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. 1996 Apr 2;93(7):2635–2639. doi: 10.1073/pnas.93.7.2635

Spectroscopic recognition of guanine dimeric hairpin quadruplexes by a carbocyanine dye.

Q Chen 1, I D Kuntz 1, R H Shafer 1
PMCID: PMC39682  PMID: 8610093

Abstract

Isolated guanine quadruplex structures have been described at high resolution both in solution and in the solid state. The existence of this unusual DNA structure in vivo and its biological significance remain to be determined. We describe the binding of 3,3'-diethyloxadicarbocyanine to dimeric hairpin guanine quadruplexes. This interaction results in a set of unique spectrophotometric signatures, none of which arises from binding to single strands or Watson-Crick duplexes. These unique signatures include a new absorbance peak (lambda max = 534 nm), an induced circular dichroism (lambda = 534-626 nm), a quenching of the dye fluorescence upon excitation with visible light, and strong energy transfer from DNA. This last effect provides the basis for detecting hairpin quadruplex structures in the presence of excess amounts of nonquadruplex DNA structures, such as single strands and Watson-Crick duplexes. The mechanism of quadruplex recognition by this dye is discussed, along with the possibility of using this dye as a probe for hairpin quadruplex structures in vitro and in vivo.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.

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