Reversal of the long-wavelength CD band of poly(dI-dC).poly(dI-dC) on specific interaction with the 53-58 peptide fragment of the lac repressor

Conformational transitions of alternating purine-pyrimidine DNAs in perchlorate ethanol solutions

Conformational transitions of poly(dA-dC).poly(dG-dT), poly(dA-dT).poly(dA-dT), and other alternating purine-pyrimidine DNAs were studied in aqueous ethanol solutions containing molar concentrations of sodium perchlorate, which is a novel solvent stabilizing non-B duplexes of DNA. Using CD and UV absorption spectroscopies, we show that this solvent unstacks bases and unwinds the B-forms of the DNAs to transform them into the A-form or Z-form. In the absence of divalent cations poly(dA-dC).poly(dG-dT) can adopt both of these conformations. Its transition into the Z-form is induced at higher salt and lower ethanol concentrations, and at higher temperatures than the transition into the A-form. Submillimolar concentrations of NiCl2 induce a highly cooperative and slow A-Z transition or Z-Z' transition, which is fast and displays low cooperativity. Poly(dA-dT).poly(dA-dT) easily isomerizes into the A-form in perchlorate-ethanol solutions, whereas high perchlorate concentrations denature the polynucleotide, which then cannot adopt the Z-form. At low temperatures, however, NiCl2 also cooperatively induces the Z'-form in poly(dA-dT).poly(dA-dT). Poly(dI-dC).poly(dI-dC) is known to adopt an unusual B-form in low-salt aqueous solution, which is transformed into a standard B-form by the combination of perchlorate and ethanol. NiCl2 then transforms poly(dI-dC).poly(dI-dC) into the Z'-form, which is also adopted by poly(dI-br5dC).poly(dI-br5dC).

Helical nature of poly(dI-dC).poly(dI-dC). Vibrational circular dichroism results

Poly(dI-dC).poly(dI-dC) was studied using vibrational circular dichroism and IR spectroscopy in both the base deformation C = O and symmetric PO2- stretching regions. VCD spectra of this duplex under low salt conditions are consistent with its having a B-form structure. Addition of 5 M NaCl leads to relatively uniform VCD intensity loss which is consistent with loss of helical structure rather than formation of an intermediate state between the B and Z forms. This duplex polymer under high salt conditions with added NiCl2 shows aggregation effects, but its IR and VCD spectra have characteristic features of the Z-form DNA conformation. The cooperative change of backbone and base pair structure upon thermal denaturation is indicated by the simultaneous collapse of the VCD at 65 degrees C in both the PO2- and C = O stretching regions. This study further demonstrates that the VCD bandshape of a specific localized nucleic acid vibrational transition can be a useful indicator of the helical handedness. The empirical conformational interpretations are supported by simulated VCD spectra, which are in excellent agreement with the experimental results, based on dipole coupling calculations.

Transitions of poly(dI-dC), poly(dI-methyl5dC) and poly(dI-bromo5dC) among and within the B-, Z-, A- and X-DNA families of conformations

It is shown, using circular dichroism spectroscopy, that poly(dI-dC) is capable to isomerize into both Z-DNA and A-DNA in concentrated NaCl + NiCl2 and trifluoroethanol solutions, respectively. This polynucleotide also undergoes a cooperative, two-state transition in ethanol into a structure which most probably is a canonical B-DNA. This implies that the conformation of poly(dI-dC) is unusual in low-salt aqueous solution. The canonical B-DNA is also adopted by poly(dI-methyl5dC) in trifluoroethanol while this polynucleotide adopts Z-DNA not only in NaCl + NiCl2 but also in the presence of MgCl2. Poly(dI-methyl5dC) partially adopts X-DNA in concentrated CsF and mainly ethanolic solutions. Poly(dI-bromo5dC) isomerizes into Z-DNA not only in concentrated NaCl even in the absence of NiCl2 but also in concentrated MgCl2. This polynucleotide transforms between two distinct variants of Z-DNA in ethanol or trifluoroethanol solutions.