Title
An FTIR and CD study of the structural effects of G-tract length and sequence context on DNA conformation in solution
Author
Martina Lindqvist, Astrid Gräslund
Year
2001
Journal
Journal of Molecular Biology
Abstract
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−1in 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−1and 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 aB-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.
Instrument
J-720
Keywords
Circular dichroism, DNA structure, Biochemistry