A subtractively optimized DNA microarray using non-sequenced genomic probes for the detection of food-borne pathogens

Jin Yong Lee; Byoung Chan Kim; Kwan Jong Chang; Joo Myung Ahn; Jee Hoon Ryu; Hyo Ihl Chang; Man Bock Gu

doi:10.1007/s12010-010-9126-6

A subtractively optimized DNA microarray using non-sequenced genomic probes for the detection of food-borne pathogens

Jin Yong Lee, Byoung Chan Kim, Kwan Jong Chang, Joo Myung Ahn, Jee Hoon Ryu, Hyo Ihl Chang, Man Bock Gu

Research output: Contribution to journal › Article › peer-review

3 Citations (Scopus)

Abstract

In this study, we present the successful detection of food-borne pathogens using randomly selected non-sequenced genomic DNA probes-based DNA microarray chips. Three food-borne pathogens, Staphylococcus aureus, Salmonella enterica subsp. enterica serovar Typhimurium (S. Typhimurium), and Bacillus cereus, were subjected for the preparation of the DNA microarray probes. Initially, about 50 DNA probes selected randomly from non-sequenced genomic DNA of each pathogen were prepared by using a set of restriction enzyme pairs. The proto-type of DNA microarray chip for detecting three different pathogens simultaneously was fabricated by using those DNA probes prepared for each pathogen. This proto-type DNA microarray has been tested with three target pathogens and additional seven bacteria, and successfully verified with a few crosshybridized probes. After this primary verification of the DNA microarray hybridization, this proto-type DNA microarray chip was redesigned and successfully optimized by eliminating a few cross-hybridized probes. The specificity of this redesigned DNA microarray chip to each pathogen was confirmed without any serious cross-hybridizations, and its multiplexing capability in its pathogen detection was found to be possible. This randomly selected nonsequenced genomic DNA probes-based DNA microarray was successfully proved to be the high-throughput simultaneous detection chip for the detection of food-borne pathogens, without knowing the exact sequence information of the target bacteria. This could be the first fabrication of DNA microarray chip for the simultaneous detection of different kinds of food-borne pathogens.

Original language	English
Pages (from-to)	183-193
Number of pages	11
Journal	Applied Biochemistry and Biotechnology
Volume	164
Issue number	2
DOIs	https://doi.org/10.1007/s12010-010-9126-6
Publication status	Published - 2011 May

Bibliographical note

Funding Information:
Acknowledgment This work was supported by a grant (code # 20080401034020) from BioGreen 21 Program, Rural Development Administration, Republic of Korea. The authors are grateful for this support.

Keywords

Cross-hybridization
DNA microarray chip
Food-borne pathogen
Multiplexed detection
Non-sequenced genomic DNA probes

ASJC Scopus subject areas

Biotechnology
Bioengineering
Biochemistry
Applied Microbiology and Biotechnology
Molecular Biology

Access to Document

10.1007/s12010-010-9126-6

Cite this

@article{085703e7b435470e9142be3df75e313b,

title = "A subtractively optimized DNA microarray using non-sequenced genomic probes for the detection of food-borne pathogens",

abstract = "In this study, we present the successful detection of food-borne pathogens using randomly selected non-sequenced genomic DNA probes-based DNA microarray chips. Three food-borne pathogens, Staphylococcus aureus, Salmonella enterica subsp. enterica serovar Typhimurium (S. Typhimurium), and Bacillus cereus, were subjected for the preparation of the DNA microarray probes. Initially, about 50 DNA probes selected randomly from non-sequenced genomic DNA of each pathogen were prepared by using a set of restriction enzyme pairs. The proto-type of DNA microarray chip for detecting three different pathogens simultaneously was fabricated by using those DNA probes prepared for each pathogen. This proto-type DNA microarray has been tested with three target pathogens and additional seven bacteria, and successfully verified with a few crosshybridized probes. After this primary verification of the DNA microarray hybridization, this proto-type DNA microarray chip was redesigned and successfully optimized by eliminating a few cross-hybridized probes. The specificity of this redesigned DNA microarray chip to each pathogen was confirmed without any serious cross-hybridizations, and its multiplexing capability in its pathogen detection was found to be possible. This randomly selected nonsequenced genomic DNA probes-based DNA microarray was successfully proved to be the high-throughput simultaneous detection chip for the detection of food-borne pathogens, without knowing the exact sequence information of the target bacteria. This could be the first fabrication of DNA microarray chip for the simultaneous detection of different kinds of food-borne pathogens.",

keywords = "Cross-hybridization, DNA microarray chip, Food-borne pathogen, Multiplexed detection, Non-sequenced genomic DNA probes",

author = "Lee, {Jin Yong} and Kim, {Byoung Chan} and Chang, {Kwan Jong} and Ahn, {Joo Myung} and Ryu, {Jee Hoon} and Chang, {Hyo Ihl} and Gu, {Man Bock}",

note = "Funding Information: Acknowledgment This work was supported by a grant (code # 20080401034020) from BioGreen 21 Program, Rural Development Administration, Republic of Korea. The authors are grateful for this support.",

year = "2011",

month = may,

doi = "10.1007/s12010-010-9126-6",

language = "English",

volume = "164",

pages = "183--193",

journal = "Applied Biochemistry and Biotechnology",

issn = "0273-2289",

publisher = "Humana Press",

number = "2",

}

TY - JOUR

T1 - A subtractively optimized DNA microarray using non-sequenced genomic probes for the detection of food-borne pathogens

AU - Lee, Jin Yong

AU - Kim, Byoung Chan

AU - Chang, Kwan Jong

AU - Ahn, Joo Myung

AU - Ryu, Jee Hoon

AU - Chang, Hyo Ihl

AU - Gu, Man Bock

N1 - Funding Information: Acknowledgment This work was supported by a grant (code # 20080401034020) from BioGreen 21 Program, Rural Development Administration, Republic of Korea. The authors are grateful for this support.

PY - 2011/5

Y1 - 2011/5

N2 - In this study, we present the successful detection of food-borne pathogens using randomly selected non-sequenced genomic DNA probes-based DNA microarray chips. Three food-borne pathogens, Staphylococcus aureus, Salmonella enterica subsp. enterica serovar Typhimurium (S. Typhimurium), and Bacillus cereus, were subjected for the preparation of the DNA microarray probes. Initially, about 50 DNA probes selected randomly from non-sequenced genomic DNA of each pathogen were prepared by using a set of restriction enzyme pairs. The proto-type of DNA microarray chip for detecting three different pathogens simultaneously was fabricated by using those DNA probes prepared for each pathogen. This proto-type DNA microarray has been tested with three target pathogens and additional seven bacteria, and successfully verified with a few crosshybridized probes. After this primary verification of the DNA microarray hybridization, this proto-type DNA microarray chip was redesigned and successfully optimized by eliminating a few cross-hybridized probes. The specificity of this redesigned DNA microarray chip to each pathogen was confirmed without any serious cross-hybridizations, and its multiplexing capability in its pathogen detection was found to be possible. This randomly selected nonsequenced genomic DNA probes-based DNA microarray was successfully proved to be the high-throughput simultaneous detection chip for the detection of food-borne pathogens, without knowing the exact sequence information of the target bacteria. This could be the first fabrication of DNA microarray chip for the simultaneous detection of different kinds of food-borne pathogens.

AB - In this study, we present the successful detection of food-borne pathogens using randomly selected non-sequenced genomic DNA probes-based DNA microarray chips. Three food-borne pathogens, Staphylococcus aureus, Salmonella enterica subsp. enterica serovar Typhimurium (S. Typhimurium), and Bacillus cereus, were subjected for the preparation of the DNA microarray probes. Initially, about 50 DNA probes selected randomly from non-sequenced genomic DNA of each pathogen were prepared by using a set of restriction enzyme pairs. The proto-type of DNA microarray chip for detecting three different pathogens simultaneously was fabricated by using those DNA probes prepared for each pathogen. This proto-type DNA microarray has been tested with three target pathogens and additional seven bacteria, and successfully verified with a few crosshybridized probes. After this primary verification of the DNA microarray hybridization, this proto-type DNA microarray chip was redesigned and successfully optimized by eliminating a few cross-hybridized probes. The specificity of this redesigned DNA microarray chip to each pathogen was confirmed without any serious cross-hybridizations, and its multiplexing capability in its pathogen detection was found to be possible. This randomly selected nonsequenced genomic DNA probes-based DNA microarray was successfully proved to be the high-throughput simultaneous detection chip for the detection of food-borne pathogens, without knowing the exact sequence information of the target bacteria. This could be the first fabrication of DNA microarray chip for the simultaneous detection of different kinds of food-borne pathogens.

KW - Cross-hybridization

KW - DNA microarray chip

KW - Food-borne pathogen

KW - Multiplexed detection

KW - Non-sequenced genomic DNA probes

UR - http://www.scopus.com/inward/record.url?scp=79956344539&partnerID=8YFLogxK

U2 - 10.1007/s12010-010-9126-6

DO - 10.1007/s12010-010-9126-6

M3 - Article

C2 - 21116735

AN - SCOPUS:79956344539

SN - 0273-2289

VL - 164

SP - 183

EP - 193

JO - Applied Biochemistry and Biotechnology

JF - Applied Biochemistry and Biotechnology

IS - 2

ER -

A subtractively optimized DNA microarray using non-sequenced genomic probes for the detection of food-borne pathogens

Abstract

Bibliographical note

Keywords

ASJC Scopus subject areas

Access to Document

Other files and links

Fingerprint

Cite this