Abstract
DNA is an important molecule in the organism. The genetic information carried by DNA regulates important biochemical reactions by replication and transcription. Many proteins selectively bind to DNA fragment to regulate these reactions. Therefore, many small molecules were designed to recognize these specific DNA sequences to block the interaction between proteins and DNA and to inhibit cancer and other disease. In this study, we designed a novel peptide contains the XPRK motif and Py residue. The sequence of the designed peptide is Gln-Hyp-Arg-Lys-(Py)4-Lys-Arg-NH2 (HyQ-10). We chose a duplex d(AGGAGAAAATAC)2 as our target. By 2D NMR spectroscopy, we got the sequential assignment of d(AGGAGAAAATAC)2. In the HyQ-10 titraion experiment, we find out that the residues around the A/T-rich site will get the larger influence. And the consecutive T site has the most stable binding. In the titration experiment, we only found out a new cross peak mode, indicating that HyQ-10 and d(AGGAGAAAATAC)2 may have only one binding mode.