title: Gold nanoparticle-based beacon to detect STAT5b mRNA expression in living cells: a case optimized by bioinformatics screen.
abstract: Messenger RNA (mRNA), a single-strand ribonucleic acid with functional gene information is usually abnormally expressed in cancer cells and has become a promising biomarker for the study of tumor progress. Hairpin DNA-coated gold nanoparticle (hDAuNP) beacon containing a bare gold nanoparticle (AuNP) as fluorescence quencher and thiol-terminated fluorescently labeled stem-loop-stem oligonucleotide sequences attached by Au-S bond is currently a new nanoscale biodiagnostic platform capable of mRNA detection, in which the design of the loop region sequence is crucial for hybridizing with the target mRNA. Hence, in this study, to improve the sensitivity and selectivity of hDAuNP beacon simultaneously, the loop region of hairpin DNA was screened by bioinformatics strategy. Here, signal transducer and activator of transcription 5b (STAT5b) mRNA was selected and used as a practical example. The results from the combined characterizations using optical techniques, flow cytometry assay, and cell microscopic imaging showed that after optimization, the as-prepared hDAuNP beacon had higher selectivity and sensitivity for the detection of STAT5b mRNA in living cells, as compared with our previous beacon. Thus, the bioinformatics method may be a promising new strategy for assisting in the designing of the hDAuNP beacon, extending its application in the detection of mRNA expression and the resultant mRNA-based biological processes and disease pathogenesis.
authors.affiliation: Department of Biomedical Engineering, China Pharmaceutical University, Nanjing, People's Republic of China.
authors.forename: Dawei
authors.initials: D
authors.lastname: Deng
authors.affiliation: Department of Biomedical Engineering, China Pharmaceutical University, Nanjing, People's Republic of China.
authors.forename: Yang
authors.initials: Y
authors.lastname: Li
authors.affiliation: Department of Biomedical Engineering, China Pharmaceutical University, Nanjing, People's Republic of China.
authors.forename: Jianpeng
authors.initials: J
authors.lastname: Xue
authors.affiliation: Department of Biomedical Engineering, China Pharmaceutical University, Nanjing, People's Republic of China.
authors.forename: Jie
authors.initials: J
authors.lastname: Wang
authors.affiliation: Department of Biomedical Engineering, China Pharmaceutical University, Nanjing, People's Republic of China.
authors.forename: Guanhua
authors.initials: G
authors.lastname: Ai
authors.affiliation: Department of Biomedical Engineering, China Pharmaceutical University, Nanjing, People's Republic of China.
authors.forename: Xin
authors.initials: X
authors.lastname: Li
authors.affiliation: Department of Biomedical Engineering, China Pharmaceutical University, Nanjing, People's Republic of China.
authors.forename: Yueqing
authors.initials: Y
authors.lastname: Gu
mesh_terms: D019295:Computational Biology / Q000379:methods*; D006046:Gold / Q000737:chemistry*; D056945:Hep G2 Cells; D006801:Humans; D053768:Metal Nanoparticles / Q000737:chemistry*; D012333:RNA, Messenger / Q000032:analysis / Q000737:chemistry / Q000235:genetics; D050799:STAT5 Transcription Factor / Q000032:analysis / Q000235:genetics / Q000378:metabolism
chemical_list: D012333:RNA, Messenger; D050799:STAT5 Transcription Factor; D006046:Gold
keywords: STAT5b mRNA; bioinformatics; gold nanoparticle; molecular beacon; visual detection