Book of Abstracts: Albany 2007
June 19-23 2007
Probing the Structural and Binding Interactions of Quadruplex DNAs with Hydroxyl radical footprinting
The ends of the linear eukaryotic chromosomes, the telomeres, are made up of repeats of a dG rich DNA sequence and the d(GGGTTA) is found in vertebrates. Telomere DNA can form quadruplex structures. Formation of these structures under physiological conditions may play a biologically significant role especially in cancer and aging. Hence, these structures are of high interest.
Quadruplex structures have been studied in vitro by many of the structural biology tools including NMR, X-ray crystallography and circular dichroism. Although some of these methods provide atomic resolution information their applications are limited by obtaining a diffractable crystal or the presence of a essentially only one structural form. Hence, alternative methods that do not have these limitations are needed. Hydroxyl radical footprinting is one such method which has the capability of providing structural information at single nucleotide resolution both in vitro as well as in vivo. Also, this method has an added advantage of being applicable to smaller amounts of DNA than methods such as NMR or crystallography.
The characteristic hydroxyl radical footprinting patterns of quadruplex DNAs of known structure can be obtained and this information used as a reference to obtain information about the structures of human telomeric repeat DNAs. The reactivity of DNA to hydroxyl radical is directly related to the solvent accessibility of the deoxyribose of the DNA. Solvent accessibilities of the DNA can be calculated from the structures and the predicted cleavage patterns compared to the observed OH radical footprinting pattern. This method will also be used to obtain structural details of binding interactions of quadruplex DNAs with small molecules and proteins both in vitro and in vivo.