ABSTRACT
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.
Subject(s)
Chemistry Techniques, Analytical/methods , DNA/chemistry , Fluorescent Dyes/chemistry , Graphite/chemistry , Immobilized Nucleic Acids/chemistry , Base Sequence , Biophysical Phenomena , Biosensing TechniquesABSTRACT
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.
Subject(s)
Biosensing Techniques , DNA/analysis , Fluorescent Dyes/chemistry , Oligonucleotides/chemistry , RNA/analysis , beta-Cyclodextrins/chemistry , Base Sequence , Drug Design , Ligands , Nucleic Acid Hybridization , Transition TemperatureABSTRACT
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.
Subject(s)
Ferrous Compounds/chemistry , Oligodeoxyribonucleotides/chemistry , beta-Cyclodextrins/chemistry , Electrochemical Techniques , Metallocenes , Oxidation-Reduction , Transition TemperatureABSTRACT
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.
