The goal of this project is to attain detailed mechanistic, structural and functional information on protein and G-Quadruplex (GQ) interactions at the single molecule level on three systems. Genome-wide computational studies have identified ~300,000 potentially GQ forming sequences (PQS) in the human genome. PQS are concentrated in telomeres and promoter sites of certain oncogenes. In addition to the well-known connection between telomeres and cancer, the concentration of PQS in promoter sites suggests a potential role in transcription level gene expression regulation. GQs were recently visualized in human cells at both telomeric and non-telomeric sites. Mutations in proteins that destabilize GQs resulted in DNA breaks, slowing of replication machinery, and genomic instability. Therefore, a better understanding of GQ-protein interactions is of critical importance We propose to study the following three systems to achieve this goal: 1) Understanding the function of GQ in telomere protection and elongation: Binding of RPA to single-stranded telomeric DNA (ssTEL) is a potential source of genomic instability as it activates ATR checkpoint. POT1/TPP1, a component of shelterin, is involved in protection of ssTEL against this pathway. However POT1/TPP1's lower concentration and lower affinity to ssTEL compared to RPA suggest the involvement of other factors in preventing RPA's access to ssTEL. On the other hand, RPA binding to ssTEL is required during telomere elongation by telomerase, as it likely removes GQ type secondary structures. How the cell manages to transition between these different modes remains unclear. We hypothesize that synergistic activity of POT1/TPP1 and GQ enhances protection of ssTEL against RPA while the dynamic nature of GQ folding/unfolding facilitates the transition to telomere elongation mode. Finally, we propose to study the influence of hnRNPA, TERRA, GQ-GQ interactions, GQ stabilizing drugs on this competition. 2) Understanding the structural and functional implications of GQ destabilization due to protein binding in its vicinity. We observed Bloom (BLM)-mediated telomeric GQ unfolding in the absence of ATP. The efficiency of this activity correlates with the binding stability of BLM to the overhang ssDNA in the vicinity of GQ. We hypothesize that binding of proteins in the vicinity of GQs significantly reduces GQ stability, facilitating efficient removal f these structures in cellular context. Such a mechanism would provide a new perspective on removal of GQs in cellular context. We will study the generality of this observation with other RecQ family helicases and establish the factors that influence it. 3) Unfolding of non-telomeric GQs by RPA: RPA, the major ssDNA binding protein in eukaryotes, is highly efficient at destabilizing GQs. We hypothesize that ssDNA binding affinity and structural arrangement of RPA's DNA binding domains (DBD) determine its efficiency in unfolding different GQs. We propose to perform systematic studies on a broad class of GQs to establish guidelines for their physiological viability.

Public Health Relevance

Elevated telomerase activity is a common feature of cancer cells while G-quadruplex (GQ) formation is known to slow down this activity. In addition, GQ formation in promoter sites of certain genes, particularly oncogenes, is known to regulate transcription level gene expression. These observations combined with the unique layered structure of GQ have recently motivated studies to develop specific drugs that target GQ to regulate telomerase activity or gene expression, which makes the proposed studies very significant in terms of their potential impact on public health.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Academic Research Enhancement Awards (AREA) (R15)
Project #
Application #
Study Section
Macromolecular Structure and Function B Study Section (MSFB)
Program Officer
Preusch, Peter
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
Kent State University at Kent
Schools of Arts and Sciences
United States
Zip Code
Mustafa, Golam; Chuang, Cho-Ying; Roy, William A et al. (2018) A force sensor that converts fluorescence signal into force measurement utilizing short looped DNA. Biosens Bioelectron 121:34-40
Maleki, Parastoo; Budhathoki, Jagat B; Roy, William A et al. (2017) A practical guide to studying G-quadruplex structures using single-molecule FRET. Mol Genet Genomics 292:483-498
Maleki, Parastoo; Ma, Yue; Iida, Keisuke et al. (2017) A single molecule study of a fluorescently labeled telomestatin derivative and G-quadruplex interactions. Nucleic Acids Res 45:288-295
Budhathoki, Jagat B; Maleki, Parastoo; Roy, William A et al. (2016) A Comparative Study of G-Quadruplex Unfolding and DNA Reeling Activities of Human RECQ5 Helicase. Biophys J 110:2585-96
Budhathoki, Jagat B; Stafford, Edward J; Yodh, Jaya G et al. (2015) ATP-dependent G-quadruplex unfolding by Bloom helicase exhibits low processivity. Nucleic Acids Res 43:5961-70
Budhathoki, Jagat B; Ray, Sujay; Urban, Vaclav et al. (2014) RecQ-core of BLM unfolds telomeric G-quadruplex in the absence of ATP. Nucleic Acids Res 42:11528-45