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 (auto associated 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 (950-800 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.

Vibrational circular dichroism signature of hemiprotonated intercalated four-stranded i-DNA

“…The negative lobe of this latter VCD feature originates from C2_O stretching of the unprotonated cytosine residues with corresponding principal absorption at 1656 cm À 1 . All the remaining absorption and VCD bands appear at the same wavenumbers as those of the unprotonated d(C) 12 and agree well with those of unprotonated poly(rC) at neutral pH [22].…”

“…3 and 4). The carbonyl absorption of s-d(C) 12 at neutral pH splits into two bands, which are shifted to higher wavenumbers for the paired cytosines by protonation of N3 from 1650 cm À 1 at pH 7.2 to 1694 and 1665 cm À 1 at lower pH [22,26]. The ring mode is shifted from 1614 to 1609 cm À 1 with somewhat lower intensity.…”

“…This band is invariably situated around 1090 cm À 1 in absorption of all DNA double helices at normal or acidic pH in parallel as well as antiparallel strands [19,22,24,26,27]. This peculiarity was first noticed in IR of d(TCCCCC) at acidic pH and was explained by a rotation of the phosphate groups stabilized by bridging water molecules [26].…”

“…Similar to poly(rC) and poly(dC), which at neutral pH form single stranded structures with stacked bases and ordered backbones [21,22], d(C) 12 also shows elements of well ordered single strands (designated here as s-d(C) 12 ). The single strong absorption of d(C) 12 at 1650 cm À 1 arises from stretching of the C2_O carbonyl group (pH 7.2 in Fig.…”

“…It is assigned as a deoxyribose vibration, which is persistently observed in the spectra of the unprotonated species [22,26]. Moreover, it is present in all spectra of DNA duplexes no matter whether they are parallel or antiparallel [19,22,24,26,27].…”