title: Nucleotide base analog pyrrolo-deoxycytidine as fluorescent probe signal for enzyme-free and signal amplified nucleic acids detection.
abstract: In the present work, an enzyme-free and signal amplified nucleic acids detection method based on the fluorescent nucleotide base analog pyrrolo-deoxycytidine (P-dC) and catalyzed hairpin assembly (CHA) has been developed. In the CHA signal amplification system, two hairpin auxiliary probes, H1 and H2, which containing a fluorescent P-dC at the end of the stem, respectively, were used as the fluorescent probes. The fluorescence of P-dC in H1 and H2 was quenched owing to the stacking interaction among the bases in the stem. In the presence of the target DNA, the catalytic assembly of H1 and H2 was triggered and the target could be released during the helix DNA H1-H2 complex formation process, then the released target was used to trigger another reaction cycle. In the H1-H2 complex, P-dC was located in the flexible single-stranded DNA (ssDNA) sticky ends instead of the rigid stem, thus resulting in the increase of fluorescence. The cycling use of the target in the CHA system amplified the fluorescence signal, and the detection limit of this method was obtained as 19pM, which is 3 orders of magnitude sensitive than the conventional fluorescent nucleotide base analogs based approach without CHA signal amplification.
authors.affiliation: College of Chemistry, Sichuan University, Chengdu 610064, China.
authors.forename: Zhijuan
authors.initials: Z
authors.lastname: Duan
authors.affiliation: College of Life Sciences, Sichuan University, Chengdu 610064, China.
authors.forename: Zhuo
authors.initials: Z
authors.lastname: Li
authors.affiliation: College of Chemistry, Sichuan University, Chengdu 610064, China. Electronic address: daijy@scu.edu.cn.
authors.forename: Jianyuan
authors.initials: J
authors.lastname: Dai
authors.affiliation: College of Chemistry, Sichuan University, Chengdu 610064, China.
authors.forename: Hongfei
authors.initials: H
authors.lastname: He
authors.affiliation: College of Chemistry, Sichuan University, Chengdu 610064, China; College of Chemical Engineering, Sichuan University, Chengdu 610065, China. Electronic address: xiaodan@scu.edu.cn.
authors.forename: Dan
authors.initials: D
authors.lastname: Xiao
mesh_terms: D015374:Biosensing Techniques / Q000379:methods*; D004247:DNA / Q000032:analysis* / Q000737:chemistry / Q000235:genetics; D003841:Deoxycytidine / Q000031:analogs & derivatives* / Q000737:chemistry; D005456:Fluorescent Dyes / Q000737:chemistry*; D055029:Inverted Repeat Sequences; D057230:Limit of Detection; D011758:Pyrroles / Q000737:chemistry*
chemical_list: D005456:Fluorescent Dyes; D011758:Pyrroles; C540526:pyrrolo-deoxycytidine; D003841:Deoxycytidine; D004247:DNA
keywords: Enzyme-free; Fluorescence; Nucleic acid; Pyrrolo-deoxycytidine; Signal amplification