SEED/2008/Day 4

Morning

 * Set up 50ul PCRs with 2 different forward RBS primers
 * 5ul 10x NovaTaq Buffer with MgCl2
 * 1ul dNTP mix (10mM each dNTP)
 * 1ul reverse primer (VR)
 * 1ul RBS specific forward primer
 * 0.25ul NovaTaq DNA polymerase
 * 0.5ul DNA template of E0050 (10ng)
 * rest PCR grade water
 * Cycle 30 times
 * 30s@94C
 * 30s@55C
 * 1m@72C
 * Pour gel

Afternoon

 * Run plasmid digest and PCRs on gel
 * Cut out bands and save in freezer

Lecture

 * Review units
 * Volume (L)
 * Mass (g)
 * Moles (mol)
 * Molecular weight (Da)
 * Concentration
 * % w/v (e.g. 1% agarose)
 * % v/v (e.g. 70% ethanol)
 * mass/volume (e.g. ng/ul)
 * molarity (e.g. 1M NaCl)
 * factors (e.g. 10x buffer)
 * Prefixes (milli, micro, nano, pico)
 * PCR discussion
 * What is Synthetic Biology?
 * Tie in Comic
 * General, Very High Level Methods (Standardization, Abstraction, Encapsulation)
 * General hierarchy (Parts, Devices, Systems)
 * Rational Design from Ground Up
 * Why should we care?
 * Project Ideas Homework Discussion
 * Environment, Energy, Medicine, Materials, Chemicals, Computing
 * Understanding of Regulation, Function, Design (Minimal systems)

Instructor Preparation

 * Oligos
 * VR: attaccgcctttgagtgagc
 * B0030.E0040-F: gaattctctagagattaaagaggagaaatactagatgcgtaaaggagaagaacttttc
 * B0031.E0040-F: gaattctctagagtcacacaggaaacctactagatgcgtaaaggagaagaacttttc
 * B0032.E0040-F: gaattctctagagtcacacaggaaagtactagatgcgtaaaggagaagaacttttc
 * B0033.E0040-F: gaattctctagagtcacacaggactactagatgcgtaaaggagaagaacttttc
 * B0034.E0040-F: gaattctctagagaaagaggagaaatactagatgcgtaaaggagaagaacttttc
 * B0035.E0040-F: gaattctctagagattaaagaggagaatactagatgcgtaaaggagaagaacttttc
 * Pairs of RBS primers to assign to groups (selected based on estimated strength):
 * B0030 & B0032
 * B0031 & B0035
 * B0033 & B0034
 * B0032 & B0033
 * B0031 & B0034
 * B0030 & B0035