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Determination of Allosteric Effects and Interstrand Bidentate Interactions in DNA‐Peptide Molecular Recognition |
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| Authors: | Yen‐Chung Chen Jonathan T. B. Huang Kee‐Ching G. Jeng Robin C. K. Yang Mo‐Kai Liao Chee‐Shan Chen Wei‐Jyun Chien Ming‐Tsair Wey Lou‐Sing Kan Leung Sheh |
| Affiliation: | 1. Department of Chemistry and Life Science Research Center, Tunghai Christian University, Taichung, Taiwan 407, R.O.C.;2. Department of Medical Research, Taichung Veterans General Hospital, Taichung, Taiwan 405, R.O.C.;3. Department of Applied Chemistry, Chaoyang University of Technology, Taichung, Taiwan 413, R.O.C.;4. Institute of Chemistry, Academia Sinica, Taipei, Taiwan 11529, R.O.C.;5. Department of Bioengineering, Tatung University, Taipei, Taiwan 104, R.O.C. |
| Abstract: | To study DNA allostery, quantitative DNase I footprinting studies were carried out on a newly designed peptide His‐Hyp‐Lys‐Lys‐(Py)4‐Lys‐Lys‐NH2 (HypKK‐10) containing the XHypKK (Hyp = hydroxyproline) and polyamide motifs. The interconnection of DNA footprints of peptides HypKK‐10 and the parent peptide PyPro‐12 supports the proposal that interaction network cooperativity is preferred in DNA‐peptide interactions between multiple recognition sites. A simple method of determining interstrand bidentate interactions between the peptide moieties and DNA bases is introduced. It is envisaged that interstrand bidentate interactions also participate in the relay of conformational changes to recognition sites on the complementary strands. Circular dichroism studies of the titration of peptide HypKK‐10 with an oligonucleotide duplex indicate that this peptide binds in a dimeric fashion to DNA in the minor groove. This work may prompt the design of new DNA binding ligands for the study of DNA‐peptide allosteric interactions and DNA interaction network. |
| Keywords: | DNA‐peptide molecular recognition Positive‐cooperative binding Footprinting Circular dichroism Interstrand bidentate interactions Interaction network |