The Dynamics of Nucleic‐Acid Single‐Strand Conformation Changes

1 The dynamics of the single‐strand conformation changes of oligo‐ and polyriboadenylic acids has been investigated by a fast temperature‐jump technique. Chemical rexalation processes have been observed in the range of 0.1 to 1 μs. The relaxation times are independent of the nucleotide concentration and also do not depend upon the pH within the range 6.9 to 9.2. The amplitudes correspond to those expected from thermal melting curves. According to these results the relaxation is assigned to the “single‐strand helix‐to‐coil” transition. 2 Measurements af different wavelengths show that the relaxation times observed in the spectral range 240 nm to 270 nm are different from those observed around 285 nm by a factor of 2 to 3. This result demonstrates that the “helix‐coil” transition of adenylic acid chains cannot be described by a simple all‐or‐none model with two reaction states. 3 As expected for a single‐strand helix‐coil transition there is a relatively small ionic strength dependence: a decrease of the salt concentration leads to an increase of the relaxation time. At high ionic strengths of monovalent ions (1 M and more) the appearance of relaxation times at 5 to 10 μs and in the ms range seem to indicate aggregation. 4 The presence of Mg 2+ leads to a strong decrease of the amplitude around 285 nm, whereas the amplitude around 245 nm remains almost unchanged; the time constant of the 245‐nm relaxation increases with increasing Mg 2+ concentration. Apparently Mg 2+ ions induce a specific shift of the riboadenylic acid chain conformation. 5 Measurements of the temperature dependence in the range of 0 to 50°C revealed an increasing rate of the conformation change with increasing temperature. The relaxation process measured around 245 nm is characterised by a higher apparent activation enthalpy than that measured around 285 nm. 6 The relaxation behaviour found for the polymer is also shown by oligoriboadenylic acids. The chain length dependence of the relaxation times is relatively small. The difference of the relaxation behaviour observed around 245 nm and around 285 nm extends to the dimer. Thus the observation of two different relaxation times cannot be explained by a cooperative effect.The relaxation time constants observed for oligo‐ and polyriboadenylic acids indicate the existence of energy barriers in the conformational transition. Similar time constants have been observed previously for the elementary process of base pairing in adenylic‐uridylic acid double helices. The observation of two relaxation time constants for the conformation change of riboadenylic acid chains demonstrates the existence of more than two different conformation states.