Help:IGEM 07 Parts Kit

The iGEM 2007 Parts Kit was shipped to teams this May. The collection of four plates contains all parts available in the Registry as of mid-Spring 2007.

Contents

Storage

Store the DNA Parts Kit with the plastic lid and the adhesive foil cover in the -20C freezer.


Usage

The DNA Parts Kit is a tool available to you to perform synthetic biology with standard biological parts. It contains dry DNA of ALL of the parts that are available in the Registry up until May 2007. You will transform the DNA into cells and make your own glycerol stocks of any part that you wish. It does not contain enough DNA to do assembly. To use the DNA in the Parts Kit follow the following instructions:

  1. Puncture a hole through the foil with a pipette tip into the well that corresponds to the Biobrick™-standard part that you want
  2. Add 15 uL of diH2O (deionized water)
  3. Take 1uL DNA and transform into your desired competent cells, plate out on a plate with the correct antibiotic* and grow overnight. Your goal here is to obtain single colonies.
  4. Pick a single colony and inoculate broth (again, with the correct antibiotic) and grow ~18 hours.
  5. Use the resulting culture to miniprep the DNA AND make your own glycerol stock (for further instruction on making a glycerol see this page).

*To know which antibiotics to use, look at the plasmid that the part is in. The naming scheme for plasmids is specifically designed to indicate antibiotic resistance.

Part location in distribution plates

Top view of plates containing dry DNA; red circle indicates well 13H

All of the DNA Parts Kit plates are Nunc 384-well plates. Unfortunately, the foil cover goes over the column and well markings. However, you can still correctly orient the plate using the two notched corners: well A1 is in the upper left corner of the plate when the long side of the plate with the notched corners is considered the bottom.

Once you have found out which well your BioBrick™ part of choice is in by searching for it in the Registry (for example well 13H in iGEM2007 DNA Parts Kit Plate 1) you want to count across the plate starting with Column 1 until you get to Column 13 and down the plate starting with Row A until you get to Row H.

MAKE SURE that the two notched corners of the plate are the BOTTOM two corners (see the top view image at left for correct orientation)


Part Searching

You can locate a part in two different ways:

Targeted search

If you know which part you are looking for, you can enter the part number in the 'Jump to Part' search box:

Partsearchbox.jpg

From here you will be taken to the part's Main Page. On the left side of the page there will be a pink box. This is the Part navigation box. The link to Physical DNA is where you will find the location of the part.

Partmainpage.jpg

The locations that appear on the Physical DNA page will correspond to the iGEM 2007 DNA Parts Kit. It will include the plate # (Plates 1-4), the well location (e.g. A12), and the plasmid that the part is in.

PhysicalDNApage2.jpg

Browsing parts

In the DNA Repositories section of the Registry, you will find this page that shows the four plates in the DNA Parts Kit. By clicking on any of the links, you will see all of the parts in each particular plate.

Availability

If you decide to do a targeted search for a particular part that you think you might want to use, you need to make sure that the part is actually available. There are many parts in the Registry that people are still working on, or decided not to continue working on anymore, therefore we never received or don't yet have the physical DNA for them. This of course means that the DNA is not available in 2007 DNA Parts Kit. The simplest way to tell whether the part is available is to look at the top right of the part's Main Page. If the part is available the top part of the box will be green and say "DNA available."

Plasmid Location

To find the plasmids that are available in the DNA Parts Kit, you need to do a targeted search (see above) for BBa_P1010. BBa_P1010 is a CcdB cell death gene that we use as the requisite part when "storing" each of the BioBrick™ plasmids. When you do the search you will go, as described above, to the Physical DNA page and see which plasmids BBa_P1010 is available in. Follow the steps above to locate, resuspend and transform the DNA.

More detailed information on the usage and features of BBa_P1010 can be found here.


BBa_I52001 is similar to BBa_P1010 in that it is the BioBrick™ part that is in the following plasmids:

  • pSB3C5
  • pSB4C5
  • pSB3T5
  • pSB4T5
  • pSB3K5
  • pSB4K5
  • pSB4A5