Steady-State and Time-Resolved Studies into the Origin of the Intrinsic Fluorescence of G‑Quadruplexes

• Published in: The journal of physical chemistry. B 2016-06, Vol.120 (23), p.5146-5158
• Main Authors: Sherlock, Madeline E, Rumble, Christopher A, Kwok, Chun Kit, Breffke, Jens, Maroncelli, Mark, Bevilacqua, Philip C
• Format: Article
• Language: English
• Subjects: Base Sequence; Circular Dichroism; Fluorescent Dyes - chemistry; G-Quadruplexes; Oligonucleotides - chemical synthesis; Oligonucleotides - chemistry; Quantum Theory; Spectrometry, Fluorescence; Temperature
• ISSN: 1520-6106; 1520-5207
• DOI: 10.1021/acs.jpcb.6b03790

Stretches of guanines in DNA and RNA can fold into guanine quadruplex structures (GQSs). These structures protect telomeres in DNA and regulate gene expression in RNA. GQSs have an intrinsic fluorescence that is sensitive to different parameters, including loop sequence and length. However, the dependence of GQS fluorescence on solution and sequence parameters and the origin of this fluorescence are poorly understood. Herein we examine effects of dangling nucleotides and cosolute conditions on GQS fluorescence using both steady-state and time-resolved fluorescence spectroscopy. The quantum yield of dGGGT­GGGT­GGGT­GGG, termed “dG3T”, is found to be modest at ∼2 × 10–3. Nevertheless, dG3T and its variants are significantly brighter than the common nucleic acid fluorophore 2-aminopurine (2AP) largely due to their sizable extinction coefficients. Dangling 5′-end nucleotides generally reduce emission and blue-shift the resultant spectrum, whereas dangling 3′-end nucleotides slightly enhance fluorescence, particularly on the red side of the emission band. Time-resolved fluorescence decays are broadly distributed in time and require three exponential components for accurate fits. Time-resolved emission spectra suggest the presence of two emitting populations centered at ∼330 and ∼390 nm, with the redder component being a well-defined long-lived (∼1 ns) entity. Insights into GQS fluorescence obtained here should be useful in designing brighter intrinsic RNA and DNA quadruplexes for use in label-free biotechnological applications.