DNA+polymorphism+notes+08 - DNA Polymorphisms J.L Marsh...

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DNA Polymorphisms J.L. Marsh 137B 11/21/08 Page 1 A] polymorphism = A DIFFERENCE IN DNA SEQUENCE BETWEEN TWO HOMOLOGS - the difference MAY AFFECT FUNCTION - eg. Thallassemias etc - or MAY NOT ALTER FUNCTION IN ANY WAY -in intron - Near but not in a gene (CLOSELY LINKED) - in 5' or 3' UT - in synonymous codons B] 2 Classes of polymorphisms 1] Single Base changes aka SNPs (including short deletions or insertions) These can be detected by 1] effect on Rest Enzyme cutting = RFLPs 2] hybridization = ASOs microarrays etc 3] Sequencing These are Binary (yes or no) 2] changes in repeat number Terms = HVR/ VNTR or MINI SATELLITES HyperVariable Repeats, Variable Number of Tandem Repeats Can be detected by 1] PCR w/ flanking unique primers (detect individual repeats) 2] Southern blotting (detect whole family at once) C] PCR = Polymerase Chain Reaction = a means of amplifying small regions of DNA many many times
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DNA Polymorphisms J.L. Marsh 137B 11/21/08 Page 2 RFLPs = Restriction Fragment Length Polymorphisms Degree of linkage is a continuum = f(location of RFLPvsMut) map units can = 0 --> 50mu linkage thus = 100% -->0% CASE I = mutation causing disease also changes restriction site. Then linkage = 100% -LUCK that mutation falls in restriction site -MstII site = CCTNAGG @ codon 6 of Hb ß Normal = 1.15 & 0.2 Mutant = 1.35kb aa5 6 7 Pro Glu Glu CCT NAG G CCT|GAG|GAG T = HbS = 1.35 Val A Lys = HbC -100% linkage BUT HbC causes a disease but does not change a restriction site CASE II restriction site change near disease Informativeness = function of 1] distance to mutation 2] freq of RFLP in gen pop If the RFLP is very frequent (e.g. like Blue/Brown eyes) the level of usefulness is lowered (not zero but lower) EXAMPLE 4kb 3.5 2.5 1 4kb 1.5 2.5 1 2 H3 = AAGCTT AAGCTT AAGCTT AAGCTA DNA HAPLOTYPE = Allele 1 AAGCTT DNA HAPLOTYPE =
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This note was uploaded on 12/13/2011 for the course BIOSCI 137 taught by Professor Staff during the Fall '11 term at UC Irvine.

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DNA+polymorphism+notes+08 - DNA Polymorphisms J.L Marsh...

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