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

• Published in: Chemistry : a European journal Vol. 19; no. 32; pp. 10526 - 10535
• Main Authors: Futamura, Akika, Uemura, Asuka, Imoto, Takeshi, Kitamura, Yusuke, Matsuura, Hirotaka, Wang, Chun-Xia, Ichihashi, Toshiki, Sato, Yusuke, Teramae, Norio, Nishizawa, Seiichi, Ihara, Toshihiro
• Format: Journal Article
• Language: English
• Published: Weinheim WILEY-VCH Verlag 05.08.2013; WILEY‐VCH Verlag
• Subjects: Base Sequence; beta-Cyclodextrins - chemistry; Biosensing Techniques; biosensors; cyclodextrin; DNA - analysis; DNA recognition; Drug Design; fluorescence; Fluorescent Dyes - chemistry; host-guest systems; Ligands; Nucleic Acid Hybridization; Oligonucleotides - chemistry; RNA - analysis; Transition Temperature; DNA recognition; biosensors; host-guest systems; fluorescence; cyclodextrin
• ISSN: 0947-6539; 1521-3765
• DOI: 10.1002/chem.201300985

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. All lit up: A nucleobase‐specific recognition system has been constructed by combining DNA/RNA‐binding fluorescent reporter ligands and oligonucleotide conjugates bearing β‐cyclodextrin (see scheme). The two molecules work cooperatively to recognize and signal the presence of specific nucleobases.