Journal
ANALYTICAL CHEMISTRY
Volume 81, Issue 7, Pages 2678-2684Publisher
AMER CHEMICAL SOC
DOI: 10.1021/ac802558f
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Funding
- National Natural Science Foundation of China [20675041]
- National Basic Research Program of China [2006CB705700]
- National Natural Science Foundation of Tianjin [08JCZDJC21200]
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G-rich sequences with the potential for quadruplex formation are common in genomic DNA. Considering that the biological functions of G-quadruplexes may well depend on their structures, the development of a sensitive structural probe for distinguishing different types of quadruplexes has received great attention. Crystal violet (CV) is a triphenylmethane dye, which can stack onto the two external G-quartets of a G-quadruplex. The ability of CV to discriminate G-quadruplexes from duplex and single-stranded DNAs has been reported by us. Herein, the ability of CV to discriminate parallel from antiparallel structures of a G-quadruplex was studied. The binding of CV to an antiparallel G-quadruplex can make its fluorescence intensity increase to a high level because of the protection of bound CV from the solvent by quadruplex end loops. The presence of side loops in parallel G-quadruplexes cannot provide bound CV such protection, causing the fluorescence intensity of CV/G-quadruplex mixture to be obviously weaker when the G-quadruplex adopts a parallel structure than that when the G-quadruplex adopts an antiparallel structure. Therefore, CV can be developed as a sensitive fluorescent biosensor for the discrimination of antiparallel G-quadruplexes from parallel G-quadruplexes and for monitoring the structural interconversion of G-quadruplexes. In addition, considering that some G-rich DNA sequences can adopt different G-quadruplex structures under Na+ or K+ ion conditions, a novel, cheap and simple K+ ion detection method was developed. This method displays a high K+ ion selectivity against Na+ ion, the change of 200 mM in Na+ ion concentration only causes a similar fluorescent signal change to 0.3 mM K+ ion.
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