Rational design for cooperative recognition of specific nucleobases using ß-cyclodextrin-modified DNAs and fluorescent ligands on DNA and RNA scaffolds.

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 ß-cyclodextrin (ß-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 ß-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 ß-CyD-ODN conjugates. For the DNA target, the ß-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 ß-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.

Cooperative DNA probing using a beta-cyclodextrin-DNA conjugate and a nucleobase-specific fluorescent ligand.

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.

DNA analysis based on toehold-mediated strand displacement on graphene oxide.

Fluorescent dye-labeled probe DNA was immobilized on fluorescence-quenching graphene oxide (GO) through a capture DNA. When targets were added, the probes were released from the GO through toehold-mediated strand exchange. Higher emission recovery and more signal contrast were achieved relative to conventional methods that are based on direct adsorption of probes.

Electrochemical signal modulation in homogeneous solutions using the formation of an inclusion complex between ferrocene and ß-cyclodextrin on a DNA scaffold.

Two DNA conjugates modified with ferrocene and ß-cyclodextrin were prepared as a pair of probes that work cooperatively for DNA sensing, in which the electrochemical signal of ferrocene on one probe was significantly "quenched" by the formation of an inclusion complex with ß-cyclodextrin of the other probe on the DNA templates.