G-Quadruplex DNA Folding and Dynamics within Duplex DNA

Abstract

The helix is the classical view of genomic DNA structure. Recent findings suggest that alternate folding motifs can play an important role in gene expression. One example is the G-Quadruplex, a single stranded DNA sequence composed of four repeat sequences of two or more G's each separated by varying spacer sequences. This structure has been suggested to affect the expression of several important genes in cancer development (c-MYC, c-KIT, VEGF)[1].Recently, immune assay based experiments have shown that G-Quadruplexes are stably found throughout the genome [2]. The dynamic properties underlying the interaction between the G-Quadruplex and its single stranded DNA complement have yet to be characterized. Preliminary studies suggest that these structures are capable of forming in response to specific cellular actions and are persistent in a biologically relevant time scale.To determine sequence dependent properties of G-Quadruplexes, we utilized a combination of Single Molecule FRET microscopy and small molecule binding fluorescence assays. We investigated biophysical properties such as stability, folding patterns, and structure persistence. These properties will help elucidate the biological roles of specific genomic quadruplexes. This knowledge will aid in interpreting the roles of the many G-Quadruplex associated proteins and may assist in the development of the next generation of chemotherapeutic agents.[1]. Patel, D et al. (2007) Nucleic Acids Research UK 35(22):7429-7455.[2]. Lam, EYN et al. (2013) Nature Communications USA 4:1796.