title: DNA-based biosensor for monitoring pH in vitro and in living cells.
abstract: DNA is a promising material for the construction of a biosensor or bioindicator because its structure is sensitive to the binding of cofactors. In the current studies, we found that a combination of two DNA oligonucleotides, 5'-TCTTTCTCTTCT-3' and 5'-AGAAAGAGAAGA-3', exhibit a novel structural transition from a Watson-Crick antiparallel duplex to a parallel Hoogsteen duplex as the pH changes from pH 7.0 to 5.0. By labeling this DNA for fluorescence resonance energy transfer, we were able to develop a sensitive pH indicator that can detect changes between pH 7.0 and 5.0. Moreover, using DNA-based hairpin parallel-stranded duplex in conjunction with fluorescence microscopy, we were able to observe the pH changes in living cells during apoptosis as an easily detected change in color. These results indicate that the DNA-based pH indicator should be useful for detecting pH changes between pH 7.0 and 5.0 in living cells.
authors.affiliation: Frontier Institute for Biomolecular Engineering Research, Konan University, 8-9-1 Okamoto, Higashinada-ku, Kobe 658-8501, Japan.
authors.forename: Tatsuo
authors.initials: T
authors.lastname: Ohmichi
authors.forename: Yasunori
authors.initials: Y
authors.lastname: Kawamoto
authors.forename: Peng
authors.initials: P
authors.lastname: Wu
authors.forename: Daisuke
authors.initials: D
authors.lastname: Miyoshi
authors.forename: Hisae
authors.initials: H
authors.lastname: Karimata
authors.forename: Naoki
authors.initials: N
authors.lastname: Sugimoto
mesh_terms: D020029:Base Pairing; D015374:Biosensing Techniques / Q000379:methods*; D045744:Cell Line, Tumor; D002942:Circular Dichroism; D004247:DNA / Q000737:chemistry* / Q000378:metabolism*; D031541:Fluorescence Resonance Energy Transfer / Q000379:methods; D006801:Humans; D006863:Hydrogen-Ion Concentration; D007202:Indicators and Reagents / Q000737:chemistry / Q000378:metabolism; D007424:Intracellular Fluid / Q000737:chemistry / Q000378:metabolism; D009690:Nucleic Acid Conformation; D009692:Nucleic Acid Heteroduplexes / Q000737:chemistry* / Q000378:metabolism*; D013056:Spectrophotometry, Ultraviolet; D014162:Transfection / Q000379:methods
chemical_list: D007202:Indicators and Reagents; D009692:Nucleic Acid Heteroduplexes; C051802:triplex DNA; D004247:DNA