Esterase 2-oligodeoxynucleotide conjugates as enzyme reporter for electrochemical detection of DNA and identification of bacterial species

Electrical Chip (E-Chip) system offers a fast, sensitive and cost-effective way to detect analyte. To improve its application of nucleic acids detection, a suitable enzyme reporter is expected. Esterase 2 (EST2) from Alicyclobacillus acidocaldarius was introduced and mutated to have an accessible cysteine residue at 118th codon. This esterase was purified by a single-step affinity chromatography with trifluoromethyl ketone as a ligand and covalently conjugated to a 5’-amino modified oligodeoxynucleotide. The purified conjugate served as a reporter enzyme for electrochemical detection of nucleic acids. Being an optimal substrate, p-aminophenylbutyrate exerts maximal signal response to EST2 in E-Chip, as determined by comparison of p-aminophenyl esters with acyl chain length from two to eight carbons. An assay of 15 pM of soluble esterase 2 in 1 ml was obtained exploiting p-aminophenylbutyrate. E-Chip detection of nucleic acids requires three essential steps: immobilization of thiol-modified capture oligodeoxynucleotides onto electrode, recruiting EST2 to electrode vicinity by means of nucleic acids hybridization, and amperometric determination of p-aminophenol produced by EST2 catalytic hydrolysis of p-aminophenylbutyrate. Generally, EST2 reporter allows a detection of approximately one million molecules/0.6 mm2 electrode. EST2 covalently attached by an oligodeoxynucleotide significantly increased the ability of mismatch discrimination as compared to the streptavidin conjugated EST2. Moreover, single nucleotide mismatch in analyte could be reliably discriminated in the set-up, as demonstrated by single nucleotide mismatch in a 49-mer oligodeoxynucleotide as well as in a 510-nucleotide ssDNA. Application of E-Chip to bacterial species identification through 16S rRNA was demonstrated. Escherichia coli and Listeria innocua were easily identified as judged by signals given by rRNA hybridization with species-specific capture ODNs. This system allows a detection of 1,000 Escherichia coli cells. As a further optimization, a stem-loop structured molecular beacon with 5’-thiol and 3’-biotin modifications was synthesized and tested on the chip using EST2-streptavidin as reporter. The presence of target oligodeoxynucleotides complementary to the whole stem-loop sequence enhanced signal for a moderate 2-fold. The future work should focus on combination of continuous flow PCR with EST2-oligodeoxynucleotide conjugate reporter to do faster and more automatic disease related DNA analysis, as well as construction of EST2 based biosensor for toxic agents detection.

Level thesis:degree_level

thesis.doctoral

Grantor dc:publisher

Universität Bayreuth

Year

2007

Author dc:creator

• Wang, Yiran

Contributors dc:contributor

• Sprinzl, Mathias

Repository record source_url

https://epub.uni-bayreuth.de/id/eprint/734/

OAI identifier oai:identifier

oai:epub.uni-bayreuth.de:734