title: G-quadruplex formation in double strand DNA probed by NMM and CV fluorescence.
abstract: G-quadruplexes (GQs) are alternative DNA secondary structures that can form throughout the human genome and control the replication and transcription of important regulatory genes. Here, we established an ensemble fluorescence assay by employing two GQ-interacting compounds, N-methyl mesoporphyrin IX (NMM) and Crystal Violet (CV). This enables quantitative measurement of the GQ folding propensity and conformation specificity in both single strand (ss) and double strand (ds) DNA. Our GQ mapping indicates that the likelihood of GQ formation is substantially diminished in dsDNA, likely due to the competition from the Watson-Crick base pairing. Unlike GQ folding sequence in ssDNA which forms both parallel and antiparallel GQs, dsDNA displays only parallel folding. Additionally, we employed single molecule FRET to obtain a direct quantitation of stably formed-, weakly folded and unfolded GQ conformations. The findings of this study and the method developed here will enable identifying and classifying potential GQ-forming sequences in human genome.
authors.affiliation: Bioengineering Department, University of Illinois; 1304 W. Springfield Ave. Urbana, IL 61801, USA.
authors.forename: Alex
authors.initials: A
authors.lastname: Kreig
authors.affiliation: Bioengineering Department, University of Illinois; 1304 W. Springfield Ave. Urbana, IL 61801, USA.
authors.forename: Jacob
authors.initials: J
authors.lastname: Calvert
authors.affiliation: Bioengineering Department, University of Illinois; 1304 W. Springfield Ave. Urbana, IL 61801, USA.
authors.forename: Janet
authors.initials: J
authors.lastname: Sanoica
authors.affiliation: Bioengineering Department, University of Illinois; 1304 W. Springfield Ave. Urbana, IL 61801, USA.
authors.forename: Emily
authors.initials: E
authors.lastname: Cullum
authors.affiliation: Bioengineering Department, University of Illinois; 1304 W. Springfield Ave. Urbana, IL 61801, USA.
authors.forename: Ramreddy
authors.initials: R
authors.lastname: Tipanna
authors.affiliation: Bioengineering Department, University of Illinois; 1304 W. Springfield Ave. Urbana, IL 61801, USA Biophysics and Computational Biology; 1110 W. Green St. Urbana, IL 61801, USA Institute for Genomic Biology; 1206 Gregory Drive, Urbana, IL 61801, USA Physics Frontier Center (Center of Physics for Living Cells), University of Illinois; 1110 W. Green St. Urbana, IL 61801, USA smyong@illinois.edu.
authors.forename: Sua
authors.initials: S
authors.lastname: Myong
mesh_terms: D004247:DNA / Q000737:chemistry*; D004277:DNA, Single-Stranded / Q000737:chemistry; D005453:Fluorescence; D031541:Fluorescence Resonance Energy Transfer; D005456:Fluorescent Dyes; D054856:G-Quadruplexes; D005840:Gentian Violet; D008652:Mesoporphyrins
chemical_list: D004277:DNA, Single-Stranded; D005456:Fluorescent Dyes; D008652:Mesoporphyrins; C065420:N-methylmesoporphyrin IX; D004247:DNA; D005840:Gentian Violet