Maurice Durand

Interaction of aromatic residues of proteins with nucleic acids. Circular dichroism studies of the binding of oligopeptides to poly(adenylic acid).

The binding of peptides containing lysyl and aromatic residues to poly(A) in its single-stranded form at pH 7 leads to a change of its circular dichroism (CD) spectrum, which is mainly due to the stacking of the aromatic amino acid with the bases of poly(A). Comparison is made between the binding of peptides having different primary structures which gives indications on the way the peptides bind to poly(A). A method is described which allows the calculation of the binding parameters from CD data. The magnitude of the association constant depends on the size of the aromatic ring and decreases in the order tryptophan greater than tyrosine greater than phenylalanine. The CD amplitude decreases linearly with the concentration of bound molecules. These results are discussed with respect to the role played by aromatic amino acids in complex formation between nucleic acids and proteins.

Interaction of lac repressor with alternating poly d (A-T) and poly d (G-C). Circular dichroism studies.

The binding of lac repressor to poly d(A-T) and d(G-C) has been studied using circular dichroism. The results indicate that the binding induces the same conformational change of both polynucleotides and perturbs the same number of nucleic acid bases (28 bases). It is shown that in 0.1 M phosphate buffer the CD measurement can be used to determine the binding constant of lac repressor to poly d(A-T). Competition experiments performed at various salt concentrations show that the stronger interaction of lac repressor for poly d(A-T) than for poly d(G-C) is based on difference in the dissociation rate of the complexes whereas the association rate for both polymers are similar.

Effect of strand orientation on the interaction of berenil with DNA triple helices

Abstract. Using circular dichroism spectroscopy the ability of berenil, a minor groove binding drug, to induce triple helix formation was investigated with two oligonucleotides designed to form two intramolecular triplexes containing T*A:T and G*G:C triplets, which differ only by the orientation of their third strand: 5′-d(G4A4G4-[T4]-C4T4C4-[T4]-G4T4G4), and 5′-d(G4T4G4-[T4]-G4A4G4-[T4]-C4T4C4), where [T4] represents a stretch of four thymine residues. We demonstrate that when added to the duplex form of these oligonucleotides, berenil induces triplex structure formation only if the orientation of third strand is antiparallel to the purine strand.

Interaction of methyl green with an oligonucleotide in intramolecular duplex and triplex conformations

Abstract Interaction of methyl green with the oligonucleotide 5′-dGGAAAAGG-[T4]-GGAAAAGG-[T4]-CCTTTTCC (where [T4] is a nucleotide sequence of four thymines) in hairpin duplex and in intramolecular triplex structures has been studied by circular dichroism. We found that methyl green binding to the duplex form shows a complex pattern, exhibiting an exciton contribution when the number of bound molecules increases. Differences between this pattern and previously published results on other DNAs reveals the presence of different types of complexes. In contrast to previous findings with the triple helix poly(dA).2poly(dT) we show that the methyl green is not totally excluded from this triplex structure made of Pur:Pur:Pyr triplets.

The Lac Repressor. Structure and Interactions

Recent results from our laboratory, on the structure and the interactions of lac repressor with the DNA are reviewed. Informations on the shape and the spatial organization of the lac repressor, its tryptic core and the headpieces were obtained by small angles neutron scattering experiments. The conformation and stability of the headpiece against thermal denaturation and tryptic hydrolysis as a function of salt concentration were also studied. Interaction between non operator DNA and the repressor or the headpieces were investigated using the photochemical cross linking method, circular dichroism, fluorescence quenching, thermal denaturation of the nucleic acid. Similitudes and differences between the headpiece and the repressor behaviours are analysed. The specific interaction between the repressor and DNA fragments containing the operator sequence were studied using circular dichroism. The interactions between the headpiece and the lac operator were also studied by fluorescence and circular dichroism. All these investigations lead to a “low resolution” model of the lac repressor and its complexes with nucleic acids.

Spectroscopic Studies on Ethidium Bromide Binding to Intramolecular Parallel and Antiparallel Triple Helices Containing T*A:T and G*G:C Triplets

Abstract The interaction of ethidium bromide (EB), a DNA intercalator, with two intramolecular triplexes 5′d(G4A4G4-[T4]-C4T4C4-[TJ-G4T4G4), 5′d(G4T4G4-[T4]-G4A4G4-[T4]-C4T4C4) ([T4]represents a stretch of 4 thymine residues) and their precursor duplexes has been investigated by circular dichroism, fluorescence and UV absorption spectroscopy. Binding of EB induces a circular dichroism band in the region around 310 nm which is positive for the duplex forms but negative for the triplex forms. We observed that the binding of EB to the duplex form does not induce the formation of the triplex structures. Thermal denaturation experiments demonstrate that EB stabilizes more the parallel triple helix than the antiparallel one. Analysis of the binding process from fluorescence measurements shows that binding constants to the triple helical forms and to the hairpin reference duplex [T4]-G4A4G4-[T4]-C4T4C4) are close. However the binding site size is larger for the triplexes (4–6 base triplets) than for the duplex (2 base pairs).

Molecular Modelling Study of the Netropsin Complexation With a Nucleic Acid Triple Helix

A detailed molecular mechanical study has been made on the complexes of netropsin with the double stranded oligonucleotide (dA)12.(dT)12 and with the triple helix (dA)12.(dT)12.(dT)12. The complexes were built using computer graphics and energy refined using JUMNA program. In agreement with circular dichroism experiments we have shown that 3 netropsins can bind the minor grooves of the triple helix and of the double helix. The groove geometry in the duplex and in the triplex is very similar. However a detailed analysis of the energetic terms shows, in agreement with thermal denaturation studies, that the affinity of netropsin toward the double helices is larger than towards triple helices.