Journal
NUCLEIC ACIDS RESEARCH
Volume 43, Issue 16, Pages 7961-7970Publisher
OXFORD UNIV PRESS
DOI: 10.1093/nar/gkv749
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Funding
- NIH Director's New Innovator Award [343 NIH 1 DP2 GM105453 A]
- American Cancer Society [Research Scholar Grant] [RSG-12-066-01-DMC]
- Human Frontier Science Program [RGP0007/2012]
- U.S. National Science Foundation Physics Frontiers Center Program [0822613]
- Division Of Physics
- Direct For Mathematical & Physical Scien [0822613] Funding Source: National Science Foundation
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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.
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