PCR Puzzle Class instructions

Start of lesson Have the following at front of the class: Template

Start of lesson continued Primers Bases

Correct base pairing is critical! Green (Guanine) pairs with yellow (Cytosine) Blue (Adenine) pairs with orange (Thymine)

The devil is in the detail! The 5’ prime and 3’ prime ends of the bases must be round the right way!

Cycle 1 - denature Spilt class in 4 pairs or groups of students Each group will copy one STRAND from the template Thus, it is important to think of a template as two strands rather than one double stranded piece of DNA

Cycle 1 - denature Two groups will do the first cycle Give Group 1 one template strand Give Group 2 the other template strand

Students comes to front to get primer One student from each group comes to front of class to get primer

Students comes to front to get primer If they have double orange in their template, pick one double blue primer The other group takes one green-blue primer

Cycle 1 - Anneal primer Each group adds primer to the template Make sure 5’ to 3’ prime is correct!

Cycle 1 - extend Students take bases required to finish strand And add the bases to complete the copy

Cycle 1 - observations When finished filling in blanks, each group brings product to front of class and put on desk or floor

Cycle 1 - observations Make observations: – How many copies do you get? – How many are just the target sequence (ie begin and end with primers)?

Cycle 2 - denature Groups 1 to 4 will do Cycle 2 Give each group a strand:

Cycle 2 – Anneal primer Each group adds appropriate primer to the template strand Make sure 5’ to 3’ prime correct way round!

Cycle 2 - extend Students take it in turns to come to front to take matching base to add to template

Cycle 2 - observations When finished filling in blanks, each group brings product to front of class and put on desk or floor

Cycle 2 - observations Make observations: – How many copies do you get? – How many are just the target sequence (ie begin and end with primers)?

Cycle 3 - denature Groups 1 to 4 will do Cycle 3 Give each group two strands:

Cycle 3 – Anneal primer Each group adds appropriate primer to the template strand Make sure 5’ to 3’ prime correct way round!

Cycle 3 - extend Students take it in turns to come to front to take matching base to add to template

Cycle 3 - observations When finished filling in blanks, each group brings product to front of class and put on desk or floor

Cycle 3 - observations How many copies do you get? How many are just the target sequence (ie begin and end with primers)? What if anything, has happened to the template? How many bases with red, black and white do you now have?