Fluorescent dyes specific for quadruplex DNA

Arthanari, Haribabu; Basu, Swarna; Kawano, Thomas L.; Bolton, Philip H.

doi:10.1093/nar/26.16.3724

Cited by 293 publications

(228 citation statements)

References 46 publications

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“…To gain further insight as to whether Lin28 RNAs contain G4s, we made use of NMM, a dye that binds selectively to G4s (52)(53)(54)(55). When it binds to G4s, NMM is excited at 399 nm and fluoresces at 614 nm (55).…”

Section: Lin28-regulated Gene Sequences Are Enriched For G-quartetmentioning

confidence: 99%

An RNA-binding Protein, Lin28, Recognizes and Remodels G-quartets in the MicroRNAs (miRNAs) and mRNAs It Regulates

O’Day

Imai

et al. 2015

Journal of Biological Chemistry

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Background: Lin28 is an evolutionary conserved RNA-binding protein that regulates miRNAs and mRNAs; Lin28 overexpression is linked to poor prognosis in cancer. Results: Lin28 binds to guanine-rich miRNAs and mRNAs that contain G-quartet structural features and remodels these structures. Conclusion: Lin28 recognition of G-quartets is a unifying feature of Lin28-regulated RNAs. Significance: Small molecules that bind to G-quartets might be useful inhibitors of Lin28 function.

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Section: Lin28-regulated Gene Sequences Are Enriched For G-quartetmentioning

confidence: 99%

An RNA-binding Protein, Lin28, Recognizes and Remodels G-quartets in the MicroRNAs (miRNAs) and mRNAs It Regulates

O’Day

Imai

et al. 2015

Journal of Biological Chemistry

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“…TMPy has more direct antitumor activity, possibly as a consequence of its ability to inhibit the telomerase enzyme (7). Binding to quadruplex DNA as well as to duplexes has been reported for TMPy and various complexes (8)(9)(10). Stabilization of G-quadruplex structures has been shown to be the mechanism whereby TMPy inhibits telomerase from catalyzing the synthesis of further linear telomere repeats.…”

mentioning

confidence: 99%

“…Stabilization of G-quadruplex structures has been shown to be the mechanism whereby TMPy inhibits telomerase from catalyzing the synthesis of further linear telomere repeats. NMR and photocleavage data have been interpreted in favor of a model with a TMPy molecule externally stacking onto guaninequadruplex structures (8)(9)(10).…”

mentioning

confidence: 99%

A DNA–porphyrin minor-groove complex at atomic resolution: The structural consequences of porphyrin ruffling

Bennett

Krah

Wien

et al. 2000

Proc. Natl. Acad. Sci. U.S.A.

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The crystal structure of a B-type DNA hexanucleotide duplex complexed with the porphyrin molecule nickel-[tetra-N-methylpyridyl] porphyrin has been solved by multiwavelength anomalous diffraction phasing and refined to an R factor of 11.5% at a resolution of 0.9 Å. The structure has been solved and refined as two crystallographically independent duplexes, stacked end to end. Contrary to expectation, the porphyrin molecule is not intercalated into the duplex but is stacked onto the ends of the two-duplex stack. The porphyrin molecule is highly buckled as a consequence of the nickel coordination, which produces large changes in local DNA structure. A second mode of porphyrin binding is apparent as a consequence of crystal packing, which places the ligand in the minor groove of an adjacent duplex. This structure thus provides, to our knowledge, the first atomic visualization of minor-groove binding for a porphyrin molecule. The geometry of groove binding provides a ready explanation for porphyrin-induced DNA strand cleavage at deoxyribose residues.DNA structure ͉ minor groove binding ͉ end capping T he interactions of cationic porphyrins with nucleic acids have received considerable attention (1, 2). Several have clinical potential as anticancer agents in photodynamic therapy (3, 4), probably as a consequence of their ability to selectively accumulate on the surface of tumor cells, become internalized, bind to genomic DNA, and then induce DNA strand cleavage. One such compound is tetra-(N-methylpyridyl) porphyrin (TMPy: Fig. 1a), which can be coordinated with a range of transition metals (1, 2, 5, 6). TMPy has more direct antitumor activity, possibly as a consequence of its ability to inhibit the telomerase enzyme (7). Binding to quadruplex DNA as well as to duplexes has been reported for TMPy and various complexes (8-10). Stabilization of G-quadruplex structures has been shown to be the mechanism whereby TMPy inhibits telomerase from catalyzing the synthesis of further linear telomere repeats. NMR and photocleavage data have been interpreted in favor of a model with a TMPy molecule externally stacking onto guaninequadruplex structures (8-10).Noncovalent interactions of TMPy and its metal complexes with duplex DNA are sequence dependent (2, 11), with intercalation occurring at 5Ј-CpG sites, as shown by NMR and other biophysical studies (12, 13) as well as molecular modeling (13,14). A crystallographic analysis (15) of the Cu 2ϩ complex of TMPy bound to the sequence 5Ј-d(CGTACG) 2 also found the ligand intercalated at this site, but with the 5Ј-end cytosine swung out in an extrahelical arrangement. By contrast, biophysical and modeling (14, 16) studies have suggested that TMPy itself (and many of its metal complexes) bind in the minor groove at A͞T sequences and perturb the double helix only to a minimal extent at such sites (16). No structural data has been reported to date on groove-binding modes. TMPy itself is a planar molecule (14, 15), and it has been assumed that the groove binding would therefore be analogou...

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Section: Some Known G-quadruplex Ligands and Their Activitiesmentioning

confidence: 99%

“…[103,104] Changes in the fluorescence properties of NMM can be used to detect G-quadruplex DNA in vitro. [103] Recently, NMM was found to up-regulate genes having promoters with a high potential for G-quadruplex formation, and it also suppressed rDNA activity in yeast. [38] The binding of rDNA (known to have a high potential for G-quadruplex formation) and the subsequent suppression of ribosome biogenesis is the reported mode of action of CX-3543 (quarfloxin), a small molecule drug candidate currently in phase II clinical trials.…”

Section: Some Known G-quadruplex Ligands and Their Activitiesmentioning

confidence: 99%

Targeting G-Quadruplex DNA with Small Molecules

Luedtke¹

2009

Chimia

101

105

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Despite a recent explosion of interest in G-quadruplex DNA, most fundamental questions regarding the possible presence and function of these intriguing structures in vivo remain unanswered. Cell-permeable G-quadruplex specific probes should provide researchers with new tools for studying these alternately folded DNA structures and their potential involvement in gene expression, chromosome stability, viral integration, and recombination. In this review, a survey of the binding affinity, specificity, and biological/pharmacological activities of some well-characterized G-quadruplex ligands is presented along with the potential importance of G-quadruplex DNA in vivo.134 CHIMIA 2009, 63, No. 3 Young AcAdemics in switzerlAnd PArt ii doi:10.2533doi:10. /chimia.2009doi:10. .134 Chimia 63 (2009 Despite a recent explosion of interest in G-quadruplex DNA, most fundamental questions regarding the possible presence and function of these intriguing structures in vivo remain unanswered. Cell-permeable Gquadruplex specific probes should provide researchers with new tools for studying these alternately folded DNA structures and their potential involvement in gene expression, chromosome stability, viral integration, and recombination. In this review, a survey of the binding affinity, specificity, and biological/pharmacological activities of some well-characterized G-quadruplex ligands is presented along with the potential importance of G-quadruplex DNA in vivo.

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Fluorescent dyes specific for quadruplex DNA

Cited by 293 publications

References 46 publications

An RNA-binding Protein, Lin28, Recognizes and Remodels G-quartets in the MicroRNAs (miRNAs) and mRNAs It Regulates

An RNA-binding Protein, Lin28, Recognizes and Remodels G-quartets in the MicroRNAs (miRNAs) and mRNAs It Regulates

A DNA–porphyrin minor-groove complex at atomic resolution: The structural consequences of porphyrin ruffling

Targeting G-Quadruplex DNA with Small Molecules

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