Sequence-directed bending of the DNA double helix is a conformational variation found in both prokaryotic and eukaryotic organisms. The utilization of bent DNA structures from various sources as specific signals recognized by an enzyme is demonstrated here using a unique endonuclease purified from trypanosomatid cells. Crithidia fasciculata nicking enzyme was previously shown to recognize specifically the bent structure found in kinetoplast DNA minicircles. The binding constant measured for this specific interaction is of two orders of magnitude higher than that measured for the binding of the enzyme to a non-curved sequence. As determined by binding competition and mobility shift electrophoresis analyses, this enzyme recognizes the sequence-directed bends associated with the origins of replication of bacteriophage λ and simian virus 40 (SV40), as well as that located within the autonomously replicating sequence (ARSl) region of the yeast S. cerevisiae.
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ACKNOWLEDGEMENTS We are grateful to Dr. Nathan Linial from the Department of Mathematics and Computer Sciences and Edna Wigderson from the Computational Center, The Hebrew University of Jerusalem, for their help and advice with the statistical analyses, and to the DNAX Research Institute of Molecular and Cellular Biology for the help in preparation of this manuscript. This study was supported in part by a grant from the Fund for Basic Research administered by the Israel Academy of Science, AID Grant No. DPE-SS42-G1-SS-4054-00 and grant No. 8500067 from the United States-Israel Binational Science Foundation (BSF), Jerusalem, Israel.