An NMR and molecular modelling analysis of d(CTACTGCTTTAG)center dot d(CTAAAGCAGTAG) reveals that the particular behaviour of TpA steps is related toedge-to-edge contacts of their base-pairs in the major groove

In a previous NMR study we detected the presence of particular motions and hydration properties within the DNA fragment d(CTACTGCTTTAG). d(CTAAAGCAGTA G). Now, we report on an NMR and molecular modelling analysis of this seque nce focusing our attention on the biologically important TpA steps. NOe and coupling constant restraints were introduced in three different modelling protocols: X-PLOR and JUMNA used with Flex and AMBER94 as force-fields. Des pite their differences the protocols produce similar mean B-DNA structures (r.m.s.d. <l Angstrom). The new information confirms our previous experimen tal results on the narrowing of the minor groove along the T8T9T10/A17A16A1 5 run and the sudden widening at the T10pA11 step ending this run. It is fu rther shown that this step displays a large positive roil with its T10:A15 and A11:T14 base-pairs likely stabilised by amino-amino and aminocarbonyl i nteractions in the major groove. A relationship between roll values and ami no-amino and amino-carbonyl distances strongly suggests that electrostatics or bifurcated hydrogen-bonds could be responsible for induction of positiv e rolls in TpA steps. Such edge-to-edge interactions could explain the slow er motions shown by the adenine A15. The influence of these interactions on the stabilisation of particular DNA conformers is discussed, using our dat a and those provided by the recent literature.