Design of two and three input molecular logic gates using non-Watson-Crick base pairing-based molecular beacons.
This study presents a single, resettable, and sensitive molecular beacon (MB) used to operate molecular-scale logic gates. The MB consists of a random DNA sequence, a fluorophore at the 5'-end, and a quencher at the 3'-end. The presence of Hg(2+), Ag(+), and coralyne promoted the formation of stable T-Hg(2+)-T, C-Ag(+)-C, and A2-coralyne-A2 coordination in the MB probe, respectively, thereby driving its conformational change. The metal ion or small molecule-mediated coordination of mismatched DNA brought the fluorophore and the quencher into close proximity, resulting in collisional quenching of fluorescence between the two organic dyes. Because thiol can bind Hg(2+) and remove it from the T-Hg(2+)-T-based MB, adding thiol to a solution of the T-Hg(2+)-T-based MB allowed the fluorophore and the quencher to be widely separated. A similar phenomenon was observed when replacing Hg(2+) with Ag(+). Because Ag(+) strongly binds to iodide, cyanide, and cysteine, they were capable of removing Ag(+) from the C-Ag(+)-C-based MB, restoring the fluorescence of the MB. Moreover, the fluorescence of the A2-coralyne-A2-based MB could be switched on by adding polyadenosine. Using these analytes as inputs and the MB as a signal transducer, we successfully developed a series of two-input, three-input, and set-reset logic gates at the molecular level.
Department of Chemistry, National Sun Yat-sen University, 70 Lienhai Rd., Kaohsiung 80424, Taiwan. tsengwl@mail.nsysu.edu.tw.
Jia-Hui
JH
Lin
Wei-Lung
WL
Tseng
D020029:Base Pairing; D001483:Base Sequence; D001600:Berberine Alkaloids / Q000032:analysis*; D015374:Biosensing Techniques; D039301:Computers, Molecular; D004247:DNA / Q000737:chemistry*; D005456:Fluorescent Dyes / Q000737:chemistry*; D008628:Mercury / Q000032:analysis*; D008969:Molecular Sequence Data; D012834:Silver / Q000032:analysis*; D013050:Spectrometry, Fluorescence
D001600:Berberine Alkaloids; D005456:Fluorescent Dyes; D012834:Silver; C000666:coralyne; D004247:DNA; D008628:Mercury