Spectroscopic comparison of different DNA structures formed by oligonucleotides

Six different nucleic acid structures including duplex, tripler and quadrup lex are formed by oligonucleotides. Their structural properties are studied in detail by four spectroscopic techniques, i.e. CD, UV, NMR and fluoresce nce. Results are: CD Spectra: The common characteristics is a negative band at 240 nm, and the spectra are different from each other in the range 260- 300 nm. Many factors such as chain direction, sugar puckering, orientation of the glycosyl bond, base stacking and sequence can effect their conformat ion and then show diversity and complexity in the spectra. UV Spectra: The UV spectra of all forms are quite similar, all of them exhibit a sharp posi tive peak around 210 nm and a broad positive band in the region of 240-280 nm. Although the bands are different in absorbance, the spectra are not cha racteristic enough to distinguish these forms. In addition, their thermal d enaturation is also observed by UV spectrum, different melting curves and p oints are shown and some thermodynamic information is provided. NMR Spectra : Since the G residues in the six samples all participate in hydrogen bond, the imino proton can not exchange with the solvent freely so as to allow a n observable resonance to arise. The resonance number and chemical shift wi ll vary with the change in base-pairing number and mode as well as the whol e geometry of its molecule. Fluorescence Spectra: The interaction mechanism s between EB and these structures are different. B type duplex and tripler adopt an intercalative mode in which the efficiency of energy transfer is r elatively high and the fluorescence of EB can not be quenched easily. While for the parallel duplex, outside binding is predominant in which energy tr ansfer can hardly happen and most of its fluorescence can be quenched. As f or the quadruplex, groove binding is possible, so the efficiency of energy transfer is higher than that in outside binding, but lower than that in int ercalative binding, and fluorescence is quenched partly.