DNA, STRs, VNTRs - Forensic Bio Exam 2

What is the structural difference between DNA and RNA on the pentose sugar?

DNA - Hydrogen on the 2’ carbon

RNA - OH group on the 2’ carbon

How are the 3’ and 5’ ends of a DNA strand identified?

3’ - Includes the hydroxy (OH) group

5’ - Includes the phosphate group

What is the difference between purines and pyrimidies?

Purines - 2 rings

Pyrimidines - 1 ring

What are the purines and pyrimidines?

Purines: adenine and guanine

Pyrimidines: cytosine, thymine, and uracil

How many hydrogen bonds are there for A-T and G-C interactions?

A-T = 2 bonds

G-C = 3 bonds

What pair of chromosomes are referred to as hemizygous?

Sex chromosomes (x and y)

What regions are DNA markers used for human identification found in?

Noncoding regions

What are genetic polymorphisms?

Sites within the genome that vary

SNPs are ____________ polymorphisms while STRs and VNTRs are ____________ polymorphisms.

Sequence ; length

What is the only marker that is not intergenic and is used for sex typing?

Amelogenin

What are SNPs?

A section of the genome that changes

SNPs usually involve how many alleles?

2 (biallelic)

STRs usually involve how many base pairs?

2 - 6 (dimeric through hexameric)

The complexity of STRs is due to what factor?

How many times the motif repeats — NOT how complex the motif itself is

How long are SNPs compared to STRs (in base pairs)?

SNPs: 1 base pair

STRs: 2-30 base pairs

Are there more SNP sites or STR sites?

SNP (300,000,000 compared to 100,000 STR sites)

What loci were first used in identifying people with SNPs?

The DQA1 loci

What SNP genotyping reaction can multiplex up to 10 reactions at once?

SNAPSHOT

What SNP sequencing technology can analyze 1.2 million markers at the same time?

Illumina Infinium Assays

What is the problem with using multiple probes for SNP identification?

A large amount of probes creates more room for probe interaction → this causes dimers that don’t actually bind to their target

Which has a higher level of multiplex capability, SNPs or STRs?

SNPs

Which has a shorter PCR product length, SNPs or STRs?

SNPs

Which has almost no stutter in testing results, SNPs or STRs?

SNPs (have less artifacts)

We need __________ SNPs to equal the informativness of STRs.

More

Is it possible to sort mixtures when analyzing SNPs?

No

T/F: SNPs can help to narrow down a suspect pool based on phenotyping.

True

What are tandem repeats?

2 more more DNA base pairs or motifs that repeat in a way that is adjacent to each other

What are also referred to as minisatellites and microsatellites?

VNTR: minisatellite

STR: microsatellite

The repeat sequence of a VNTR is at least how many base pairs?

6

How many times does a VNTR repeat?

5 to 50

What’s larger, STRs or VNTRs?

VNTRs

In VNTRs, what differs between individuals: the motif or the number of repeats?

The number of repeats

What indicates a particular genotype based off of a VNTR?

A particular number of tandem repeats at a given locus

What is an RFLP?

Restriction Fragment Length Polymorphism

What was used in the first historical method for forensic DNA testing?

RFLPs and VNTRs

What is the function of an endonuclease?

To cut the core repeat region of a VNTR

What is an important part of what’s contained within specific probes?

Complementary sequence of the fragment of DNA that the probe detects for

What does the single-locus probe technique create?

A DNA profile from one mutation

What are the two types of probe detection for VNTRs?

Radioisotope labeling and enzyme-conjugated probes

What is the multi-locus probing technique?

Method that detects multiple VNTR loci at the same time

Many VNTRs contain a sequence rich in which base pairs?

G-C

What is the process of probe stripping?

DNA is denatured with heat to remove each probe — probes are added one at a time and removed before the next is added

What is the “bin” in terms of VNTR standardization?

The range of DNA fragments that differ by only a few repeating units

T/F: You can distinguish between two VNTRs that differ by only one or two repeating units.

False

T/F: Longer DNA sequences are more susceptible to degradation.

True

What is a DNA drop-out?

No allele is detected — no evidence of DNA on a gel, etc.

What is partial restriction digestion?

When the DNA is not fully cleaved

What is star activity?

When too much DNA is cleaved

What is partial stripping?

When a probe is not completely removed before the next probe is applied

What is the main problem that results from issues like probe stripping, partial restriction, star activity, etc.?

Individuals that are homozygous may look heterozygous due to these issues causing multiple different bands to form

What is band shifting?

When two samples from the same individual look different between different runs (based on temperature, etc.)

What is AFLP?

An RFLP modification that adds PCR (A = Amplification)

Where do STRs occur?

In between genes in the noncoding regions

What is the core repeat region and the flanking regions?

Core: Tandemly repeated sequences

Flanking: Conserved region surrounding the core

T/F: Flanking regions are always conserved.

True

What is the other 3-letter acronym for STRs?

SSR (Simple Sequence Repeat)

How many nucleotides are in each repeat of all 13 CODIS STR loci?

4 (Tetranucleotides)

What are the characteristics of simple repeats?

Contain units of identical length and sequence

What are the characteristics of compound repeats?

Comprised of two or more adjacent simple repeats

What are the characteristics of complex repeats?

Contain several repeat blocks of variable unit length

T/F: Two STR loci can be on the same chromosome.

True

T/F: The further away two loci are on a chromosome, the less related they are.

True