Autonomous replication of nucleic acids by polymerization/nicking enzyme/DNAzyme cascades for the amplified detection of DNA and the aptamer-cocaine complex

Anal Chem. 2013 Sep 3;85(17):8196-203. doi: 10.1021/ac4013094. Epub 2013 Aug 15.

Abstract

The progressive development of amplified DNA sensors and aptasensors using replication/nicking enzymes/DNAzyme machineries is described. The sensing platforms are based on the tailoring of a DNA template on which the recognition of the target DNA or the formation of the aptamer-substrate complex trigger on the autonomous isothermal replication/nicking processes and the displacement of a Mg(2+)-dependent DNAzyme that catalyzes the generation of a fluorophore-labeled nucleic acid acting as readout signal for the analyses. Three different DNA sensing configurations are described, where in the ultimate configuration the target sequence is incorporated into a nucleic acid blocker structure associated with the sensing template. The target-triggered isothermal autonomous replication/nicking process on the modified template results in the formation of the Mg(2+)-dependent DNAzyme tethered to a free strand consisting of the target sequence. This activates additional template units for the nucleic acid self-replication process, resulting in the ultrasensitive detection of the target DNA (detection limit 1 aM). Similarly, amplified aptamer-based sensing platforms for cocaine are developed along these concepts. The modification of the cocaine-detection template by the addition of a nucleic acid sequence that enables the autonomous secondary coupled activation of a polymerization/nicking machinery and DNAzyme generation path leads to an improved analysis of cocaine (detection limit 10 nM).

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Aptamers, Nucleotide / analysis*
  • Aptamers, Nucleotide / chemistry
  • Aptamers, Nucleotide / genetics
  • Cocaine / analysis*
  • Cocaine / chemistry
  • Cocaine / genetics
  • DNA Replication* / genetics
  • DNA, Catalytic / analysis*
  • DNA, Catalytic / chemistry
  • DNA, Catalytic / genetics
  • Nucleic Acid Amplification Techniques
  • Nucleic Acids / analysis*
  • Nucleic Acids / chemistry
  • Nucleic Acids / genetics
  • Polymerization*

Substances

  • Aptamers, Nucleotide
  • DNA, Catalytic
  • Nucleic Acids
  • Cocaine