Studies On The Interaction Mechanism Of Arginine And/or Tryptophan With CtDNA

Deoxyribonucleic acid (DNA) is the basic genetic material of life. DNA is a major target for antiviral, anticancer and antibiotic drugs, it could be damaged under various conditions especially interact with some molecules, so it could be applied in various type of therapy.Amino acid drug is a kind of small molecular compound with special physiological function and most widely used as biochemical drug, the amino acids and amino acid derivatives are possible to be the new research fields of drugs. Protein and polypeptide drugs are generally a group of the most effective and natural therapeutics, have been broadly applied in many therapeutic areas. Among them, most of the polypeptide can be used as drug precursors.The study on the interaction between amino acid, protein and polypeptide drugs and DNA has become an active research area in biochemistry and life science in recent years. However, little work is focused on investigating the interaction mechanism between the drug-loaded delivery complex and DNA at the molecular level.Understanding the modes of amino acid drug, protein and polypeptide drugs binding to DNA and DNA binding affinity and cleavage mechanism can help us to understand the mechanism of drugs on molecular level and to provide guidance for the design of new DNA-targeted drugs.In the first part, the interaction between L-Arg and calf thymus DNA (ctDNA) in sodium acetate-acetic acid buffer(pH=4) was investigated with the use of neutral red (NR) dye as a spectral probe coupled with UV-vis absorption, fluorescence, and circular dichroism (CD) spectroscopy technique. The UV absorption spectroscopy indicated that L-Arg interacted with ctDNA via electrostatic force and the fluorescence enhancing of the DNA-NR system verified the electrostatic interaction. In addition, detectable changes in the CD spectrum of ctDNA in the presence of L-Arg indicated conformational changes in the DNA double helix after interaction with the drug. Docking studies were found to corroborate the experimental results. All these results prove that this drug interacts with ctDNA via an electrostatic binding mode.In the second part, the interaction between L-Trp and calf thymus DNA (ctDNA) in physiologieal condition was investigated by UV-vis absorption, fluorescence, and circular dichroism (CD) spectroscopy technique. The experiment demonstrated that the fluoresenee of L-Trp could be quenehed by DNA, the binding mechanism was proved to be the statie quenehing proeess according to the deesealating binding constant along with the esealating temperatures. From the UV-visible spectra between L-Trp and DNA, it was coneluded that there was not interealation binding mode between L-Trp and DNA. For further effect of ionic Strength study, the electrostatic interaction could be eliminated. A kind of groove binding mode may existed according to the effect of I-. In a word, we can get a conclusion that L-Trp can interact with DNA, and the groove binding mode was mainly existed.In the third part, the interaction between Trp-Arg dipetide (WR) and calf thymus DNA (ctDNA) in pH7.4Tris-HCl buffer was investigated by multi-spectroscopic techniques and molecular modeling. The fluorescence spectroscopy and UV absorption spectroscopy indicated that WR interacted with ctDNA in a minor groove binding mode and the binding constant was4.1×103. The ionic strength effect and single-stranded DNA (ssDNA) quenching illustrated that electrostatic interaction and groove binding coexisted between them. Circular dichroism spectroscopy (CD) was employed to measure the conformation change of ctDNA in the presence of WR. The molecular modeling results and the hydrogen bond and Van der Waals were main acting forces. All the above methods can be widely used to investigate the interaction of peptide with nucleic acids, which contributes to design the structure of new and efficient drugs.In the fourth part, the interaction of WAR with ctDNAwas studied by means of absorption, fluorescence spectra, circular dichroism (CD) spectroscopy and molecular modeling. Information such as binding constants and quenching constant at various temperatures were calculated, it was proved that the quenehing belonged to static fiuorescene quenching. The results of UV-vis and fluorescence spectra indieated the major mode of binding was groove binding of WAR with ctDNA and same result can be drawn from the effect of native and denatured DNA experiment. The ionic strength effect illustrated that electrostatic binding also existed between them. The molecular modeling results showed that WAR tended to bind in the major groove, and the hydrogen bond and Van der Waals were main acting forces.