Book of Abstracts: Albany 2003

category image Albany 2003
Conversation 13
Abstract Book
June 17-21 2003

A-tract in a 31mer Hairpin DNA

Adenine-tract or A-tract is known to be a segment formed by a number of consecutive adenines in a double helix DNA. DNA molecules with A-tracts play an important role in biology, since A-tracts interact with drugs or proteins more easily than other motifs. The single stranded 31mer DNA, d(G1A2A3G4A5C6T7T8G9G10A11A12A13A14G15A16A17T18T19T20 T21C22C23A24A25G26T27C28T29T30C31), has unusually high adenine fraction (11/31>35%). This A-rich sequence was shown by NMR to form a stable hairpin double helix in solution with a GAA hairpin. Thirteen imino resonances were unambiguously assigned. In the variable temperature experiments, the imino resonance did not disappear until the temperature was above 60°C, implying that the melting temperature of the hairpin duplex was close to 60°C. Over 700 NOE correlations were identified. In addition to normal intra-residue and inter-residue NOE correlations, this sequence exhibited abundant long range NOEs, including inter-step A11H2-C22H1?, A12H2-T21H1?, A13H2-T20H1? and A14H2-T19H1? correlations. These inter-step correlations were indicative of a structure bend at the A-tract motif.

Relaxation editing technique was applied to selectively observe the adenine H2 resonances. This technique helped identify the 11 adenine H2 resonances out of 42 severely overlapped signals in the region between 7 and 8.2 ppm. Adenine-H2-only NOESY spectrum was obtained, which clearly mapped the adenine-adenine connectivity in the sequence.

Keywords Adenine-rich DNA, A-tract, DNA Bend, Relaxation-edited NOESY.

Xian Mao
William H. Gmeiner*

Department of Biochemistry
Wake Forest University School of Medicine
Winston Salem, NC 27157-1016