Warren, Christopher L. and Kratochvil, Natasha C. S. and Hauschild, Karl E. and Foister, Shane and Brezinski, Mary L. and Dervan, Peter B. and Phillips, George N., Jr. and Ansari, Aseem Z. (2006) Defining the sequence-recognition profile of DNA-binding molecules. Proceedings of the National Academy of Sciences of the United States of America, 103 (4). pp. 867-872. ISSN 0027-8424 http://resolver.caltech.edu/CaltechAUTHORS:WARpnas06
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Determining the sequence-recognition properties of DNA-binding proteins and small molecules remains a major challenge. To address this need, we have developed a high-throughput approach that provides a comprehensive profile of the binding properties of DNA-binding molecules. The approach is based on displaying every permutation of a duplex DNA sequence (up to 10 positional variants) on a microfabricated array. The entire sequence space is interrogated simultaneously, and the affinity of a DNA-binding molecule for every sequence is obtained in a rapid, unbiased, and unsupervised manner. Using this platform, we have determined the full molecular recognition profile of an engineered small molecule and a eukaryotic transcription factor. The approach also yielded unique insights into the altered sequence-recognition landscapes as a result of cooperative assembly of DNA-binding molecules in a ternary complex. Solution studies strongly corroborated the sequence preferences identified by the array analysis.
|Additional Information:||© 2006 by The National Academy of Sciences of the USA Contributed by Peter B. Dervan, November 11, 2005. Published online before print January 17, 2006, 10.1073/pnas.0509843102 We thank D. Page and C. Kendziorski for helpful discussions and L. Vanderploeg for help with the figures. We gratefully acknowledge the support of the University of Wisconsin Industrial and Economic Development Research Program and the National Foundation–March of Dimes (A.Z.A.), Computation and Informatics in Biology and Medicine Training Grant T15LM007359 (to C.L.W.), and National Institutes of Health Grant GM51747 (to P.B.D.). Conflict of interest statement: No conflicts declared.|
|Subject Keywords:||chemical genomics; ligand–DNA recognition|
|Usage Policy:||No commercial reproduction, distribution, display or performance rights in this work are provided.|
|Deposited By:||Archive Administrator|
|Deposited On:||10 Nov 2006|
|Last Modified:||26 Dec 2012 09:16|
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