Chapter 7 Analyzing DNA and gene structure, variation and expression. Sequencing and genotyping DNA Standard/manual DNA sequencing using dideoxynucleotide chain terminators ddATP, ddGTP, ddCTP, and ddTTP. . 07_01.jpg. 07_02.jpg. 07_02_2.jpg.
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- RSPs: single nucleotide polymorphism may cause a loss or gain in a restriction site generating an RSP. Used in identifying carriers for some disease causing genes.
- VNTR: use of PCR or Southern blot hybridization to identify differences in the number of microsatellite tandem repeats.
2. Identifying coding sequences (genes) in cloned DNA (e.g. libraries) and establishing their structure
-i- coding sequences are highly conserved
-ii- presence, in coding sequences, of open reading frames (ORFs).
-iii- vertebrate coding sequences are often associated with CpG islands.
-i- Exon trapping uses an artificial RNA splicing assay.
-ii- cDNA selection by heteroduplex formation using magnetic beads capture identifies expressed sequences in genomic clones.
-iii- To obtain full length cDNA of any gene, a cDNA library is screened using a probe (an oligonucleotide of the gene) and a set of overlapping truncated cDNA clones are produced. Then, RACE-PCR (rapid amplification of cDNA ends) is a technique used to extend the 5’ and/or 3’ ends of a short cDNA clone to onbtain a full length cDNA.
-iv- Mapping transcription start site could be achieved by S1 nuclease protection or primer extension.
3. Studying gene expression S1 nuclease protection or primer extension.