title: Bacterial discrimination by means of a universal array approach mediated by LDR (ligase detection reaction).
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.
authors.affiliation: 1Dipartimento di Scienze e Tecnologie Biomediche, Universita' di Milano, via F.lli Cervi, 93 20090 Segrate (MI), Italy. ebusti@biosearch.it
authors.forename: Elena
authors.initials: E
authors.lastname: Busti
authors.forename: Roberta
authors.initials: R
authors.lastname: Bordoni
authors.forename: Bianca
authors.initials: B
authors.lastname: Castiglioni
authors.forename: Paolo
authors.initials: P
authors.lastname: Monciardini
authors.forename: Margherita
authors.initials: M
authors.lastname: Sosio
authors.forename: Stefano
authors.initials: S
authors.lastname: Donadio
authors.forename: Clarissa
authors.initials: C
authors.lastname: Consolandi
authors.forename: Luigi
authors.initials: L
authors.lastname: Rossi Bernardi
authors.forename: Cristina
authors.initials: C
authors.lastname: Battaglia
authors.forename: Gianluca
authors.initials: G
authors.lastname: De Bellis
mesh_terms: D001419:Bacteria / Q000235:genetics / Q000302:isolation & purification*; D011088:DNA Ligases / Q000378:metabolism; D004269:DNA, Bacterial / Q000032:analysis; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D011786:Quality Control; D012336:RNA, Ribosomal, 16S / Q000032:analysis / Q000235:genetics; D017422:Sequence Analysis, DNA
chemical_list: D004269:DNA, Bacterial; D012336:RNA, Ribosomal, 16S; D011088:DNA Ligases