From: Duggan et.al. Nature Genetics 21:10-14, 1999 Microarray-Based Assays (The Basics) Each feature or “spot” represents a specific expressed gene (mRNA). The fluorescent intensity of each feature correlates with the expression level of the gene (mRNA) in the samples under investigation.

The Key to Nucleic Acid Detection is “Sequence-Specific Affinity” CAGTAACGGTTCAGTAACGGTT 5’ 3’ GTCATTGCCAAGTCATTGCCAA 5’ 3’ “GC” content (base paring) generally dictates thermodynamics of complementary binding. Tm = Melting Temperature Microarray-Based Assays (The Basics)

“PROBE” is DNA spotted (attached) to the solid substrate (non-fluorescent glass slide). “TARGET” is the fluorescence labeled cDNA representation of the mRNA and is hybridized to the probe. Microarray-Based Assays (The Basics)

384-well plate Microarray Production Microarray Imaging Microarray Hybridization Microarray Raw Data Analysis Microarray Statistical Data Analysis Biological Samples

Microarray Oligonucleotide Probe Design System Experimental Assessment of DNA Binding BehaviorExperimental Assessment of DNA Binding Behavior Design and ImplementationDesign and Implementation

1) AGCCCGATGATGAGCGACTCACCACGGGCCACGGCTTCTGACTCTCTTT0 2) AGCCCGATGATGAGCGACTCACCAGGGGCCACGGCTTCTGACTCTCTTT1 3) AGCCCGATGATGAGCCACTCACCACGGGCCAGGGCTTCTGACTCTCTTT2 4) AGCCCGATGATCAGCGACTCACCTCGGGCCACGGCATCTGACTCTCTTT3 5) AGCCCCATGATCAGCGAGTCACCTCGGGCCACGCCTTCTGACTCTCTTT5 Normalized Target/Probe Microarray Oligonucleotide Probes 32  C 42  C 52  C Assessment of Sequence-Specific Cross-Reactivity/Cross-Hybridization Microarray Oligonucleotide ProbesMismatched Base Pairs Kane, MD et. al. Gene Cloning and Expression Technologies (2002) Ch. 35:

yicK cDNA yabM cDNA yeiO cDNA Yick_337 Yick_884 Yick_GAP Yeio_997 Yeio_469 Yeio_GAP Yabm_392 Yabm_552 Yabm_GAP A. B. Assessment of Sequence-Specific Cross-Reactivity/Cross-Hybridization Kane, MD et. al. Nucleic Acids Res. (2000) 28:

80% Overall Homology (Cross-hybridization detected); Yick_337 gcgtacttctgagtagttttgcttccaccgcaaacccgcaaatgttcgcc |||| |||| || || |||| || ||||| |||||||||||||| ||| yeiO 335 gcgtctttcttagcagctttggctcgaccgctaacccgcaaatgtttgcc 74% Overall Homology (No cross-hybridization detected); yicK 471 gttatcgggccaccgctcgcttatgaactggcaatgggatttagttttaa || || || |||||||| ||||||| | || ||||| || || |||| Yeio_469 gtcattggcccaccgctggcttatgccttagcgatgggtttcagctttac 14 Nucleotides; 6 (42%) GC 8 Nucleotides; 6 (75%) GC A. B. Assessment of Sequence-Specific Cross-Reactivity/Cross-Hybridization Kane, MD et. al. Nucleic Acids Res. (2000) 28:

Probe Pair “variable region” DAP Overlap w/ Conserved Region “conserved regions” DAP  Assessment of Sequence-Specific Cross-Reactivity/Cross-Hybridization Kane, MD et. al. Nucleic Acids Res. (2000) 28:

Length of Complementary Base Pairing with DAP  cDNA DAP  cDNA Signal (Cy3) DAP cDNA Signal (Cy5) Assessment of Sequence-Specific Cross-Reactivity/Cross-Hybridization Kane, MD et. al. Nucleic Acids Res. (2000) 28:

Length of Continuous Complementary Base Pairing with Non-Target (DAP  ) cDNA Ratio of Target Signal (DAP) to Non-Target Signal (DAP  ) Ratio of Target/Non-Target Cross-Hybridization Kane, MD et. al. Nucleic Acids Res. (2000) 28: Assessment of Sequence-Specific Cross-Reactivity/Cross-Hybridization

Microarray Oligonucleotide Probe Design System Experimental Assessment of DNA Binding BehaviorExperimental Assessment of DNA Binding Behavior Design and ImplementationDesign and Implementation

Microarray Oligonucleotide Probe Design System Objective: Computationally Design Gene-Specific Microarray Probes Commercial Objective: Produce and Sell Pre-Printed Oligo-Probe Microarrays Remove Redundant Entries Confirm RNA vs. Genomic DNA Confirm Species Selection on Each Gene Identify Longest mRNA Identify Splice/Isoform Variants (Segments) Contigs Used to Increase EST Sequence Quality Sequence QC Target Gene List Obtain Sequence Info Genomic Sequence Database Data Flow

Microarray Oligonucleotide Probe Design System AGAAGAAGCCGATGATGACGAGGACGATGAGGATGGTGATGAGGTAGAGGAAGAGGCTGAGGAACCCTAC… Sequence QC Target Gene List Obtain Sequence Info Genomic Sequence Database Probe Design Oligonucleotide Probe Length = bases

Microarray Oligonucleotide Probe Design System 1)Accept if GC content range = 40%-60% 2)Reject 4 or more contiguous bases of G or C (2ndary Structure) 3)Reject palindromic-hairpin sequences greater than 7 bases (2ndary Structure) 4)Reject known splice site sequences 5)Accepted if Calculated Tm = 52.4  C ± 4.0  C 6)No more than 75% homology within the target region of non-target genes. 7)No more than 14 contiguous base pairs with non-target genes. AGAGCACGCGGAGGAGCGTGCGCGGGGGCCCCGGGAGACGGCGGCGGTGGCGGCGCGGGCAGAGCAAGGA… 46 bases 82.6% GC (failure) >4 cont. G or C (failure) AGAAGAAGCCGATGATGACGAGGACGATGAGGATGGTGATGAGGTAGAGGAAGAGGCTGAGGAACCCTAC… 46 bases 54.3% GC Sequence QC Target Gene List Obtain Sequence Info Genomic Sequence Database Probe Design Primary Probe Evaluation

Microarray Oligonucleotide Probe Design System 1)Accept if GC content range = 40%-60% 2)Reject 4 or more contiguous bases of G or C (2ndary Structure) 3)Reject palindromic-hairpin sequences greater than 7 bases (2ndary Structure) 4)Reject known splice site sequences 5)Accept if Calculated Tm = 52.4  C ± 4.0  C 6)No more than 75% homology within the target region of non-target genes. 7)No more than 14 contiguous base pairs with non-target genes. Basic Local Alignment Search Tool (BLAST) against published sequences in target species. Parse BLAST Output Accept/Reject Candidate Probe Sequence QC Target Gene List Obtain Sequence Info Genomic Sequence Database Probe Design Primary Probe Eval Secondary Probe Evaluation

Microarray Oligonucleotide Probe Design System Target Gene List Sequence QC DNA Sequences Redundant Entries Wrong Species Probe Design High Quality mRNA Primary Probe Evaluation Secondary Probe Evaluation GC Rich/Poor 2ndary Structure Known Splice Site Cross-Hybridization Potential Rank Acceptable Probes Optimal Probes: Nearest to Desired Tm Probe Annotated: GInumber_start_length Obtain Sequence Info Genomic Sequence Database

Microarray Oligonucleotide Probe Design System Target Gene List Sequence QC Probe Design Primary Probe Evaluation Secondary Probe Evaluation Rank Acceptable Probes Obtain Sequence Info Genomic Sequence Database Desk Top PC 500 mhz 512 meg RAM Dedicated PC 1 ghz 1 gig RAM SYSTEM PERFORMANCE X  50 genes/hour generating 2 probes for each target gene (mRNA). File-Based Communication

Number of Spots Spot Size Replicates MICROARRAY SPOTTER Solid Substrate (slide) Functional Surface Chemistry DNA Probes Oligonucleotide Probes cDNA (PCR) Probes Design Synthesis Purification Clones Amplification Purification DNA Microarrays Record File (.gal file) Processing Chemistry Storage Delivery Pre-Hybridization Chemistry HYBRIDIZATION IMAGING Raw Data Image (.tif file) Gene Specific Data Biological/Bioinformatics Analysis Time, Temp, Buffers, Wash Resolution, Region of Interest Raw Data Analysis Spot Finding, Background Subtraction, Signal Intensity, Normalization Sample Control Sample Test Sample RNA Isolation RT (Fluorescence) Labeling STUDY DESIGN and OBJECTIVES