Effect of flanking bases on quadruplex stability and Watson-Crick duplex competition

Guanine-rich DNA sequences have the ability to fold into four-stranded structures called G-quadruplexes, and are considered as promising anticancer targets. Although the G-quadruplex structure is composed of quartets and interspersed loops, in the genome it is also flanked on each side by numerous bases. The effect of loop length and composition on quadruplex conformation and stability has been well investigated in the past, but the effect of flanking bases on quadruplex stability and Watson-Crick duplex competition has not been addressed. We have studied in detail the effect of flanking bases on quadruplex stability and on duplex formation by the G-quadruplex in the presence of complementary strands using the quadruplex-forming sequence located in the promoter region of the c-kit oncogene. The results obtained from CD, thermal difference spectrum and UV melting demonstrated the effect of flanking bases on quadruplex structure and stability. With the increase in flank length, the increase in the more favorable Delta H-vH is accompanied by a striking increase in the unfavorable Delta S-vH, which resulted in a decrease in the overall Delta G(vH) of quadruplex formation. Furthermore, CD, fluorescence and isothermal titration calorimetry studies demonstrated that the propensity to attain quadruplex structure decreases with increasing flank length.