title: Optimal DNA templates for rolling circle amplification revealed by in vitro selection.
abstract: Rolling circle amplification (RCA) has been widely used as an isothermal DNA amplification technique for diagnostic and bioanalytical applications. Because RCA involves repeated copying of the same circular DNA template by a DNA polymerase thousands of times, we hypothesized there exist DNA sequences that can function as optimal templates and produce more DNA amplicons within an allocated time. Herein we describe an in vitro selection effort conducted to search from a random sequence DNA pool for such templates for phi29 DNA polymerase, a frequently used polymerase for RCA. Diverse DNA molecules were isolated and they were characterized by richness in adenosine (A) and cytidine (C) nucleotides. The top ranked sequences exhibit superior RCA efficiency and the use of these templates for RCA results in significantly improved detection sensitivity. AC-rich sequences are expected to find useful applications for setting up effective RCA assays for biological sensing.
authors: Departments of Biochemistry and Biomedical Sciences and Chemistry and Chemical Biology, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1 (Canada).|The Ministry-Province Jointly Constructed Base for State Key Laboratory, Shenzhen Key Laboratory of Chemical Biology, The Graduate School at Shenzhen, Tsinghua University, Shenzhen, Guangdong 518055 (P. R. China).|School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055 (P. R. China).
authors: Yu
authors: Y
authors: Mao
authors: Departments of Biochemistry and Biomedical Sciences and Chemistry and Chemical Biology, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1 (Canada).
authors: Meng
authors: M
authors: Liu
authors: Departments of Biochemistry and Biomedical Sciences and Chemistry and Chemical Biology, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1 (Canada).
authors: Kha
authors: K
authors: Tram
authors: Departments of Biochemistry and Biomedical Sciences and Chemistry and Chemical Biology, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1 (Canada).
authors: Jimmy
authors: J
authors: Gu
authors: Department of Medicine, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1 (Canada).
authors: Bruno J
authors: BJ
authors: Salena
authors: The Ministry-Province Jointly Constructed Base for State Key Laboratory, Shenzhen Key Laboratory of Chemical Biology, The Graduate School at Shenzhen, Tsinghua University, Shenzhen, Guangdong 518055 (P. R. China). jiangyy@sz.tsinghua.edu.cn.
authors: Yuyang
authors: Y
authors: Jiang
authors: Departments of Biochemistry and Biomedical Sciences and Chemistry and Chemical Biology, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1 (Canada). liying@mcmaster.ca.
authors: Yingfu
authors: Y
authors: Li
mesh_terms: D052157:Aptamers, Nucleotide / Q000737:chemistry; D017103:Bacillus Phages / Q000201:enzymology; D001483:Base Sequence; D015374:Biosensing Techniques / Q000379:methods*; D004270:DNA, Circular / Q000737:chemistry* / Q000378:metabolism; D004259:DNA-Directed DNA Polymerase / Q000378:metabolism; D021141:Nucleic Acid Amplification Techniques / Q000379:methods*
chemical_list: D052157:Aptamers, Nucleotide; D004270:DNA, Circular; D004259:DNA-Directed DNA Polymerase
keywords: DNA; biosensors; circular templates; in vitro selection; rolling circle amplification