Simulation of double-stranded branch point migration

B. H. Robinson; N. C. Seeman

doi:10.1016/S0006-3495(87)83386-6

Simulation of double-stranded branch point migration

B. H. Robinson, N. C. Seeman

Chemistry

Research output: Contribution to journal › Article › peer-review

Abstract

A structural and dynamic model has been developed for the branch point formed when two DNA double helices exchange strands during genetic recombination. This model, which generalizes most previous structural models, maintains the twofold symmetry inherent in the covalent and hydrogen bonded structure, yet has three degrees of freedom about virtual bonds, constituting a simplified junction. Using this structural model, a three-step dynamic model for branch point migration has been developed: longitudinal diffusion about the virtual bonds to achieve a structure in which the helix axes are approximately parallel; opening of the base pairs; and rotary diffusion about the helix axis to effect a migratory event. The model, which includes the possible role of electrostatic interactions, solves problems inherent in previous treatments. We find that no significant electrostatic torques arise that promote branch point migration. The absence of a kinetic mechanism to circumvent thermodynamic barriers due to mispairing suggests that an energy source is used for those situations in living systems.

Original language	English (US)
Pages (from-to)	611-626
Number of pages	16
Journal	Biophysical journal
Volume	51
Issue number	4
DOIs	https://doi.org/10.1016/S0006-3495(87)83386-6
State	Published - 1987

ASJC Scopus subject areas

Biophysics

Access to Document

10.1016/S0006-3495(87)83386-6

Cite this

@article{0e770cdc09654ed299628cc5e8dbce4e,

title = "Simulation of double-stranded branch point migration",

abstract = "A structural and dynamic model has been developed for the branch point formed when two DNA double helices exchange strands during genetic recombination. This model, which generalizes most previous structural models, maintains the twofold symmetry inherent in the covalent and hydrogen bonded structure, yet has three degrees of freedom about virtual bonds, constituting a simplified junction. Using this structural model, a three-step dynamic model for branch point migration has been developed: longitudinal diffusion about the virtual bonds to achieve a structure in which the helix axes are approximately parallel; opening of the base pairs; and rotary diffusion about the helix axis to effect a migratory event. The model, which includes the possible role of electrostatic interactions, solves problems inherent in previous treatments. We find that no significant electrostatic torques arise that promote branch point migration. The absence of a kinetic mechanism to circumvent thermodynamic barriers due to mispairing suggests that an energy source is used for those situations in living systems.",

author = "Robinson, {B. H.} and Seeman, {N. C.}",

note = "Funding Information: We are grateful to Drs. Robert Warner and Richard Fishel for pre- publication materials. We would like to thank Dr. J. M. Schurr for valuable discussions and information about torsional correlation lengths and Dr. Neville R. Kallenbach for many helpful suggestions. We would also like to thank Ms. Kathleen A. McDonough for assistance in model building. Ms. Diane B. Robinson and Mr. Ryland Loos drew the figures, and Mr. Robert Speck made the photographs. Computational facilities were kindly provided by the SUNY/Albany Computer Center and by the University of Washington Computer Center. This work has been supported by a Basil O'Connor Starter Grant from The March of Dimes Birth Defects Foundation, Grants GM-26467, GM-29554, and ES-001 17 from the National Institutes of Health (NIH), and Grant PCM-8216762 from the National Science Foundation. N. C. Seeman is a recipient of an NIH Research Career Development Award.",

year = "1987",

doi = "10.1016/S0006-3495(87)83386-6",

language = "English (US)",

volume = "51",

pages = "611--626",

journal = "Biophysical journal",

issn = "0006-3495",

publisher = "Biophysical Society",

number = "4",

}

TY - JOUR

T1 - Simulation of double-stranded branch point migration

AU - Robinson, B. H.

AU - Seeman, N. C.

N1 - Funding Information: We are grateful to Drs. Robert Warner and Richard Fishel for pre- publication materials. We would like to thank Dr. J. M. Schurr for valuable discussions and information about torsional correlation lengths and Dr. Neville R. Kallenbach for many helpful suggestions. We would also like to thank Ms. Kathleen A. McDonough for assistance in model building. Ms. Diane B. Robinson and Mr. Ryland Loos drew the figures, and Mr. Robert Speck made the photographs. Computational facilities were kindly provided by the SUNY/Albany Computer Center and by the University of Washington Computer Center. This work has been supported by a Basil O'Connor Starter Grant from The March of Dimes Birth Defects Foundation, Grants GM-26467, GM-29554, and ES-001 17 from the National Institutes of Health (NIH), and Grant PCM-8216762 from the National Science Foundation. N. C. Seeman is a recipient of an NIH Research Career Development Award.

PY - 1987

Y1 - 1987

N2 - A structural and dynamic model has been developed for the branch point formed when two DNA double helices exchange strands during genetic recombination. This model, which generalizes most previous structural models, maintains the twofold symmetry inherent in the covalent and hydrogen bonded structure, yet has three degrees of freedom about virtual bonds, constituting a simplified junction. Using this structural model, a three-step dynamic model for branch point migration has been developed: longitudinal diffusion about the virtual bonds to achieve a structure in which the helix axes are approximately parallel; opening of the base pairs; and rotary diffusion about the helix axis to effect a migratory event. The model, which includes the possible role of electrostatic interactions, solves problems inherent in previous treatments. We find that no significant electrostatic torques arise that promote branch point migration. The absence of a kinetic mechanism to circumvent thermodynamic barriers due to mispairing suggests that an energy source is used for those situations in living systems.

AB - A structural and dynamic model has been developed for the branch point formed when two DNA double helices exchange strands during genetic recombination. This model, which generalizes most previous structural models, maintains the twofold symmetry inherent in the covalent and hydrogen bonded structure, yet has three degrees of freedom about virtual bonds, constituting a simplified junction. Using this structural model, a three-step dynamic model for branch point migration has been developed: longitudinal diffusion about the virtual bonds to achieve a structure in which the helix axes are approximately parallel; opening of the base pairs; and rotary diffusion about the helix axis to effect a migratory event. The model, which includes the possible role of electrostatic interactions, solves problems inherent in previous treatments. We find that no significant electrostatic torques arise that promote branch point migration. The absence of a kinetic mechanism to circumvent thermodynamic barriers due to mispairing suggests that an energy source is used for those situations in living systems.

UR - http://www.scopus.com/inward/record.url?scp=0023322696&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=0023322696&partnerID=8YFLogxK

U2 - 10.1016/S0006-3495(87)83386-6

DO - 10.1016/S0006-3495(87)83386-6

M3 - Article

C2 - 3580487

AN - SCOPUS:0023322696

SN - 0006-3495

VL - 51

SP - 611

EP - 626

JO - Biophysical journal

JF - Biophysical journal

IS - 4

ER -

Simulation of double-stranded branch point migration

Abstract

ASJC Scopus subject areas

Access to Document

Other files and links

Fingerprint

Cite this