Bacterial discrimination by means of a universal array approach mediated by LDR (ligase detection reaction).

Elena Busti, Roberta Bordoni, Bianca Castiglioni, Paolo Monciardini, Margherita Sosio, Stefano Donadio, Clarissa Consolandi, Luigi Rossi Bernardi, Cristina Battaglia, Gianluca De Bellis

Research output: Contribution to journalArticle

Abstract

BACKGROUND: PCR amplification of bacterial 16S rRNA genes provides the most comprehensive and flexible means of sampling bacterial communities. Sequence analysis of these cloned fragments can provide a qualitative and quantitative insight of the microbial population under scrutiny although this approach is not suited to large-scale screenings. Other methods, such as denaturing gradient gel electrophoresis, heteroduplex or terminal restriction fragment analysis are rapid and therefore amenable to field-scale experiments. A very recent addition to these analytical tools is represented by microarray technology. RESULTS: Here we present our results using a Universal DNA Microarray approach as an analytical tool for bacterial discrimination. The proposed procedure is based on the properties of the DNA ligation reaction and requires the design of two probes specific for each target sequence. One oligo carries a fluorescent label and the other a unique sequence (cZipCode or complementary ZipCode) which identifies a ligation product. Ligated fragments, obtained in presence of a proper template (a PCR amplified fragment of the 16s rRNA gene) contain either the fluorescent label or the unique sequence and therefore are addressed to the location on the microarray where the ZipCode sequence has been spotted. Such an array is therefore "Universal" being unrelated to a specific molecular analysis. Here we present the design of probes specific for some groups of bacteria and their application to bacterial diagnostics. CONCLUSIONS: The combined use of selective probes, ligation reaction and the Universal Array approach yielded an analytical procedure with a good power of discrimination among bacteria.

Original languageEnglish
Pages (from-to)27
Number of pages1
JournalBMC Microbiology
Volume2
Issue number1
Publication statusPublished - Sep 20 2002

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Ligases
Ligation
rRNA Genes
Bacteria
Polymerase Chain Reaction
Denaturing Gradient Gel Electrophoresis
Oligonucleotide Array Sequence Analysis
Sequence Analysis
Technology
DNA
Population

ASJC Scopus subject areas

  • Microbiology (medical)

Cite this

Busti, E., Bordoni, R., Castiglioni, B., Monciardini, P., Sosio, M., Donadio, S., ... De Bellis, G. (2002). Bacterial discrimination by means of a universal array approach mediated by LDR (ligase detection reaction). BMC Microbiology, 2(1), 27.

Bacterial discrimination by means of a universal array approach mediated by LDR (ligase detection reaction). / Busti, Elena; Bordoni, Roberta; Castiglioni, Bianca; Monciardini, Paolo; Sosio, Margherita; Donadio, Stefano; Consolandi, Clarissa; Rossi Bernardi, Luigi; Battaglia, Cristina; De Bellis, Gianluca.

In: BMC Microbiology, Vol. 2, No. 1, 20.09.2002, p. 27.

Research output: Contribution to journalArticle

Busti, E, Bordoni, R, Castiglioni, B, Monciardini, P, Sosio, M, Donadio, S, Consolandi, C, Rossi Bernardi, L, Battaglia, C & De Bellis, G 2002, 'Bacterial discrimination by means of a universal array approach mediated by LDR (ligase detection reaction).', BMC Microbiology, vol. 2, no. 1, pp. 27.
Busti E, Bordoni R, Castiglioni B, Monciardini P, Sosio M, Donadio S et al. Bacterial discrimination by means of a universal array approach mediated by LDR (ligase detection reaction). BMC Microbiology. 2002 Sep 20;2(1):27.
Busti, Elena ; Bordoni, Roberta ; Castiglioni, Bianca ; Monciardini, Paolo ; Sosio, Margherita ; Donadio, Stefano ; Consolandi, Clarissa ; Rossi Bernardi, Luigi ; Battaglia, Cristina ; De Bellis, Gianluca. / Bacterial discrimination by means of a universal array approach mediated by LDR (ligase detection reaction). In: BMC Microbiology. 2002 ; Vol. 2, No. 1. pp. 27.
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