N‐methylmesoporphyrin IX fluorescence as a reporter of strand orientation in guanine quadruplexes

Abstract

Guanine quadruplexes (GQ) are four‐stranded DNA structures formed by guanine‐rich DNA sequences. The formation of GQs inhibits cancer cell growth, although the detection of GQs in vivo has proven difficult, in part because of their structural diversity. The development of GQ‐selective fluorescent reporters would enhance our ability to quantify the number and location of GQs, ultimately advancing biological studies of quadruplex relevance and function. N‐methylmesoporphyrin IX (NMM) interacts selectively with parallel‐stranded GQs; in addition, its fluorescence is sensitive to the presence of DNA, making this ligand a possible candidate for a quadruplex probe. In the present study, we investigated the effect of DNA secondary structure on NMM fluorescence. We found that NMM fluorescence increases by about 60‐fold in the presence of parallel‐stranded GQs and by about 40‐fold in the presence of hybrid GQs. Antiparallel GQs lead to lower than 10‐fold increases in NMM fluorescence. Single‐stranded DNA, duplex, or i‐motif, induce no change in NMM fluorescence. We conclude that NMM shows promise as a ‘turn‐on’ fluorescent probe for detecting quadruplex structures, as well as for differentiating them on the basis of strand orientation.

DNA Triplexes‐Guided Assembly of G‐Quadruplexes for Constructing Label‐free Fluorescent Logic Gates

“…The sequences of S2 M1 and S2 M2 are 5′‐GGGACGGG‐3’ and 5′‐GTGGAGGG‐3′, respectively. As shown in Figure S2 (Supporting Information), the NMM fluorescence was weakly sensitive to pH over a range from 5.2 to 8.0, which is in line with the previous results . When NMM was incubated with S2 M1 and S2 M2, the NMM fluorescence increased slightly and remained insensitive to pH changes in the absence of K + .…”

G-Quadruplexes Act as Sequence Dependent Chaperones via Protein Oligomerization

“…2A) (18), and distinct from a control sequence (sequence 42) that had poor chaperone activity and no polyG motif. This supposition was further supported by examining the emission spectra of Nmethylmesoporphyrin IX (NMM), a well characterized parallel quadruplex binding fluorophore (19,20). The NMM spectra indicated that all three sequences formed parallel quadruplexes at the concentration used in aggregation assays, unlike the ssDNA control ( Fig.…”

“…N-methylmesoporphyrin IX (NMM) Fluorescence NMM is a well characterized fluorophore that increases fluorescence when bound to parallel quadruplexes (19). The emission spectra of 10 μM NMM was measured using an excitation wave length of 399 nm, and an emission range of 550 to 750 nm in the presence of 1 μM DNA.…”

Label-free detection of microRNA based on coupling multiple isothermal amplification techniques

“…S4. NMM is an anionic porphyrin with a good structural selectivity for G-quadraplex313233. It has weak fluorescence signal by itself, but exhibits a dramatic fluorescence enhancement after binding to G-quadruplex.…”