Stanford/BIOE44:Module 3:Day1: Difference between revisions

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==Getting Started==


===Useful tools===
===Useful tools===

Revision as of 10:30, 27 April 2010

Home        People        Schedule        Key Info.        OWW Basics       
DNA Engineering        Devices        Synthesis        Baking        Testing

M2: Day 1 - What to measure?

Introduction

Your primary goal today is to identify an environmental pollutant that can be via a genetically encoded sensor. Your goal is to be able to specific the standardized DNA encoding your new sensor by 3p this Thursday, so that we can place the DNA synthesis orders at that time. Overall, you should design a device that receives as input an environmental pollutant and that produces a PoPS signal as output (so that your sensor device can be connected to one or more PoPS-based color generators). Please consider today's class notes for starting hints and materials regarding environmental pollutants that might be worth detecting.

Reprise From Last Thursday

What happened with our gel extractions?

What did Isis do?

I had a hunch that the isopropanol step was messing up our gel extractions so I decided to test this. I also prepared some color generators and vectors.

  1. I digested 10ul K274003, K274100, K274200 with XbaI/PstI and K274220 (pSB2k3 vector) with EcoRI/PstI. This is roughly 2ug of DNA for each.
  2. For K274003 (this is what I used to test the gel extractions) I separated the digestion into 3 wells on a gel. The other digests each got their own well. (0.8% agarose)
  3. I cut out each band and gel extracted with and without isopropanol for the K274003 pieces. The rest were extracted with a Zymo kit.
  4. After extraction I ran 0.5ul on a gel to determine concentration (this is the gel in the image below).

The Results

Gel extraction test.
Gel extraction test.

Legend

Label Meaning Concentration
1kb ladder NEB 1kb ladder
003 with IP Part K274003 (green generator) cut at XbaI/PstI and gel extracted using Qiagen kit with isopropanol step included. 50 ng/ul
003 without IP Part K274003 (green generator) cut at XbaI/PstI and gel extracted using Qiagen kit with no isopropanol step. 50 ng/ul
003 Zymo Part K274003 (green generator) cut at XbaI/PstI and gel extracted using Zymo kit. ~75 ng/ul
100 XbaI/PstI Part K274100 (red generator) cut at XbaI/PstI, gel extracted with Zymo kit 250 ng/ul
200 XbaI/PstI Part K274200 (orange generator) cut at XbaI/PstI, gel extracted with Zymo kit 250 ng/ul
pSB2K3 EcoRI/PstI Vector pSB2K3 cut at EcoRI/PstI, gel extracted with Zymo kit 150 ng/ul

Getting Started

Useful tools

Literature

Sequence Viewing and Manipulation