Abstract 1999 Investigations of G-Triplex DNA formation by Surface Plasmon Resonance

The G-quadruplex (G4) is a four-stranded secondary DNA structure that can form from guanine-rich DNA, such as telomeric DNA, that is stabilized by a variety of physiologically relevant cations. The intramolecular folding process of telomeric G4 DNA from single-stranded DNA proceeds through an intermediate structure, a three-stranded G-triplex (G3) DNA. In certain cases, truncated telomeric and other G4 DNA forming sequences have been shown to fold into stable G3 structures, but the generality of this phenomenon is not well established. Due to the propensity of truncated G4 sequences to form multimolecular species in solution instead of intramolecularly folded structures, we have sought to develop a new method for studying G3 structures under conditions that preclude competing intermolecular G4 structure formation. The objective of this study is to employ surface plasmon resonance (SPR) techniques to characterize the formation of G-triplex DNA structures. We have identified a specific truncated form of the G4 DNA forming sequence in the c-MYC promoter that adopts a stable G3 structure. We performed SPR on this and a control, single-stranded DNA oligonucleotide using single-stranded DNA binding proteins and hemin to probe for folding under a variety of ion conditions. We find that single-stranded DNA binding proteins do not interact with the folded G-triplex formed by the truncated c-MYC sequence; whereas, the G4 DNA ligand hemin selectively binds to the G3 structure and not single-stranded DNA. These studies indicate that the c-MYC G4 may fold through a G3 intermediate that can be stabilized by potassium, calcium, or lithium cations. Furthermore, they provide a framework for G-triplex investigation in which intramolecular structure formation is ensured. This work was supported in part by NSF grant CHE-1955432, the Partnership for Research and Education in Materials (PREM) NSF Grant DMR-212204, and the South Texas Doctoral Bridge Program funded by the NIH through the R25 Bridges to the Doctorate Program (GM102783).