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Sequences and their Properties
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Nucleotides DNA A, T, G, C RNA A, U, G, C
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Annealing Two opposing forces affect annealing
Nucleic acids can base pair with their reverse complement sequence Two opposing forces affect annealing Hydrogen bonds favours annealing Phosphate groups favours denaturation
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Annealing-Melting Point (Tm)
The Tm is the temperature at which 50% of the nucleic acid molecules are in a single stranded state (or double stranded) The Tm is a function of: Percentage G:C Ionic composition of the environment The percentage of complementarity Estimate of Tm for oligos =2(#A:T) + 4(#G:C)
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Tm Vs percentage G:C % Double stranded Temperature (C) (38%) G+C (52%)
50 100 (38%) G+C (52%) (58%) (66%) % Double stranded Temperature (C)
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Tm Vs Conc. of Positive Ions
(0.1M NaCl) 50 100 (0.2M NaCl) (0.5M NaCl) % Double stranded Temperature (C)
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Tm Vs percentage of Complementarity
(25%) 50 100 (50%) (100%) % Double stranded Temperature (C)
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Stringency Percentage of complementarity required to allow the formation of stable duplexes The Tm influences the stringency conditions required to allow annealing A high stringency requires a high level of complementarity GATCCGGTTATTA vs GATCCGGTTATTA CTAGGCCAATAAT CTTGGACGATAAT
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Parameters that Influence Stringency
[salt] = High stringency Temperature = High stringency [salt] = ? Temperature = ?
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Hybridization Stringency
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Genetics and Biometrics
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Definitions Locus Gene
The position of a coding or non coding genetic element Gene All the nucleotide elements required for the expression of a transcript Promoter, ORF, introns, exons, etc.
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Genetic Definitions (Cont’d)
Allele Version of a genetic element at a given locus Everyone necessarily has two alleles for each genomic locus The two alleles may be the same Homozygotes The two alleles may be different Heterozygote A population of individuals may have multiple alleles of a genomic locus
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Genetic Definitions (Cont’d)
Genotype: Nucleic acid sequence responsable for the phenotype Physical detection by molecular techniques Phenotype: Trait that can be distinguished resulting from a genotype Several different genotypes may have the same phenotype
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The Differences Between individuals of the same sex
<0.5% Between humans and chimpanzes <2%
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Molecular Markers Characteristics of the nucleotide sequence
The phenotype often corressponds to a specific genotype Restriction polymorphisms (RFLP) Length polymorphisms (VNTR) Variable number of tandem repeats Single nucleotide polymorphisms (SNP)
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Length Polymorphisms - RFLP
Based on the presence or absence of a restriction site at a given poistion Ex. The enzyme EcoR1 recognizes and cleaves the sequence: GAATTC A single base mutation abolishes the site GAGTTC
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Detection of Genomic RFLP
1 2 Polymorphism A B E A+B * E Genome 1 Genome 2 2 possible phenotypes 2 alleles can be distinguished Several possible genotypes 18
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Detection of RFLP by PCR
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Length Polymorphisms Minisatellites and Microsatellites:
Sequences repeated in tandem Highly variable number of repetitions between individuals; thus several alleles Length polymorphisms Molecular phenotype=Genotype Minisatellites Low distribution throughout the genome Mostly found within telomeres Microsatellites: High distribution throughout the genome VNTR
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Length polymorphisms - VNTRs
The number of repetitions = different lengths = different alleles = different genotypes = different molecular phenotypes
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Length Polymorphisms - VNTR
DNA Region where tandem copies of di-, tri- or tetra repeated units are located Examples: Dinucleotide repeat GTGTGTGTGTGT…… Trinucléotide repeat ACGACGACGACG…… Tetranucléotide repeat TATCTATCTATC……
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VNTR (Cont’d) Highly variable number of repetitions individuals
Thus several alleles within a population CA Allele 1 Allele 2 Allele 3 Different fragment lengths would be generated by a digestion at the indicated positions
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Detection of VNTR by PCR
AGCTGCTTAATGCTGCTGCTGCTGCTGCTGCATAACATTGC Individual 1 AGCGGCTTAATGCTGCTGCATAACATTGC Individual 2 1 2 Amplification & gel separation 24
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Biometrics
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VNTR Profile From whom does the blood come from? 26
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VNTR Profile Bob Luc Paul Tom Marc Who is Bob’s father? 27
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Determing number of loci
Determine both extremes In this case 8 and 13 Dertermine max and min for each extreme In the case of 8: max 8, min 4 In the case of 13: max 13, min 7 Determine range 7-8 loci What is maximum number of homozygous loci if number of bands is 13?
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