Physical studies of the interaction of a calf thymus helix-destabilizing protein with nucleic acids

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Abstract
UP1, a calf thymus protein that destabilizes both DNA and RNA helices, dramatically accelerates the conversion of the inactive conformers of several small RNA molecules to their biologically active forms. Using circular dichroic [CD] and spectrophotometric methods, the interaction of this protein with a variety of synthetic polynucleotides and yeast tRNA3Leu was studied. As judged by perturbations in polynucleotide ellipticity or UV absorbance, the secondary structures of the single-stranded helices poly(A) and poly(C), as well as the double-stranded helices poly[d(A-T)] and poly(U.cntdot.U), are largely destroyed upon interaction with UP1 at low ionic strength. This effect can be reversed by an increase in [Na+]: half the UP1-induced perturbation of the poly(A) CD spectrum is removed at 0.05 M Na+. The variation of poly(A) ellipticity and UV absorbance with [UP1]/[poly(A)]p is used to determine the length of single-stranded polynucleotide chain covered by the protein: 7 .+-. 1 residues. A model is presented in which the specificity of UP1 for single strands and their concomitant distortion are a consequence of maximal binding of nucleic acid phosphates to a unique matrix of basic residues on the protein. Analogous to the effect on polynucleotides, UP1-facilitated renaturation of yeast tRNA3Leu follows the partial destruction of the inactive tRNA''s secondary structure. At the tRNA absorbance maximum, UP1 effects a hyperchronic change of 10%, representing 1/3 of the secondary structure of the inactive conformer. This change is clearly observable as a perturbation of the tRNA''s CD spectrum.