A-like guanine-guanine stacking in the aqueous DNA duplex of d(GGGGCCCC)

We have used CD spectroscopy, NMR spectroscopy and unrestrained molecular d ynamics to study conformational properties of a DNA duplex formed by the se lf-complementary octamer d(GGGGCCCC). Its unusual CD spectrum contains feat ures indicating A-like stacking of half of the bases, whereas the other hal f stack in a B-like fashion. Unrestrained molecular dynamics simulations co nverged to a stable B-like double-helix of d(GGGGCCCC). However, the double -helix contained a central hole whose size was half of that occurring in st ructure A. In the canonical structure B, the hole does not exist at all bec ause the base-pairs cross the double-helix centre. The cytosine bases were stacked in the duplex of B(GGGGCCCC) as in structure B, while stacking of t he guanine bases displayed features characteristic for structure A. NMR spe ctroscopy revealed that the A-like guanine-guanine stacking was accompanied by an increased tendency of the deoxyribose rings attached to the guanine bases to be puckered in an A-like fashion. Otherwise, the duplex of d(GGGGC CCC) showed no clash, no bend and no other significant deviation from struc ture B. The present analysis demonstrates a remarkable propensity of the gu anine runs to stack in an A-like fashion even within the B-DNA framework. T his property explains why the oligo(dG). oligo(dC) tracts switch into struc ture A so easily. Secondly, this property may influence replication, becaus e structure A is replicated more faithfully than structure B. Thirdly, the oligo(dG) runs might have played an important role in early evolution, when DNA took on functions that originally evolved on RNA. Fourthly, the presen t study extends the vocabulary of DNA secondary structures by the heteronom ous duplex of d(GGGGCCCC) in which the B-like strand of oligo(dC) is bound to the A-like strand of oligo(dG). (C) 2001 Academic Press.