Influence of Dangling Ends and Surface-Proximal Tails of Targets on Probe-Target Duplex Formation in 16S rRNA Gene-Based Diagnostic Arrays (cid:1) †

Dangling ends and surface-proximal tails of gene targets influence probe-target duplex formation and affect the signal intensity of probes on diagnostic microarrays. This phenomenon was evaluated using an oligonucleotide microarray containing 18-mer probes corresponding to the 16S rRNA genes of 10 waterborne patho- gens and a number of synthetic and PCR-amplified gene targets. Signal intensities for Klenow/random primer-labeled 16S rRNA gene targets were dissimilar from those for 45-mer synthetic targets for nearly 73% of the probes tested. Klenow/random primer-labeled targets resulted in an interaction with a complex mixture of 16S rRNA genes (used as the background) 3.7 times higher than the interaction of 45-mer targets with the same mixture. A 7-base-long dangling end sequence with perfect homology to another single-stranded

[1]  D. Tautz,et al.  Tests of rRNA hybridization to microarrays suggest that hybridization characteristics of oligonucleotide probes for species discrimination cannot be predicted , 2006, Nucleic Acids Research.

[2]  H. Insam,et al.  Comparison of different labeling methods for the production of labeled target DNA for microarray hybridization. , 2006, Journal of microbiological methods.

[3]  Erdogan Gulari,et al.  On-chip non-equilibrium dissociation curves and dissociation rate constants as methods to assess specificity of oligonucleotide probes , 2006, Nucleic acids research.

[4]  Michael B. Eisen,et al.  Rapid quantitative profiling of complex microbial populations , 2006, Nucleic acids research.

[5]  Lei Zhang,et al.  Position of the fluorescent label is a crucial factor determining signal intensity in microarray hybridizations , 2005, Nucleic acids research.

[6]  Nicolas Peyret,et al.  Thermodynamic properties of DNA sequences: characteristic values for the human genome , 2005, Bioinform..

[7]  F. Raymond,et al.  Correlation between microarray DNA hybridization efficiency and the position of short capture probe on the target nucleic acid. , 2005, BioTechniques.

[8]  Heribert Insam,et al.  Design and application of an oligonucleotide microarray for the investigation of compost microbial communities. , 2005, Journal of microbiological methods.

[9]  Michael Wagner,et al.  16S rRNA Gene-Based Oligonucleotide Microarray for Environmental Monitoring of the Betaproteobacterial Order “Rhodocyclales” , 2005, Applied and Environmental Microbiology.

[10]  C. Gibas,et al.  Secondary structure in the target as a confounding factor in synthetic oligomer microarray design , 2005, BMC Genomics.

[11]  Wen-Tso Liu,et al.  Evaluating single-base-pair discriminating capability of planar oligonucleotide microchips using a non-equilibrium dissociation approach. , 2004, Environmental microbiology.

[12]  Douglas R Call,et al.  Amplicon secondary structure prevents target hybridization to oligonucleotide microarrays. , 2004, Biosensors & bioelectronics.

[13]  Jean-Marie Rouillard,et al.  Potential of DNA microarrays for developing parallel detection tools (PDTs) for microorganisms relevant to biodefense and related research needs. , 2004, Biosensors & bioelectronics.

[14]  M. P. Beaudet,et al.  Possible sources of dye-related signal correlation bias in two-color DNA microarray assays. , 2004, Analytical biochemistry.

[15]  M. Zuker,et al.  Prediction of hybridization and melting for double-stranded nucleic acids. , 2004, Biophysical journal.

[16]  E. Gulari,et al.  In situ synthesis of oligonucleotide microarrays. , 2004, Biopolymers.

[17]  Jizhong Zhou,et al.  Evaluation of 50-mer oligonucleotide arrays for detecting microbial populations in environmental samples. , 2004, BioTechniques.

[18]  Ulrich Melcher,et al.  Molecular Detection and Identification of Influenza Viruses by Oligonucleotide Microarray Hybridization , 2003, Journal of Clinical Microbiology.

[19]  N. Stralis-Pavese,et al.  Development and validation of a diagnostic microbial microarray for methanotrophs. , 2003, Environmental microbiology.

[20]  M. Zuker,et al.  OligoArray 2.0: design of oligonucleotide probes for DNA microarrays using a thermodynamic approach. , 2003, Nucleic acids research.

[21]  Darrell P. Chandler,et al.  Sequence versus Structure for the Direct Detection of 16S rRNA on Planar Oligonucleotide Microarrays , 2003, Applied and Environmental Microbiology.

[22]  Gabrielle Prefontaine,et al.  Rapid Identification of Escherichia coli Pathotypes by Virulence Gene Detection with DNA Microarrays , 2003, Journal of Clinical Microbiology.

[23]  D. Stahl,et al.  Direct Profiling of Environmental Microbial Populations by Thermal Dissociation Analysis of Native rRNAs Hybridized to Oligonucleotide Microarrays , 2003, Applied and Environmental Microbiology.

[24]  Rudolf Amann,et al.  Optimization Strategies for DNA Microarray-Based Detection of Bacteria with 16S rRNA-Targeting Oligonucleotide Probes , 2003, Applied and Environmental Microbiology.

[25]  B. Pettitt,et al.  Surface electrostatic effects in oligonucleotide microarrays: control and optimization of binding thermodynamics. , 2003, Biopolymers.

[26]  B. Ward,et al.  Oligonucleotide Microarray for the Study of Functional Gene Diversity in the Nitrogen Cycle in the Environment , 2003, Applied and Environmental Microbiology.

[27]  J. Fleming,et al.  Fingerprinting of prokaryotic 16S rRNA genes using oligodeoxyribonucleotide microarrays and virtual hybridization. , 2003, Nucleic acids research.

[28]  G. Churchill.  Fundamentals of experimental design for cDNA microarrays , 2002, Nature Genetics.

[29]  P. Riccelli,et al.  Melting studies of dangling-ended DNA hairpins: effects of end length, loop sequence and biotinylation of loop bases. , 2002, Nucleic acids research.

[30]  D. Stahl,et al.  Parallel Characterization of Anaerobic Toluene- and Ethylbenzene-Degrading Microbial Consortia by PCR-Denaturing Gradient Gel Electrophoresis, RNA-DNA Membrane Hybridization, and DNA Microarray Technology , 2002, Applied and Environmental Microbiology.

[31]  Zuhong Lu,et al.  Label-free hybridization detection of a single nucleotide mismatch by immobilization of molecular beacons on an agarose film. , 2002, Nucleic acids research.

[32]  G L Andersen,et al.  Sequence-specific identification of 18 pathogenic microorganisms using microarray technology. , 2002, Molecular and cellular probes.

[33]  R. Shippy,et al.  An assessment of Motorola CodeLink microarray performance for gene expression profiling applications. , 2002, Nucleic acids research.

[34]  John J. Kelly,et al.  Single-Base-Pair Discrimination of Terminal Mismatches by Using Oligonucleotide Microarrays and Neural Network Analyses , 2002, Applied and Environmental Microbiology.

[35]  E. Leproust,et al.  A flexible light-directed DNA chip synthesis gated by deprotection using solution photogenerated acids. , 2001, Nucleic acids research.

[36]  F. Brockman,et al.  Direct Detection of 16S rRNA in Soil Extracts by Using Oligonucleotide Microarrays , 2001, Applied and Environmental Microbiology.

[37]  Jiasen Lu,et al.  Assessment of the sensitivity and specificity of oligonucleotide (50mer) microarrays. , 2000, Nucleic acids research.

[38]  A. Vologodskii,et al.  The kinetics of oligonucleotide replacements. , 2000, Journal of molecular biology.

[39]  E. Southern,et al.  Molecular interactions on microarrays , 1999, Nature Genetics.

[40]  R. Blake,et al.  Thermodynamic effects of formamide on DNA stability. , 1996, Nucleic acids research.

[41]  K U Mir,et al.  Arrays of complementary oligonucleotides for analysing the hybridisation behaviour of nucleic acids. , 1994, Nucleic acids research.

[42]  A. Thiel,et al.  Direct fluorescence analysis of genetic polymorphisms by hybridization with oligonucleotide arrays on glass supports. , 1994, Nucleic acids research.

[43]  D. Lane.  16S/23S rRNA sequencing , 1991 .

[44]  J. Hartley,et al.  Use of uracil DNA glycosylase to control carry-over contamination in polymerase chain reactions. , 1990, Gene.