Ethanol-induced structural transitions of DNA on mica

Ye Fang; Thomas S. Spisz; Jan H. Hoh

doi:10.1093/nar/27.8.1943

Ethanol-induced structural transitions of DNA on mica

Ye Fang, Thomas S. Spisz, Jan H. Hoh

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Abstract

The effect of ethanol on the structure of DNA confined to mica in the presence of Mg²⁺ was examined by varying the ethanol concentration and imaging the DNA by atomic force microscopy. Contour length measurements of the DNA show a transition from all-B-form at 0% ethanol to all-A-form at > 25% ethanol. At intermediate ethanol concentrations, contour lengths suggest that individual molecules of air-dried DNA are trapped with mixed compositions of A-form and B-form. The relative composition depends on the ethanol concentration. Fitting the length distributions at intermediate ethanol concentrations to a simple binomial model results in an upper bound estimate for the A-form and B-form domains of ~ 54 bp in the individual molecules. In addition to length changes, the apparent persistence length of DNA decreases with increasing ethanol concentration. At high concentrations of ethanol (> 20%), DNA formed several higher order structures, including flower shaped condensates and toroids.

Original language	English (US)
Pages (from-to)	1943-1949
Number of pages	7
Journal	Nucleic acids research
Volume	27
Issue number	8
DOIs	https://doi.org/10.1093/nar/27.8.1943
State	Published - Apr 15 1999
Externally published	Yes

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Genetics

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title = "Ethanol-induced structural transitions of DNA on mica",

abstract = "The effect of ethanol on the structure of DNA confined to mica in the presence of Mg2+ was examined by varying the ethanol concentration and imaging the DNA by atomic force microscopy. Contour length measurements of the DNA show a transition from all-B-form at 0% ethanol to all-A-form at > 25% ethanol. At intermediate ethanol concentrations, contour lengths suggest that individual molecules of air-dried DNA are trapped with mixed compositions of A-form and B-form. The relative composition depends on the ethanol concentration. Fitting the length distributions at intermediate ethanol concentrations to a simple binomial model results in an upper bound estimate for the A-form and B-form domains of ~ 54 bp in the individual molecules. In addition to length changes, the apparent persistence length of DNA decreases with increasing ethanol concentration. At high concentrations of ethanol (> 20%), DNA formed several higher order structures, including flower shaped condensates and toroids.",

author = "Ye Fang and Spisz, {Thomas S.} and Hoh, {Jan H.}",

note = "Funding Information: We thank Dr Qi-Chun Tang of the Johns Hopkins University School of Medicine for providing the linear 1968 bp DNA used. This work was supported by NIH grants HGO1518 (J.H.H.), and internal research and development funds from the Johns Hopkins University Applied Physics Laboratory (T.S.S.).",

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doi = "10.1093/nar/27.8.1943",

language = "English (US)",

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AU - Fang, Ye

AU - Spisz, Thomas S.

AU - Hoh, Jan H.

N1 - Funding Information: We thank Dr Qi-Chun Tang of the Johns Hopkins University School of Medicine for providing the linear 1968 bp DNA used. This work was supported by NIH grants HGO1518 (J.H.H.), and internal research and development funds from the Johns Hopkins University Applied Physics Laboratory (T.S.S.).

PY - 1999/4/15

Y1 - 1999/4/15

N2 - The effect of ethanol on the structure of DNA confined to mica in the presence of Mg2+ was examined by varying the ethanol concentration and imaging the DNA by atomic force microscopy. Contour length measurements of the DNA show a transition from all-B-form at 0% ethanol to all-A-form at > 25% ethanol. At intermediate ethanol concentrations, contour lengths suggest that individual molecules of air-dried DNA are trapped with mixed compositions of A-form and B-form. The relative composition depends on the ethanol concentration. Fitting the length distributions at intermediate ethanol concentrations to a simple binomial model results in an upper bound estimate for the A-form and B-form domains of ~ 54 bp in the individual molecules. In addition to length changes, the apparent persistence length of DNA decreases with increasing ethanol concentration. At high concentrations of ethanol (> 20%), DNA formed several higher order structures, including flower shaped condensates and toroids.

AB - The effect of ethanol on the structure of DNA confined to mica in the presence of Mg2+ was examined by varying the ethanol concentration and imaging the DNA by atomic force microscopy. Contour length measurements of the DNA show a transition from all-B-form at 0% ethanol to all-A-form at > 25% ethanol. At intermediate ethanol concentrations, contour lengths suggest that individual molecules of air-dried DNA are trapped with mixed compositions of A-form and B-form. The relative composition depends on the ethanol concentration. Fitting the length distributions at intermediate ethanol concentrations to a simple binomial model results in an upper bound estimate for the A-form and B-form domains of ~ 54 bp in the individual molecules. In addition to length changes, the apparent persistence length of DNA decreases with increasing ethanol concentration. At high concentrations of ethanol (> 20%), DNA formed several higher order structures, including flower shaped condensates and toroids.

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JO - Nucleic acids research

JF - Nucleic acids research

IS - 8

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Ethanol-induced structural transitions of DNA on mica

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