title: Restriction site tagged (RST) microarrays: a novel technique to study the species composition of complex microbial systems.
abstract: We have developed a new type of microarray, restriction site tagged (RST), for example NotI, microarrays. In this approach only sequences surrounding specific restriction sites (i.e. NotI linking clones) were used for generating microarrays. DNA was labeled using a new procedure, NotI representation, where only sequences surrounding NotI sites were labeled. Due to these modifications, the sensitivity of RST microarrays increases several hundred-fold compared to that of ordinary genomic microarrays. In a pilot experiment we have produced NotI microarrays from Gram-positive and Gram-negative bacteria and have shown that even closely related Escherichia coli strains can be easily discriminated using this technique. For example, two E.coli strains, K12 and R2, differ by less than 0.1% in their 16S rRNA sequences and thus the 16S rRNA sequence would not easily discriminate between these strains. However, these strains showed distinctly different hybridization patterns with NotI microarrays. The same technique can be adapted to other restriction enzymes as well. This type of microarray opens the possibility not only for studies of the normal flora of the gut but also for any problem where quantitative and qualitative analysis of microbial (or large viral) genomes is needed.
authors.affiliation: Microbiology and Tumor Biology Center, Department of Cell and Molecular Biology, Karolinska Institute, 171 77 Stockholm, Sweden. eugzab@ki.se
authors.forename: Eugene R
authors.initials: ER
authors.lastname: Zabarovsky
authors.forename: Lev
authors.initials: L
authors.lastname: Petrenko
authors.forename: Alexei
authors.initials: A
authors.lastname: Protopopov
authors.forename: Olga
authors.initials: O
authors.lastname: Vorontsova
authors.forename: Alexey S
authors.initials: AS
authors.lastname: Kutsenko
authors.forename: Yanyan
authors.initials: Y
authors.lastname: Zhao
authors.forename: Gelena
authors.initials: G
authors.lastname: Kilosanidze
authors.forename: Veronika
authors.initials: V
authors.lastname: Zabarovska
authors.forename: Elian
authors.initials: E
authors.lastname: Rakhmanaliev
authors.forename: Bertil
authors.initials: B
authors.lastname: Pettersson
authors.forename: Vladimir I
authors.initials: VI
authors.lastname: Kashuba
authors.forename: Olle
authors.initials: O
authors.lastname: Ljungqvist
authors.forename: Elisabeth
authors.initials: E
authors.lastname: Norin
authors.forename: Tore
authors.initials: T
authors.lastname: Midtvedt
authors.forename: Roland
authors.initials: R
authors.lastname: Möllby
authors.forename: Gösta
authors.initials: G
authors.lastname: Winberg
authors.forename: Ingemar
authors.initials: I
authors.lastname: Ernberg
mesh_terms: D001419:Bacteria / Q000235:genetics; D001665:Binding Sites / Q000235:genetics; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D015252:Deoxyribonucleases, Type II Site-Specific / Q000378:metabolism*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D017422:Sequence Analysis, DNA; D013045:Species Specificity
chemical_list: D004269:DNA, Bacterial; D015252:Deoxyribonucleases, Type II Site-Specific; C038565:GCGGCCGC-specific type II deoxyribonucleases