Direct profiling of environmental microbial populations by thermal dissociation analysis of native rRNAs hybridized to oligonucleotide microarrays.
Oligonucleotide microarrays were used to profile directly extracted rRNA from environmental microbial populations without PCR amplification. In our initial inspection of two distinct estuarine study sites, the hybridization patterns were reproducible and varied between estuarine sediments of differing salinities. The determination of a thermal dissociation curve (i.e., melting profile) for each probe-target duplex provided information on hybridization specificity, which is essential for confirming adequate discrimination between target and nontarget sequences.
El Fantroussi
Said
S
Department of Civil and Environmental Engineering, University of Washington, Seattle 98195, USA.
Urakawa
Hidetoshi
H
Bernhard
Anne E
AE
Kelly
John J
JJ
Noble
Peter A
PA
Smidt
H
H
Yershov
G M
GM
Stahl
David A
DA
D001419:Bacteria / Q000235:genetics*; D005618:Fresh Water / Q000382:microbiology*; D019015:Geologic Sediments / Q000382:microbiology*; D009693:Nucleic Acid Hybridization / Q000379:methods*; D020411:Oligonucleotide Array Sequence Analysis; D015345:Oligonucleotide Probes; D012335:RNA, Ribosomal / Q000235:genetics*; D012680:Sensitivity and Specificity; D013696:Temperature
D015345:Oligonucleotide Probes; D012335:RNA, Ribosomal