Regulation And Application Of Polymorphic Structures Of G-rich Oligonucleotides

In this research, regulation of quadruplex-duplex competition and condensation of polymorphic oligonucleotides are systematically investigated, as well as their application in the fields of anticancer drug mechanism, nanoparticle systhesis and DNA nanomachine.Firstly, effects of natural anticancer isoflavones on the structural competition of human telomeric G-quadruplex d[AG₃(T₂AG₃)₃] (AG22) and its related Watson-Crick duplex are investigated by thermodynamic and kinetic methods respectively. Isoflavones can stabilize the G-quadruplex structure but destabilize its corresponding Watson-Crick duplex and this discriminated interaction is intensified by molecular crowding environments. Kinetic experiments indicate that the dissociation rate of quadruplex (kobs290 nm) is decreased by ₄0.3 % at the daidzin/DNA molar ratio of 1.0 in K+ whereas in Na+ the observed rate constant (kobs295 nm) is reduced by 12.0 %. Furthermore, glycosidic daidzin significantly induces a structural transition of the polymorphic G-quadruplex into the antiparallel conformation in K+ solution. Next, effects of terminal variations on the structural competition between the G-quadruplex and the Watson-Crick duplex are investigated quantitatively by thermodynamic parameters (ΔH,ΔS,ΔG25) using G-rich sequences containing two G-tracts with different 5'terminal residues from Oxytricha nova telomeric DNAs. Decreasing guanines or increasing thymines at 5'end of d[G₄T₄G₄] destabilizes the quadruplex but favors the duplex at equibrilium. Further, silver nanoparticles are synthesized templated by d[G₄T₄G₄], d[G3T₄G₄], d[G2T₄G₄], as well as their corresponding duplexes. In the case of G-quadruplexes, the silver nanoparticles are in the range of 10²0 nm without fluorescence. For the double-stranded systems, silver nanoclusters are detected with the fluorescence emission at 708 nm, 615 nm and 610 nm respectively by decreasing 5'guanines of d[G₄T₄G₄].Finally, effects of secondary structures on spermine-induced condensation of polymorphic oligonucleotides are investigated both in dilute and crowding solutions. In dilute solution, parallel G-quadruplexes display condensed and network-like aggregates in the presence of spermine, whereas hybrid-type and antiparallel structures form nanoparticles with average radius of 2.0 nm. G-rich oligonucleotides which exhibit structural transition to parallel conformation under crowding conditions can form large condensates in the presence of spermine, which exhibit cholesteric liquid crystalline. In contrast, oligonucleotides which adopt antiparallel conformation in crowding solution form small nanoparticles with average radius of 2.8 nm. At acidic pH value under crowding condition, C-rich oligonucleotides form condensed aggregates with a size distribution of 30¹00 nm, which exhibit cholesteric liquid crystalline. Environmental stimuli involving pH and temperature regulate condensation and resolubilization of C-rich oligonucleotides reversibly. A new class of DNA logic gates has been constructed based on the regulation of condensation/resolubilization of G-rich or C-rich oligonucleotides.