1. Chapter 14 Jizhong Zhou and Dorothea K. Thompson

4. Cont.,

9. complementary to both sense and antisense strands Two sets of probes - complementary to both sense and antisense strands of the target sequence. 8N probes Detecting all the substitutions in a target sequence with N base pairs, 8N probes are needed.

12. Gain-of-signal analysisLoss-of-signal analysis with two colors

18. Dideoxyribonucleotide triphosphates, labeled with different fluorescent dyes Probes are attached to the array surface via a 5’-linkage Hybridized with the probes on the microarrays Hybridized target sequences and oligonucleotide probes serve as templates Extension of primers for single-base Determined with a fluorescence microscope

21. Genotyping sequence variations, Single-base mismatch prevents ligation, A G/T mismatch at the 3’- end to be ligated inhibits the reaction by up to 1,000-fold.

26. desired gene fragment 1. Amplify the desired gene fragment from genomic DNA. PCR-based cloning methods 2. Recover the desired gene fragments from natural environments using PCR-based cloning methods. oligonucleotide probes 3. Use oligonucleotide probes. 0.85% Sequences that show 0.85% identity can be used as specific probes for FGAs.

29. Both pure cultures and soil community samples. Sensitivity of the 50-mer is 10 times < PCR based FGAs and 100 times < community genome arrays Genomic DNA from a pure culture of nirS Genomic DNA from surface soil

33. Membrane-based reverse sample genome probing, Membrane-based reverse sample genome probing, arraying substrate and signal detection strategies. Different from RSGP in terms of the arraying substrate and signal detection strategies. fabrication and fluorescence- based detection. Use nonporous surface for fabrication and fluorescence- based detection. Miniaturized microarray. Miniaturized microarray. Bacterial artificial chromosomes (BAC)- Bacterial artificial chromosomes (BAC)-based cloning approach.

36. SNPs the most frequent type of variation in the human genome and experimental organisms. Approaches for design probe and array for hybridization, SBE’s need and its types, Conventional detection limits, Functional and quantitative analysis of result, Other types of array.