Triple Helical Polynucleotidic Structures: An FTIR Study Of The C⁺ · G · C Triplet

Abstract

Triple helixes containing one homopurine poly dG or poly rG strand and two homopyrimidine poly dC or poly rC strands have been prepared and studied by FTIR spectroscopy in H₂O and D₂O solutions. The spectra are discussed by comparison with those of the corresponding third strands (autoassociated or not) and of double stranded poly dG · poly dC and poly rG · poly rC in the same concentration range and salt conditions. The triplex formation is characterized by the study of the base-base interactions reflected by changes in the spectral domain involving the in-plane double bond vibrations of the bases. Modifications of the initial duplex conformation (A family form for poly rG · poly rC, B family form for poly dG · poly dC) when the triplex is formed have been investigated. Two spectral domains (950800 and 1450–1350 cm⁻¹) containing absorption bands markers of the N and S type sugar geometries have been extensively studied. The spectra of the triplexes prepared starting with a double helix containing only riboses (poly rC⁺ · poly rG · poly rC and poly dC⁺ · poly rG · poly rC) as well as that of poly rC⁺ · poly dG · poly dC present exclusively markers of the North type geometry of the sugars. On the contrary in the case of the poly dC⁺ · poly dG · poly dC triplex both N and S type sugars are shown to coexist. The FTIR spectra allow us to propose that in this case the sugars of the purine (poly dG) strand adopt the S type geometry.