Energetics of B-Z junction formation in a sixteen base-pair duplex DNA

Mitchel J. Doktycz; Albert S. Benight; Richard D. Sheardy

doi:10.1016/0022-2836(90)90297-Y

Energetics of B-Z junction formation in a sixteen base-pair duplex DNA

Mitchel J. Doktycz, Albert S. Benight, Richard D. Sheardy

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

20 Scopus citations

Abstract

We report analysis of the NaCl-induced B-Z transition in a 16 base-pair duplex DNA with sequence designed such that when NaCl is increased the left half of the molecule undergoes the B-Z transition while the right half remains in the B-form. An equilibrium thermodynamic model based on the body of available published experimental data and the recent theoretical work of Soumpasis, which indicate, in the salt range above ~0.9 m-NaCl, the transition free-energy of B-Z conversion in DNA is a linear function of the NaCl concentration, is employed. Analysis of the B-Z transition of the junction-containing molecule indicates the B-Z junction formed in this 16 base-pair DNA is composed of approximately three base-pairs and has a free energy of formation of ~4.7 kcal/mol junction. These values for the junction are in excellent agreement with published estimates of B-Z junction size and energy derived from much longer DNA pieces.

Original language	English
Pages (from-to)	3-6
Number of pages	4
Journal	Journal of Molecular Biology
Volume	212
Issue number	1
DOIs	https://doi.org/10.1016/0022-2836(90)90297-Y
State	Published - Mar 5 1990
Externally published	Yes

Funding

This work was supported by grants GM-39471 from the National Institutes of Health (ASB), and DMB-8616358 from the National Science Foundation (RDS).

Funders	Funder number
National Science Foundation
National Institutes of Health	DMB-8616358
National Institute of General Medical Sciences	R29GM039471
Research Down Syndrome

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title = "Energetics of B-Z junction formation in a sixteen base-pair duplex DNA",

abstract = "We report analysis of the NaCl-induced B-Z transition in a 16 base-pair duplex DNA with sequence designed such that when NaCl is increased the left half of the molecule undergoes the B-Z transition while the right half remains in the B-form. An equilibrium thermodynamic model based on the body of available published experimental data and the recent theoretical work of Soumpasis, which indicate, in the salt range above ~0.9 m-NaCl, the transition free-energy of B-Z conversion in DNA is a linear function of the NaCl concentration, is employed. Analysis of the B-Z transition of the junction-containing molecule indicates the B-Z junction formed in this 16 base-pair DNA is composed of approximately three base-pairs and has a free energy of formation of ~4.7 kcal/mol junction. These values for the junction are in excellent agreement with published estimates of B-Z junction size and energy derived from much longer DNA pieces.",

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AU - Doktycz, Mitchel J.

AU - Benight, Albert S.

AU - Sheardy, Richard D.

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N2 - We report analysis of the NaCl-induced B-Z transition in a 16 base-pair duplex DNA with sequence designed such that when NaCl is increased the left half of the molecule undergoes the B-Z transition while the right half remains in the B-form. An equilibrium thermodynamic model based on the body of available published experimental data and the recent theoretical work of Soumpasis, which indicate, in the salt range above ~0.9 m-NaCl, the transition free-energy of B-Z conversion in DNA is a linear function of the NaCl concentration, is employed. Analysis of the B-Z transition of the junction-containing molecule indicates the B-Z junction formed in this 16 base-pair DNA is composed of approximately three base-pairs and has a free energy of formation of ~4.7 kcal/mol junction. These values for the junction are in excellent agreement with published estimates of B-Z junction size and energy derived from much longer DNA pieces.

AB - We report analysis of the NaCl-induced B-Z transition in a 16 base-pair duplex DNA with sequence designed such that when NaCl is increased the left half of the molecule undergoes the B-Z transition while the right half remains in the B-form. An equilibrium thermodynamic model based on the body of available published experimental data and the recent theoretical work of Soumpasis, which indicate, in the salt range above ~0.9 m-NaCl, the transition free-energy of B-Z conversion in DNA is a linear function of the NaCl concentration, is employed. Analysis of the B-Z transition of the junction-containing molecule indicates the B-Z junction formed in this 16 base-pair DNA is composed of approximately three base-pairs and has a free energy of formation of ~4.7 kcal/mol junction. These values for the junction are in excellent agreement with published estimates of B-Z junction size and energy derived from much longer DNA pieces.

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Energetics of B-Z junction formation in a sixteen base-pair duplex DNA

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