WEEK 4 Flashcards
What are SNPs?
- Single Nucleotide Polymorphisms
- SIMPLEST variant of a DNA sequence is one base pair difference between two alleles
What can SNPs change in the restriction enzyme behaviour?
- The ability for it to cut the surrounding sequence
What is a Restriction Fragment Length Polymorphism?
- Method used to detect small differences (SNPs) by using a restriction enzyme to cut sequence and seeing where it cuts or doesn’t cut
How do we detect RFLP?
- Using PCR from genomic DNA followed by restriction enzyme digestion –> Design primers to then carry out the polymorphism chain reaction.
What is a limitation of RFLP?
- Not every SNP you’re interested in will cut a restriction enzyme site!
What are two methods to detect SNPs that do not cause changes in restriction sites?
- Allele specific oligonucleotide hybridisation (you can identify a SNP in ANY part of the genome
- Allele specific PCR
Why are SNPs good for mapping?
- They are VERY COMMON in the genome
How often does the SNP occur?
- Every 1000 bp in the genome –> Human genome = 3 000 000 kbp so about 3 million SNPs
What is a limitation of SNPs?
- Each SNP occurs as ONLY 2 alleles! and the second category of DNA sequence polymorphism has MANY alleles
What are micro and mini satellites?
- Short DNA sequences that occur in a VARIABLE number of tandem repeats in a genome
What does the number of micro and mini satellite repeats vary between?
- Varies between INDIVIDUALS AND between the two chromosomes in individual
What is a micro-satellite (short tandem repeat, STR) defined as?
- 2-10 base pair repeat of a DNA sequence
What is a mini-satellite (Or Variable Number of Tandem Repeats, VNTR) defined as?
- 10-100 base pair repeat of a DNA sequence
How are mini-satellites and micro-satellites detected?
- Old fashion way= Southern Hybridisation using the repeat sequence as a probe
- New cool way= PCR using sequences on each side of the repeat as primers
What are the satellite alleles inheritance?
- Co-dominant
How often do satellite markers occur?
- Once every 10 000 bp so 300 000 satellite loci
What 3 areas are satellite markers used in due to the many alleles they have (number of repeats) and high level of polymorphism?
- DNA profiling and forensic genetics
- High resolution genetic mapping
- Ecological genetics and conservation biology
In mapping with DNA markers what does the ‘phase’ mean?
- Which alleles are together (eg. A1+B1)
What is the haplotype?
- the genotype for CLOSELY linked genes on a SINGLE chromosome
What are the benefits of genetic mapping?
- Can use to tell if a disorder is caused by one gene or by DIFFERENT genes
- Genes whose DNA sequence is not yet known (only its mutant phenotype) can be cloned from their map location
- Assists with identifying disease loci in combination with the whole exome/genome sequencing
- Nearby markers can be used as a tag of a desired gene in plant and animal breeding (marker assisted breeding)
- Closely linked DNA markers are useful in genetic counselling e..g Huntington disease
If a gene locus and a DNA marker locus are r map units apart, what is the probability that she has inherited the gene disease allele if she has inherited a SNP A4? (i.e. Formula)
1- (r/100)
What are three reasons why DNA fingerprinting and profiling are possible?
- genomic DNA sequence is stable (unless mutation)
- All cells in body have same DNA (unless mutation)
- DNA is UNIQUE (huge variation between individuals) –> humans have a lot of genetic diversity
How can DNA be detected from fingerprinting and how does it work?
- With mini satellite loci
- Digestion of genomic DNA with restriction enzyme and perform SOUTHERN BLOT
- Use a probe COMPLEMENTARY to the repeat to detect ALL repeat loci at ONCE
- fingerprint of bands will come up
Which technique is used to detect DNA from mini satellites?
- A southern blot