Oligonucleotide microchips as genosensors for determinative and environmental studies in microbiology

The utility of parallel hybridization of environmental nucleic acids to many oligonucleotides immobilized in a matrix of polyacrylamide gel pads on a glass slide (oligonucleotide microchip) was evaluated. Oligonucleotides complementary to small-subunit rRNA sequences of selected microbial groups, encompassing key genera of nitrifying bacteria, were shown to selectively retain labeled target nucleic acid derived from either DNA or RNA forms of the target sequences. The utility of varying the probe concentration to normalize hybridization signals and the use of multicolor detection for simultaneous quantitation of multiple probe-target populations were demonstrated.

[1]  A. Mirzabekov,et al.  Sequence analysis by hybridization with oligonucleotide microchip: identification of beta-thalassemia mutations. , 1997, Gene.

[2]  M. Wagner,et al.  Phylogenetic probes for analyzing abundance and spatial organization of nitrifying bacteria , 1996, Applied and environmental microbiology.

[3]  D. Stahl,et al.  Characterization of universal small-subunit rRNA hybridization probes for quantitative molecular microbial ecology studies , 1996, Applied and environmental microbiology.

[4]  A. Mirzabekov,et al.  Theoretical analysis of the kinetics of DNA hybridization with gel-immobilized oligonucleotides. , 1996, Biophysical journal.

[5]  A. Mirzabekov,et al.  Chemical methods of DNA and RNA fluorescent labeling. , 1996, Nucleic acids research.

[6]  Daniel B. Oerther,et al.  The oligonucleotide probe database , 1996, Applied and environmental microbiology.

[7]  A. Mirzabekov,et al.  DNA analysis and diagnostics on oligonucleotide microchips. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[8]  D. Stahl.  Application of phylogenetically based hybridization probes to microbial ecology , 1995 .

[9]  K. Schleifer,et al.  Phylogenetic identification and in situ detection of individual microbial cells without cultivation. , 1995, Microbiological reviews.

[10]  K. Schleifer,et al.  In situ Identification of Ammonia-oxidizing Bacteria , 1995 .

[11]  D. Stahl,et al.  Evolutionary relationships among ammonia- and nitrite-oxidizing bacteria , 1994, Journal of bacteriology.

[12]  N. Pace,et al.  Remarkable archaeal diversity detected in a Yellowstone National Park hot spring environment. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[13]  A. Mirzabekov,et al.  DNA sequencing by hybridization--a megasequencing method and a diagnostic tool? , 1994, Trends in biotechnology.

[14]  G. Sayler,et al.  Quantitative Relationship between Naphthalene Catabolic Gene Frequency and Expression in Predicting PAH Degradation in Soils at Town Gas Manufacturing Sites , 1993 .

[15]  J R Saunders,et al.  The phylogeny of autotrophic ammonia-oxidizing bacteria as determined by analysis of 16S ribosomal RNA gene sequences. , 1993, Journal of general microbiology.

[16]  D A Stahl,et al.  Use of rRNA fluorescence in situ hybridization for measuring the activity of single cells in young and established biofilms , 1993, Applied and environmental microbiology.

[17]  P. V. von Hippel,et al.  Betaine can eliminate the base pair composition dependence of DNA melting. , 1993, Biochemistry.

[18]  E. Delong.  Archaea in coastal marine environments. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[19]  E. Southern,et al.  Parallel analysis of oligodeoxyribonucleotide (oligonucleotide) interactions. I. Analysis of factors influencing oligonucleotide duplex formation. , 1992, Nucleic acids research.

[20]  D. M. Ward,et al.  Ribosomal RNA Analysis of Microorganisms as They Occur in Nature , 1992 .

[21]  Lysov YuP,et al.  A method for DNA sequencing by hybridization with oligonucleotide matrix. , 1991, DNA sequence : the journal of DNA sequencing and mapping.

[22]  R. Amann,et al.  Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations , 1990, Applied and environmental microbiology.

[23]  S. Giovannoni,et al.  Genetic diversity in Sargasso Sea bacterioplankton , 1990, Nature.

[24]  M. Salimans,et al.  Rapid and simple method for purification of nucleic acids , 1990, Journal of clinical microbiology.

[25]  B Flesher,et al.  Use of phylogenetically based hybridization probes for studies of ruminal microbial ecology , 1988, Applied and environmental microbiology.

[26]  C. Woese,et al.  Bacterial evolution , 1987, Microbiological reviews.

[27]  N. Pace,et al.  The Analysis of Natural Microbial Populations by Ribosomal RNA Sequences , 1986 .

[28]  C R Woese,et al.  The phylogeny of purple bacteria: the alpha subdivision. , 1984, Systematic and applied microbiology.

[29]  J. Sambrook,et al.  Molecular Cloning: A Laboratory Manual , 2001 .

[30]  M. S. Finstein,et al.  Length of incubation for enumerating nitrifying bacteria present in various environments. , 1975, Applied microbiology.