How are areas of DNA that don’t code for proteins (genes) used by our cells? How can we make use of these areas?

Types of Non-coding DNA (DNA base sequences that do not code for proteins)

Not Just “Junk” DNA - New York Times (9/5/12) http://www.nytimes.com/2012/09/06/science/far-from-junk-dna-dark-matter-proves-crucial-to-health.html?_r=0 ENCODE Nature Database: http://www.nature.com/encode/

Polymorphism Definition: variations in form Polymorphisms can be single bases or thousands of bases Polymorphism may or may not have physical (phenotypic) effects on an organism Single Nucleotide Polymorphism (SNP): differences in single nucleotides

Short Tandem Repeats (STRs) STR: short sequence of DNA (2-8 bps) that is repeated over and over ; occur in multiple regions of one person’s DNA People differ in the NUMBER of STR REPEATS ; differences in repeats used for identifying or comparing individuals (i.e. DNA FINGERPRINTING) Also called “microsatellites”

How can we use STRs to do “DNA Fingerprinting or DNA Profiling”? DNA Fingerprinting: a general method for identifying individuals based on their DNA (specifically through the use of STRs) Involves three smaller lab procedures: DNA Extraction Polymerase Chain Reaction (PCR) Gel Electrophoresis

Polymerase Chain Reaction (PCR) Purpose: to “amplify” DNA Procedure uses a machine called a “thermocycler” to quickly make LOTS of copies of DNA PCR – Interactive Lab http://learn.genetics.utah.edu/content/labs/pcr/

Polymerase Chain Reaction (PCR) 1. Denaturing DNA 2. Primer Annealing 3. Extension

What are 4 differences between DNA Replication and PCR? Similarities? Place for DNA polymerase to attach to DNA strand RNA primers DNA primers Separates the two strands of DNA Helicase Heat Name of enzyme that elongates new strand of DNA DNA polymerase Taq or other thermophillic DNA polymerase What the primers are made out of (DNA or RNA?) RNA DNA Products Leading & Lagging Strand – Okazaki Fragments NO Leading & Lagging Strand – NO Okazaki Fragments Items that are common in both situations that has not already been mentioned. Nucleotides are needed for elongation, some enzyme to bring nucleotides, DNA serves as template for new strand

DNA Fingerprinting using Gel Electrophoresis After DNA is amplified: Treat DNA with Restriction Enzymes -cut DNA at specific sequences (between STRs) Results in different sized fragments due the variation in size of STRs between individuals Fragments are color dyed, then loaded into a agarose gel which is powered by an electrical source Run electric current through gel and DNA fragments move along agarose gel resulting in “banding patterns” Banding patterns are used to identify individuals

DNA Restriction Enzymes • Evolved by bacteria to protect against viral DNA infection •

Enzyme Site Recognition • Each enzyme digests (cuts) DNA at a specific sequence = restriction site • Restriction site Palindrome Fragment 2 Fragment 1

Gel Electrophoresis: Setup Electrical current carries negatively-charged DNA through gel towards positive (red) electrode

Gel Electrophoresis Results: Smaller bands move farther on gel. Ladder used to measure the number of base pairs that make up each band.

DNA Fingerprinting for Paternity Tests

DNA in the News : Solving Mysteries with DNA Profiling http://genetics.thetech.org/original_news/news16 http://www.nature.com/bmt/journal/v29/n3/full/1703360a.html