The binding of ethidium bromide with DNA: interaction with single- and double-stranded structures.

P O Vardevanyan,H G Davtyan,A T Karapetyan,A P Antonyan,M A Parsadanyan

doi:10.1038/emm.2003.68

P O Vardevanyan, H G Davtyan + Show 3 more

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https://doi.org/10.1038/emm.2003.68

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Abstract

The pH-induced helix-coil transition of DNA and its complexes with EtBr is carried out at acidic pH in a wide interval of change of concentration ratio of EtBr/DNA. The binding isotherms of EtBr on double and single-stranded DNA at pH = 7.0 and pH = 3.0 (t = 25(o)C) are obtained by absorption and fluorimetric methods. Binding constants (K) and number of bases (n), corresponding to one binding site were determined. Non fluorescent "strong" complex with ds-DNA at pH = 7.0 and t = 25(o)C as well as "strong" and "weak" complexes with ss-DNA at pH = 3.0 and t = 25(o)C are revealed.

Highlights

The existing data oninteraction of ethidium bromide (EtBr) with DNA specifies that this ligand can form several types of complexes with double stranded DNA (ds-DNA) and single stranded DNA (ss-DNA)(Karapetian et al.,1996,Vardevanyanetal.,2000)
It is necessary to note that the research of behaviour of ss-DNA in a solution is connected with certain difficulties.Itis connected with occurrenceofintermolecularas wellasintramolecular bindingin diluted solutions that carryin essential contributiontotheenthalpyofintermolecularbinding att=25oC(Seanger,1987; Graves,1993).Theearlier reported data showed a high affinity and selective binding ofthe antibiotic actinomycin D (AMD) with ss-DNA.Ethidium Bromide(EtBr)alsoshowsbinding specificity with ss-oligonucleotide sequences(Veselkov et al, 1997, Vardevanyan et al, 2000)
Existing experimental data for complex formation of EtBr with ss-polynucleotides are relevant to conditions, not excluding presence of ds-sitesin DNA(Borisova et al, 1998)

Summary

Introduction

The existing data oninteraction of EtBr with DNA specifies that this ligand can form several types of complexes with ds-DNA and ss-DNA(Karapetian et al.,1996,Vardevanyanetal.,2000). It is necessary to note that the research of behaviour of ss-DNA in a solution is connected with certain difficulties.Itis connected with occurrenceofintermolecularas wellasintramolecular bindingin diluted solutions that carryin essential contributiontotheenthalpyofintermolecularbinding att=25oC(Seanger,1987; Graves,1993).Theearlier reported data showed a high affinity and selective binding ofthe antibiotic actinomycin D (AMD) with ss-DNA.Ethidium Bromide(EtBr)alsoshowsbinding specificity with ss-oligonucleotide sequences(Veselkov et al, 1997, Vardevanyan et al, 2000). It is possibletoassumethattheselectivitycomplexformation of ligands with certain single-stranded sequences plays an important role in functioning of biologically active substancesin processes connected withtranscription andreplication of DNA. Existing experimental data for complex formation of EtBr with ss-polynucleotides are relevant to conditions, not excluding presence of ds-sitesin DNA(Borisova et al, 1998)

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