The quadruplex-duplex structural transition of polyriboguanylic acid

The vibrational infrared (IR) absorption and vibrational circular dichroism (VCD) spectral changes of polyriboguanylic acid (polyG) as a function of time, temperature and pH have been investigated to establish how changes in spectral features relate to the structural modifications of polyG. From the progression of IR and VCD spectral features with respect to time, it is observed that stabilization of the quadruplex structure at pH 6.4 (near-neutral environment) takes place within 5 days. This stabilization process is most clearly evidenced by a downshift of the carbonyl absorption band and the corresponding positive VCD couplet, from 1689 to approximately 1682 cm(-1) in time. Time-induced spectral modifications also indicated that, in an acidic environment (pH 3.1) and within a 5 day waiting period, polyG develops a duplex structure. An additional positive VCD couplet associated with an absorption band at 1589 cm(-1) is identified as a marker of the polyG duplex structure. From the progression of spectral features with respect to temperature at pH 6.4, it is found that heating induces structural changes that favor the formation of a duplex structure. This duplex structure, at pH 6.4, would not form at room temperature simply by the passage of time. When polyG is in an acidic environment (pH 3.1), heating accelerates the conversion to the duplex structure that could also be obtained with passage of time at that pH. On the basis of the comparison of experimental and quantum theoretical VCD spectra for polyG, the key spectral signature for the quadruplex form is considered to be a single positive VCD couplet, while the spectral signature for a duplex form is considered to contain an additional positive VCD couplet at a lower frequency.