Helix-coil equilibria of poly (rA) · poly (rU) |
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Authors: | RD Blake |
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Institution: | Department of Biochemical Sciences, Frick Chemical Laboratory, Princeton University, Princeton, New Jersey 08540, USA |
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Abstract: | Absorbance melting curves of the double-stranded (rA) · (rU) helix, made with fractionated homopolynucleotides of matched length, have been obtained over a 15-fold range of Na+] and 30° range of temperature. An excellent fit of the observed profiles was obtained with theoretical curves calculated on the basis of the simplest interpretation for the occurrence of particular equilibria 1–3]; the complete molecular partition function being evaluated by the power series method developed by Applequist 4–6]. The stability constant was evaluated from literature values for the calorimetric enthalpy. The loop closure exponent was best represented by 2.22 ± 0.04 for the mismatching loop mode of melting and 1.22 for the matching mode and was independent of Na+] and temperature. Assuming the applicability of the nonintersecting random walk value of 1.9 ± 0.1, these results would suggest a slight bias toward matched loop formation during melting of homopolynucleotides that might be expected to form only mismatched loops. The value of the stacking parameter at 60°C was only ~6% higher than that at 30°C, 0.0221 (0.0184 for the matching case). Calculated melting curves indicate the occurrence of a fifth-order phase transition when the mean helix length is only ~13 base-pairs, or about one full turn of the helix. |
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Keywords: | Present address: Department of Biochemistry Hitchner Hall University of Maine Orono Maine 04473 USA |
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