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Nucleic Acids Research, 2001, Vol. 29, No. 2 499-505
© 2001 Oxford University Press

Solution structure and dynamics of GCN4 cognate DNA: NMR investigations

Purnima Khandelwal, S. C. Panchal, P. K. Radha and R. V. Hosur*

Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai 400 005, India

A 12 bp long GCN4-binding, self-complementary duplex DNA d(CATGACGTCATG)2 has been investigated by NMR spectroscopy to study the structure and dynamics of the molecule in aqueous solution. The NMR structure of the DNA obtained using simulated annealing and iterative relaxation matrix calculations compares quite closely with the X-ray structure of ATF/CREB DNA in complex with GCN4 protein (DNA-binding domain). The DNA is also seen to be curved in the free state and this has a significant bearing on recognition by the protein. The dynamic characteristics of the molecule have been studied by 13C relaxation measurements at natural abundance. A correlation has been observed between sequence-dependent dynamics and recognition by GCN4 protein.

* To whom correspondence should be addressed. Tel: +91 22 215 2971; Fax: +91 22 215 2110; Email: hosur{at}tifr.res.in Present addresses: Purnima Khandelwal, Biophysics Research Division, University of Michigan, 930 North University Avenue, Ann Arbor, MI 48109, USA P. K. Radha, Department of Molecular Biology and the Skaggs Institute of Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA


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A. I. Dragan, Y. Liu, E. N. Makeyeva, and P. L. Privalov
DNA-binding domain of GCN4 induces bending of both the ATF/CREB and AP-1 binding sites of DNA
Nucleic Acids Res., September 30, 2004; 32(17): 5192 - 5197.
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