Rational Design for Cooperative Recognition of Specific Nucleobases Using β‐Cyclodextrin‐Modified DNAs and Fluorescent Ligands on DNA and RNA Scaffolds

Abstract

We propose a binary fluorimetric method for DNA and RNA analysis by the combined use of two probes rationally designed to work cooperatively. One probe is an oligonucleotide (ODN) conjugate bearing a β-cyclodextrin (β-CyD). The other probe is a small reporter ligand, which comprises linked molecules of a nucleobase-specific heterocycle and an environment-sensitive fluorophore. The heterocycle of the reporter ligand recognizes a single nucleobase displayed in a gap on the target labeled with the conjugate and, at the same time, the fluorophore moiety forms a luminous inclusion complex with nearby β-CyD. Three reporter ligands, MNDS (naphthyridine-dansyl linked ligand), MNDB (naphthyridine-DBD), and DPDB (pyridine-DBD), were used for DNA and RNA probing with 3'-end or 5'-end modified β-CyD-ODN conjugates. For the DNA target, the β-CyD tethered to the 3'-end of the ODN facing into the gap interacted with the fluorophore sticking out into the major groove of the gap site (MNDS and DPDB). Meanwhile the β-CyD on the 5'-end of the ODN interacted with the fluorophore in the minor groove (MNDB and DPDB). The results obtained by this study could be a guideline for the design of binary DNA/RNA probe systems based on controlling the proximity of functional molecules.

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.…”

Catalytic Formation of Luminescent Complex Clusters Based on Autonomous Strand Exchange Reaction of DNA

“…The precise introduction of functional molecules into these scaffolds can provide unique DNA-based materials and interfaces such as luminescent molecular sensors, 1−5 conductive wires, 6−11 chiral selective catalysts, 12−15 and microenvironments for DNA-templated reactions. 16−19 For several years, we have been studying DNA-templated reactions such as metal complex formation, 20−22 photochemical reactions, 23−25 supramolecular inclusion complex formation, 26,27 and allosteric assembly of DNA conjugates. 28 In a series of studies, we found that luminescent lanthanide (Ln) complexes could be successfully formed by sequence-specific hybridization between a template and two DNA conjugates carrying ethylenediaminetetraacetic acid (EDTA) and 1,10phenanthroline (phen) as metal-capturing and sensitizer moieties, respectively.…”

“…For several years, we have been studying DNA-templated reactions such as metal complex formation, − photochemical reactions, − supramolecular inclusion complex formation, , and allosteric assembly of DNA conjugates . In a series of studies, we found that luminescent lanthanide (Ln) complexes could be successfully formed by sequence-specific hybridization between a template and two DNA conjugates carrying ethylenediaminetetraacetic acid (EDTA) and 1,10-phenanthroline (phen) as metal-capturing and sensitizer moieties, respectively.…”

Prototropically Allosteric Probe for Superbly Selective DNA Analysis

“…This strategy is intriguingly straightforward, but its implementation into practice usually requires case-dependent presynthesis of the incorporators and subsequent challenging modification of DNA. Another universal and attractive strategy is introduction of local structures into DNA, such as an abasic site (AP site), − a bulge site, ,, a gap site, , etc., which provide cavities ready for the exogenous probe binding. In these structures, only the target nucleotides are left unpaired to be recognized and the probe manipulation is more flexible since the covalent attachment of incorporators into DNA is unnecessarily required.…”

“…In these structures, only the target nucleotides are left unpaired to be recognized and the probe manipulation is more flexible since the covalent attachment of incorporators into DNA is unnecessarily required. Upon entering into these sites, the signal probes report the type of SNP with changes in, for example, dielectric-environment-dependent fluorescence, self-folding-sensitive emission, and some photophysical behaviors, including excited-state intramolecular proton transfer (ESIPT), photoinduced electron transfer (PET), etc. − …”