title: Arrest of rolling circle amplification by protein-binding DNA aptamers.
abstract: Certain DNA polymerases, such as ϕ29 DNA polymerase, can isothermally copy the sequence of a circular template round by round in a process known as rolling circle amplification (RCA), which results in super-long single-stranded (ss) DNA molecules made of tandem repeats. The power of RCA reflects the high processivity and the strand-displacement ability of these polymerases. In this work, the ability of ϕ29DNAP to carry out RCA over circular templates containing a protein-binding DNA aptamer sequence was investigated. It was found that protein-aptamer interactions can prevent this DNA polymerase from reading through the aptameric domain. This finding indicates that protein-binding DNA aptamers can form highly stable complexes with their targets in solution. This novel observation was exploited by translating RCA arrest into a simple and convenient colorimetric assay for the detection of specific protein targets, which continues to showcase the versatility of aptamers as molecular recognition elements for biosensing applications.
authors.affiliation: Department of Biochemistry and Biomedical Sciences and Department of Chemistry and Chemical Biology, McMaster University, 1280 Main St. W., Hamilton, ON, L8S 4K1 (Canada); Department of Chemistry and Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Tsinghua University, Beijing, 100084 (P. R. China).
authors.forename: Lida
authors.initials: L
authors.lastname: Wang
authors.forename: Kha
authors.initials: K
authors.lastname: Tram
authors.forename: Monsur M
authors.initials: MM
authors.lastname: Ali
authors.forename: Bruno J
authors.initials: BJ
authors.lastname: Salena
authors.forename: Jinghong
authors.initials: J
authors.lastname: Li
authors.forename: Yingfu
authors.initials: Y
authors.lastname: Li
mesh_terms: D052157:Aptamers, Nucleotide / Q000096:biosynthesis* / Q000737:chemistry*; D004268:DNA-Binding Proteins / Q000737:chemistry*; D004259:DNA-Directed DNA Polymerase / Q000737:chemistry*; D021141:Nucleic Acid Amplification Techniques / Q000379:methods; D009841:Oligonucleotides / Q000096:biosynthesis* / Q000737:chemistry*
chemical_list: D052157:Aptamers, Nucleotide; D004268:DNA-Binding Proteins; D009841:Oligonucleotides; D004259:DNA-Directed DNA Polymerase
keywords: aptamers; biosensors; molecular competition; protein detection; rolling circle amplification