Synthesis and properties of novel oligonucleotide conjugates

Stilbene diether (SE) linkers can form the most stable DNA hairpins to date. SE diols form edge-to-face H-aggregate in aqueous solution. The crystal structure of a SE-bridged hairpin confirms that it adopts a B-form structure in which SE is pi-stacked with the adjacent base pair. The "pinwheel" structure of four SEs in an unsymmetric unit is the first observation of an isolated "pinwheel" structure and is consistent with aggregate formation by SE diols in aqueous solution. SE can serve as a source of electrons for photoinjection into DNA, and may function as a hole trap in studies of electron transport in DNA.;The driving force dependence of photoinduced electron transfer dynamics in duplex DNA has been investigated for sixteen synthetic DNA hairpins in which an acceptor chromophore serves as a linker connecting two complementary oligonucleotide arms containing a single donor nucleobase located either adjacent to the linker or separated from the linker by two unreactive base pairs. The dynamics of charge separation and charge recombination have been determined by means of sub-picosecond time-resolved transient absorption spectroscopy and the results were analyzed using quantum mechanical Marcus theory. This analysis provides intimate details about electron transfer processes in DNA including the distance dependence of the electronic coupling between the acceptor and nucleobase donor and the solvent and nuclear reorganization energies.;SE and stilbene dicarboxyamide (SA) linked intramolecular parallel triplex systems have been prepared. An exciton coupled CD band has been observed in the CD spectra of these DNA triplex conjugates. The intramolecular triple helical structure provides a new way to control the distance and dihedral angle of two chromophores, and useful information for investigating the exciton coupled effect in other helical structures. The distance dependence of electron transfer, the value of beta (0.4 A -1), in T:AT triplex conjugates is smaller than the beta value in hairpin systems (0.7 A-1). Overall, the T:AT triplex provides a better electron transfer medium than the B-form duplex, but they are still not molecular wires.;Thermal dissociation kinetics of SE linked G-quadruplexes have been investigated. A dissociation mechanism has been proposed based on temperature dependent UV ad CD spectra. Both the length of the linker and sequence component have big effects on the stability of G-quadruplexes.