. Studies over the past decade with asymmetric analogs of Holliday junctions have shown that the four arms stack to generate two stacking domains. This arrangement of arms results in two strands with a roughly helical structure, and two that contain a crossover structure connecting the domains. Both parallel and antiparallel orientations of the helical strands are possible, although the antiparallel orientation is favored. In principle, there are two possible isomers of the Holliday junction, depending on which pairs of strands contain the crossover structure; isomerization between these two structures is key to many molecular models of recombination. Isomerization of parallel domain structures entails large end-to-end helical rotations if braiding of the crossover strands is to be avoided. We have examined the ability of the crossover strands to braid. This has been done by employing a double crossover molecule, whose termini are all hairpin loops. Such a molecule is a catenane of two single strands of DNA, whose linking number is a function of the sign of the node at the crossover. We have prepared linking standards by means of topological protection techniques, and have compared them to the catenane formed by the double crossover molecule. We find no evidence for braiding of the strands. Furthermore, no braided structures can be detected when the double crossover molecule is treated with Escherichia coli DNA topoisomerase I in the presence of varying amounts of Mg2+ cations.

KW - DNA catenanes

KW - DNA topology

KW - Holliday junctions

KW - Recombination

KW - Topological protection

UR - http://www.scopus.com/inward/record.url?scp=0028330515&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=0028330515&partnerID=8YFLogxK

U2 - 10.1006/jmbi.1994.1121

DO - 10.1006/jmbi.1994.1121

M3 - Article

VL - 236

SP - 91

EP - 105

JO - Journal of Molecular Biology

JF - Journal of Molecular Biology

SN - 0022-2836

IS - 1

ER -