Cooperative DNA Probing Using a β-Cyclodextrin−DNA Conjugate and a Nucleobase-Specific Fluorescent Ligand

Abstract

A single nucleotide polymorphism (SNP) base on the target is displayed at a gap in a ternary duplex carrying beta-cyclodextrin-modified DNA. A stable tandem duplex forms regardless of the type of SNP base. A nucleobase-specific ligand is then added to this system. The dansyl moiety in the ligand is expected to form a luminous inclusion complex with nearby beta-CyD, only when the ligand recognizes the specific base displayed in the gap.

A label-free and sensitive fluorescent method for the detection of uracil-DNA glycosylase activity

“…1A). A dSpacer [28][29][30][31][32][33] (1 0 ,2 0 -dideoxyribose, an artificial non-base spacer in DNA, abbreviated as ''dSp'' and …”

“…1A). A dSpacer [28][29][30][31][32][33] (1 0 ,2 0 -dideoxyribose, an artificial non-base spacer in DNA, abbreviated as ''dSp'' and a Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and shown in the blue structure in Fig. 1A) binding fluorophore, named 2-amino-5,6,7-trimethyl-1,8-naphthyridine (ATMND), is allowed to bind the dSpacer opposite to a uracil site in the DNA duplex (DNA-U/DNA-X) through 3 complementary hydrogen bonds and p-p stacking.…”

Recent Progress in Abasic Site-binding Small Molecules for Detecting Single-base Mutations in DNA

“…The ratiometric signal was indeed effective, and the strategy would be sufficiently flexible for further design of this class of probes to detect all possible mutations. Also, since the naphthyridine (ATMND) moiety can bind to the other non-Watson-Crick base pairing sites in the DNA duplex as demonstrated in our previous work, [63][64][65][66][67][68][69][70][71][72] ATMND-DBD would have a potential for further applications such as gap site binding in a binary fluorometric method, 63,64 detecting mismatches in trinucleotide repeats, 65 and affinity-labeling in aptamer assays or molecular beacons.…”

Zn2+-cyclen-based complex enable a selective detection of single-stranded thymine-rich DNA in aqueous buffer

“…It is of important significance to develop fluorescent probes for detecting nucleic acids with specific sequences because the sequence of nucleotides represents the genetic information that relates to physiological functions in living organisms (Szalay and Golovchenko, 2015;Mamanova et al, 2010;Doré et al, 2004;Ihara et al, 2009;Granzhan et al, 2014). Most nucleic acid probes show poor selectivity for DNA with different sequences since they mainly recognize nucleic acids by intercalation (Dragan et al, 2009;Chiang et al, 2008;Friedman et al, 1990), groove binding (Zhu et al, 2011a(Zhu et al, , 2011b, electrostatic interaction (Tong et al, 2006;Hong et al, 2008Hong et al, , 2010, hydrogen bond (Xu et al, 2014a(Xu et al, , 2014b or coordination interactions (Zhu et al, 2014(Zhu et al, , 2016Wang, 2015;Hu, 2015).…”