Specific Recognition And Stabilization Of G-quadruplexes By Cationic Porphyrin Under Molecular Crowding Conditions

G-quadruplexes are special secondary structures adopted in some guanine(G)-rich DNA sequences with a high potential to form G-quadruplexes are found inmany genomic regions with biological significance. Ligands targetingG-quadruplexes are considered good candidates for anticancer drugs.In recent years, a large number of G-quadruplex ligands have been reported, butmost studies focused on the interactions between the tested ligands and monomericG-quadruplexes that have only one G-quadruplex unit. Additionally, most of currentstudies are carried out under dilute conditions. However, the~200-nucleotidetelomeric G-rich single-stranded overhang has the potential to fold into consecutiveG-quadruplex structures (multimeric G-quadruplexes) containing several units.Ligands that can selectively bind to the pocket between two adjacent G-quadruplexunits might be more suitable ligands for telomeric G-quadruplex and better telomeraseinhibitors. As we known, very few ligands have been reported that target multimericG-quadruplex structures. Studies on interactions between small-molecule ligands andmultimeric G-quadruplexes could provide new possibilities for anticancer drug design.On the other hand, living cells are crowded with many biomacromolecules includingnucleic acids, polysaccharides, and proteins, as well as soluble and insolublecomponents. These crowding conditions can greatly affect the structure and stabilityof G-quadruplexes. More importantly, some ligands are significantly less effective oreven lose the ability to stabilize G-quadruplexes under crowding conditions. Soresearch under crowding conditions conforms to the reality in the cell more. Excepttelomeres, G-quadruplex sequences have been found to present in many otheressential regions of human genome, such as promoter of oncogenes, immunoglobulinswitch and insulin regulatory regions. G-quadruplex structure in genome is supportedby several observations. G-quadruplex/duplex competition in long double-strandedDNA has rarely been studied.Based on these considerations, the following aspects were included in this thesis:1) Using a combination of spectroscopic (UV, fluorescence and CD) techniques,we demonstrated that TMPipEOPP, a cationic porphyrin derivative designed by us,can also perfectly discriminate G-quadruplexes from duplex, single-stranded andtriplex DNAs under molecular crowding conditions utilizing the dramatic effects ofG-quadruplexes on UV-vis absorption signal, solution color and fluorescence signal of TMPipEOPP.2) Meanwhile, TMPipEOPP was demonstrated as a promising multimerictelomeric G-quadruplex ligand under molecular crowding conditions. It could highlyspecifically recognize G-quadruplexes. It could also promote the formation ofG-quadruplexes and stabilize them. We demonstrated for the first time that the pocketsize between two adjacent G-quadruplex units strongly affects interactions betweenligands and multimeric G-quadruplexes.3) The above job also provides the possibility for the identification ofG-quadruplex embedding in double-stranded DNA. We used TMPipEOPP to studyG-quadruplex formation in long double-stranded DNA under both dilute andmolecular crowding condition. We proved (G)-rich DNA sequences embedding indouble-stranded DNA can fold into G-quadruplex under molecular crowdingconditions.by the dramatic effects of UV-vis absorption signal and fluorescence signalof TMPipEOPP.4) Furthermore, by changing the side arm substituents of TMPipEOPP, wesynthesized another new cationic porphyrin m-TMPipEOPP derivative to introduce anew route for screening anticancer drugs targeting telomeric G-quadruplexes.