An FTIR and CD study of the structural effects of G-tract length and sequence context on DNA conformation in solution

Fourier transform infrared (FTIR) and CD spectroscopy have been used to investigate the structural effects of G-tract length and flanking sequence on the conformation of DNA G-tracts in aqueous solution. Particularly, a possible predisposition for A-form features has been probed, since this may be important for protein-DNA interactions. Five different G-tract-containing DNA duplexes have been studied: d[CATGGCCATG]2, d[CATGGGCCCATG]2, d[CATGGGGCCCCATG]2, d[AGGGGCCCCT]2, and d[TGGGGCCCCA]2. In addition, a DNA duplex lacking a G-tract center was probed (d[CATATGCATATG]2). The CD and FTIR results show that the G-tract-containing sequences are all in a dominating B-DNA conformation in solution. However, certain spectral variations reflect structural effects of sequence context and G-tract length. CD spectra and FTIR results in the 1800–1500 cm−1 region show that the base-stacking pattern is greatly affected by the sequence context. The FTIR backbone 1250–1000 cm−1 region shows the antisymmetric non-bridging phosphate vibration around 1225 cm−1 in all sequences, demonstrating the overall B-conformation of the backbone. The FTIR sugar 900–800 cm−1 region shows variable contributions of two bands around 865 cm−1 and 840 cm−1, reflecting the N and S-type of sugar pucker. The relative intensities of the 865 cm−1 and 840 cm−1 bands have been proposed in the literature to quantitatively yield the contribution of N and S-type of sugar pucker, respectively. This correlation is supported by the present study. Furthermore, the contributions of N-type sugar in the DNA sequences studied indicate structural propensities that agree with trends in reported crystal structures of the same sequences: (1) d[CATGGCCATG]2, for which FTIR shows the lowest contribution of N-type sugar puckering in solution, crystallizes in a B-like conformation; (2) d[AGGGGCCCCT]2, with the highest degree of N-type sugar puckering of all the sequences studied, crystallizes in an A-like conformation; (3) d[CATGGGCCCATG]2, with an N-type contribution intermediate between that of d[CATGGCCATG]2 and d[AGGGGCCCCT]2, crystallizes in an A/B intermediate conformation.