MadSci Network: Biochemistry

Re: Can more Ethidium Bromide insert into RNA than DNA both of which have the same length?

Date: Sat Jan 13 07:05:30 2007
Posted By: Sebastien De Landtsheer, Undergraduate, Immunology, Laboratoire National de Santé
Area of science: Biochemistry
ID: 1163062575.Bc

Hello, Your question is very interesting. It all depends if you mean binding, or intercalation, or fluorescence...

The discussion here would be very long, that's why I give you the references of the articles I've found. Contact me (by replying to the email you receive containing this answer) if you cannot get the pdfs.

See the study on eilatin complexes by Luedtke et al. in Nucleic Acids Research (Luedtke NW, Hwang JS, Nava E, Gut D, Kol M, Tor Y. The DNA and RNA specificity of eilatin Ru(II) complexes as compared to eilatin and ethidium bromide. (2003) Nucleic Acids Research. October 1; 31(19): 5732–5740). There they compare affinities of varying intercalating agents on different nucleic acids (DNA/RNA, ds/ss etc).

See also Vardevanyan et al in EXPERIMENTAL and MOLECULAR MEDICINE (Vardevanyan PO, Antonyan AP, Parsadanyan MA, Davtyan HG, Karapetyan AT. (2003) The binding of ethidium bromide with DNA: interaction with single- and double-stranded structures. Experimental and Molecular Medicine, Vol. 35, No. 6, 527-533).

Hope that helps...

[Moderator's note: The paper by Luedtke et al. suggests that Ethidium bromide reaches maximum saturation at about 3 molecules per 10 base pairs of double-stranded DNA or RNA, but also presents data suggesting a wide range of binding affinities for DNA and RNA molecules of very different compositions. The paper by Vardevanyan et al. presents a wide range of ethidium binding values for several different modes of binding, in single- and double-stranded DNA molecules at differnet pH values. ]

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