Published online 12 July 2004
Nucleic Acids Research, Vol. 32 No. 12 © Oxford University Press 2004; all rights reserved
Measuring specific interaction of transcription factor ZmDREB1A with its DNA responsive element at the molecular level
Institute of Chemistry, Chinese Academy of Sciences, Beijing 100080, China and 1 Department of Biological Sciences and Biotechnology, Tsinghua University, Beijing 100084, China
* To whom correspondence should be addressed. Tel: +86 10 62650024; Fax: +86 10 62650024; Email: xfang{at}iccas.ac.cn
Correspondence may also be addressed to Chunli Bai. Email: clbai{at}iccas.ac.cn
The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors
Received April 21, 2004; Revised and Accepted June 23, 2004
Specific interactions between transcription factors and DNA responsive elements are of fundamental importance in understanding how genetic regulatory proteins control gene transcription. Here we have developed a new method of using atomic force microscopy (AFM) to quantitatively study the single molecular specific interaction between ZmDREB1A, a transcription factor from maize, and its DNA responsive element, dehydration-responsive element (DRE) with core sequence A/GCCGAC. It was found that ZmDREB1A bound to both DRE ACCGAC and GCCGAC efficiently. The single molecular interaction forces of ZmDREB1A with DRE A/GCCGAC were determined to be 101 ± 5 and 108 ± 3 pN, respectively. The point mutation of ZmDREB1A in its DNA-binding domain or single base substitution of the DRE core sequence greatly reduced the binding affinity, demonstrating the high sensitivity of the AFM measurements. AFM is expected to be a simple, quick, sensitive and reliable method that offers valuable information for the characterization of transcription factors and the identification of their potential DNA responsiveelements in functional genomics research.