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Nucleic Acids Research, 1977, Vol. 4, No. 5 1349-1360
© 1977

Articles

Ethidium analogues with improved resolution in the dye-buoyant density procedure*

Bruce Hudson, John H. Dawson, Russell Desiderio and Carol W. Mosher

Department of Chemistry, Stanford University Stanford, CA 94305 Bio-Organic Chemistry Department, Life Sciences Division, Stanford Research Institute Menlo Park, CA 94025, USA

Received January 12, 1977.

Analogues of ethidium chloride with large quaternary side chains have been synthesized and evaluated for improved resolution in the dye-buoyant density system for the separation of open and closed circular DNA. These compounds are similar to propidium which differs from ethidium by the replacement of an ethyl group by a methyldiethylaminopropyl group. The new analogues contain a triethylamino group attached to a methylene chain with 3, 5 or 7 carbons. With PM2 DNA the observed separation for propidium is 1.97 times that of ethidium and the new dyes show separations relative to ethidium of 2.27, 2.66 and 2.77. A correlation is established between the mass of the dye component and the observed separation which is rationalized on the basis of the four component thermodynamics describing this system.

*Dedicated to Jerome Vinograd.


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