Final Exam Extra Material

DNA and Crime

What did Dr. Alec Jefferys figure out?

Dr. Alec Jeffreys developed DNA fingerprinting techniques that allow for the identification of individuals based on their unique DNA patterns, revolutionizing forensic science and genetic research. First using Restriction Fragment Length Polymorphisms (RFLP)

What is RFLP?

Restriction Fragment Length Polymorphism is a technique used to identify variations in DNA sequences by cutting DNA with specific enzymes and analyzing the resulting fragment lengths.

What is a restriction enzyme?

An enzyme produced chiefly by certain bacteria, having the property of cleaving DNA molecules at or near a specific sequence of bases.

Where do restriction enzymes cut a DNA molecule?

At the palindromic repeat of the specific gene.

How can a restriction site be protected from digestion?

By methylation of the bases at the restriction site, which prevents the enzyme from recognizing and cutting the DNA.

What is produced when the ALUl and Haelll genes are cut with restriction enzymes?

blunt ends are formed

What is produced when the BAmHI, HindIII, and EcoRI genes are cut with restriction enzymes?

Sticky ends are formed which are overlapping.

What is the first step of RFLP?

Isolate DNA samples from samples from the crime scene and suspects

What is the second step of RFLP?

Treat DNA with Restriction Enzymes

What is the Third step of Restriction Fragment Length Polymorphism?

Label DNA with radioactive markers

What is the fourth step of RFLP?

Electrophorese labeled DNA

What is the Fifth step of RFLP?

Expose to X-ray film

Other than DNA fingerprinting in forensics, what is RFLP used for?

Paternity tests.

What did Dr. Alec JEffereys discover as a more efficient way to determine DNA other than RFLP?

Variable Number Tandem Repeat or VNTR

What is VNTR?

A method of analyzing DNA that focuses on variations in the number of tandemly repeated sequences (minisatellites), useful in genetic profiling and paternity testing.

What are the similarities between RFLP and VNTR?

• Isolate DNA from Sample a

• Electrophorese

How do RFLP and VNTR differentiate in signal formation?

RFLP uses restriction enzymes to cut the DNA. VNTR uses specific primers to access regions of interest using PCR.

In RFLP what yields different band patterns?

The number of specific cut sites in DNA

In VNTR what yields different band patterns?

The number of tandem repeat units.

Why is VNTR more effective than RFLP?

We can use PCR to increase the amount of DNA in VNTR versus RFLP whcih requires a lot of DNA, making it take longer and be much more expensive.

In forensics what is DNA fingerprointing used for?

Most often to exclude someone from a crime

In a DNA tree what is a standard?

A reference sample used to compare genetic data and determine relationships between individuals.

What is a ladder in a DNA tree?

A set of known size markers used to determine the size of DNA fragments in a gel electrophoresis.

If there is one restriction site, then …

There will be two bands after gel electrophoresis.

If there is no restriction site, then …

There will be one band after gel electrophoresis.

If there is two restriction site, then …

There will be three bands after gel electrophoresis.

Who was the first man ever exonerated based on DNA evidence?

Richard Buckland

Who was the first person convicted with DNA evidence in the USA?

Tommy Lee Andrews

What is the STR?

Short Tandem Repeat, a type of DNA sequence used in forensic analysis and genetic profiling. It measures the exact number of repeats in the amplified region.

What is an analysis that is a common method in molecular biology which is used to compare specific loci on DNA from two or more samples. A short tandem repeat is a microsatellite, consisting of a unit of two to thirteen nucleotides repeated several dozen times in a row on the DNA strand?

Short Tandem Repeats

How is an STR formed?

Through strand slippaged by misaligning repeat STRS which ill result in an addition or deletion from the repeats (Microsatellites)

What is the first step of STR?

Isolate DNA samples from crime scene and suspects

What is the second step of STR?

Amplify the isolated DNA using PCR

What is the third step of STR?

Label the DNA fragments with fluorescent dyes before separating them by size using gel electrophoresis.

What is the fourth step of STR?

Capillary electrophoresis is used to separate the labeled DNA fragments based on size and then analyze them.

What is the fifth step of STR?

The final step is to interpret the DNA profiles to match samples and identify individuals using laser detection.

If one peak appears on an STR the individual is …

homozygous for that allele.

If two peaks appear on an STR the individual is …

heterozygous for that allele.

If three or more peaks appear on an STR the individual is …

the sample is tainted and contains at least one other person, possibly more

What is the repeat length in VNTR and STR?

VNTR repeats are 10-100 bp in length, STR repeats are 2-6 bp in length

What is the DNA sequence length in VNTR and STR?

VNTR sequences are between 50 - 5000 bp in length. STRsequences are generally less than 500bp in length.

What type of DNA are VNTR and STR found?

VNTR is often found in heterochromatin. STR is often found in euchromatin although it does occur all over the genome.

What are the benefits of STR?

It lends very well to PCR, with the number of repeats being highly variable. In addition the small size allows separation from other areas of the chromosome resulting in quicker results. These are microsatellites.

What are the down sides of VNTR?

It can be cumbersome and time consumeing, making it hard to tell lots of alleles apart. These repeats tend to occur at the end of chromosomes and require a lot of DNA. They are made of minisatellites.

What is CODIS?

CODIS is the FBI's Combined DNA Index System, which allows for the storage and comparison of DNA profiles from crime scenes and convicted offenders to help solve crimes.

How many loci are used in the CODIS system?

CODIS uses 13 core loci for DNA profiling and 7 recently added loci, which enables comparison and matching between DNA samples.

What is the probability of two people matching the DNA if 13 loci are used in CODIS?

1 in huundreds of billiions

What three methods of STR data are collected and stored in CODIS?

Whole Genome STR, Y-STR, and Mitochondrial mt-STR

When looking at the amel (amelogenin) STR which is on the sex chromosome what differentiates male from female?

The presence of one peak on an STR reading indicated female and the presence of two peaks indicates male.

What is the first step to how CODIS works?

Collect DNA Evidence

What is the second step to how CODIS works?

Generate DNA profile

What is the third step to how CODIS works?

Submit Profile to CODIS

What is the fourth step to how CODIS works?

Search Indices for Match

What is a Partial CODIS match?

A situation where a submitted DNA profile does not match completely, but shares enough similarities with another profile to suggest a possible connection or relationship. (Familial Heritage)

What is the purpose of Y-STR?

To analyze male DNA and trace paternal lineage through specific regions of the Y chromosome. Allowing law enforcement to reduce the suspect pool by 50% and identify male relatives.

What is the purpose of mt-STR?

To analyze the lineage of an individual from the mothers side and identify possible suspects with the use of ancestory DNA test.

Who did DNA profiles from ancestry website help identify?

The Golden State Killer, Joseph DeAngelo, through familial DNA matching.

What is PARABON DNA phenotyping?

A process that predicts physical appearance and ancestry based on DNA, aiding law enforcement in identifying suspects. Using the SNPs that have been discovered (about 100,000 of them)

What is an SNP?

Single nucleotide polymorphism, a variation at a single base pair in DNA. This is the most common type of genetic variation found in humans, is almost always biallelic, and one SNP may only occur in 1% of the population. This allows us to use them for markers of Genetic similarity.

What is Forensic DNA Phenotyping?

A technique used to predict physical characteristics of individuals from DNA samples, often employed in criminal investigations to help identify unknown perpetrators. Currently Eye, Skin, and Hair color are identified, while height, baldness, and age are being developed. This technology assists law enforcement in narrowing down suspects based on genetic factors.

What is the pitfall/exception to DNA phenotyping?

Individuals can artificially alter their appearance and there are legal issues with the idea of Biological witnesses.