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 inv estigate the structural effects of G-tract length and flanking sequence on the conformation of DNA G-tracts in aqueous solution. Particularly, a possi ble predisposition for A-form features has been probed, since this may be i mportant for protein-DNA interactions. Five different G-tract-containing DN A duplexes have been studied: d[CATGGCCATG](2), d[CATGGGCCCATG](2), d[CATGG GGCCCCATG](2), d[AGGGGCCCCT](2), and d[TGGGGCCCCA](2). In addition, a DNA d uplex 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 domina ting B-DNA conformation in solution. However, certain spectral variations r eflect structural effects of sequence context and G-tract length. CD spectr a and FTIR results in the 1800-1500 cm(-1) region show that the base-stacki ng pattern is greatly affected by the sequence context. The FTIR backbone 1 250-1000 cm(-1) region shows the antisyn-Lmetric non-bridging phosphate vib ration around 1225 cm(-1) in all sequences, demonstrating the overall B-con formation of the backbone. The FTIR sugar 900-800 cm(-1) region shows varia ble contributions of two bands around 865 cm(-1) and 840 cm(-1), reflecting the N and S-e of sugar pucker. The relative intensities of the 865 cm and 840 cm- bands have been proposed in the literature to quantitatively yield the contribution of N and S-type of sugar pucker, respectively. This correl ation 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-t ype 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[CATGG GCCCATG](2), with an N-type contribution intermediate between that of d[CAT GGCCATG](2) and d[AGGGGCCCCT](2), crystallizes in an A/B intermediate confo rmation. (C) 2001 Academic Press.