Under certain conditions DNAs and RNAs can give rise to particular structures different from a typical double helix form; among them hairpins and loops, triple helices, and four-way junctions. These structures are frequently essential to let the polynucleotide exert a given function. Molecules that interfere with a structure selected among several can have fundamental (positive or negative) implications in the biochemistry of a certain process. On this basis, our group is carrying out since some years an analysis of the ability of small molecules to stabilise, under given experimental conditions, peculiar DNAs and RNAs forms like multi-strand aggregates [1] or triple helices [2]. In this communication we will present a short overview of the results on the above topic with particular focus to the last system analysed: the DAPI/DNA system. DAPI (4',6-diamidino-2-phenylindole) is a fluorescent stain that is used extensively in fluorescence microscopy [3]. Is was found to bind strongly to A-T rich regions in DNA, principally as a minor groove binder. On the other hand, indications on intercalation have also been found. Absorbance, fluorescence and viscosimetric titrations together with T-jump kinetic experiments have been done on the DAPI/DNA system to get new information on the very complex mode of binding of this fluorescent dye to polynucleotides. The results of these experiments will be discussed.

Small molecules that are able to induce large conformation changes in polynucleotides: the DAPI/DNA system

BIVER, TARITA;SECCO, FERNANDO;VENTURINI, MARCELLA;
2011

Abstract

Under certain conditions DNAs and RNAs can give rise to particular structures different from a typical double helix form; among them hairpins and loops, triple helices, and four-way junctions. These structures are frequently essential to let the polynucleotide exert a given function. Molecules that interfere with a structure selected among several can have fundamental (positive or negative) implications in the biochemistry of a certain process. On this basis, our group is carrying out since some years an analysis of the ability of small molecules to stabilise, under given experimental conditions, peculiar DNAs and RNAs forms like multi-strand aggregates [1] or triple helices [2]. In this communication we will present a short overview of the results on the above topic with particular focus to the last system analysed: the DAPI/DNA system. DAPI (4',6-diamidino-2-phenylindole) is a fluorescent stain that is used extensively in fluorescence microscopy [3]. Is was found to bind strongly to A-T rich regions in DNA, principally as a minor groove binder. On the other hand, indications on intercalation have also been found. Absorbance, fluorescence and viscosimetric titrations together with T-jump kinetic experiments have been done on the DAPI/DNA system to get new information on the very complex mode of binding of this fluorescent dye to polynucleotides. The results of these experiments will be discussed.
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Utilizza questo identificativo per citare o creare un link a questo documento: http://hdl.handle.net/11568/144416
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