G-quadruplex formation in double strand DNA probed by NMM and CV fluorescence

Alex Kreig, Jacob Calvert, Janet Sanoica, Emily Cullum, Ramreddy Tipanna, Sua Myong

Research output: Contribution to journalArticlepeer-review


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) andCrystal 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.

Original languageEnglish (US)
Pages (from-to)7961-7970
Number of pages10
JournalNucleic acids research
Issue number16
StatePublished - Jul 11 2015
Externally publishedYes

ASJC Scopus subject areas

  • Genetics


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