BISC 219/F10: Lab 6

Lab 6: Series2 Forward Genetics Project

Complementation Analysis
From your complementation analysis, you have discovered the name of your dpy gene of interest. To learn more, you can enter the dpygene name into the C. elegans database: | Wormbase at http://www.wormbase.org Wormbase

Click on the link to Wormbase above and enter your gene name into the box at the top of the page and click Search. It will either bring you directly to that page or it will bring you to a page with mutiple hits - click on the link that provides a definition for what the gene does.

On this new page you should find all the known information about this particular gene. Its name, who named it, what the gene encodes - if that is known, and much more. At the bottom will be a list of references - or a link to a list of references. If you are looking at your dumpy gene information, read further. Does it appear that you are working with a well characterized gene?

Spend some time with Wormbase and marvel at all the hard work and years of research that went into discovering all this information about this tiny little nematode that causes us no harm (non-parasitic). Why do you think so many smart people have devoted so much of their time and energy to working out the genetics of "appearance or movement challenged" little worms? We will talk more about model organisms and the power of functional and comparative genomics in our next series.

Sequencing Analysis

Sequencing a portion of our genes of interest will provide us with direct evidence of the nature of the mutation (i.e: point mutation or deletion) in the mutant worms. It will help us make conclusions whether or not this mutation has been previously characterized or not. This knowledge will be useful to establish a link with the type of functional defect present in the protein produced by the mutated gene.

There are three major steps in a sequencing reaction, which are repeated for 25 cycles in a thermocycler:

1. Denaturation at 94°C: During the denaturation, the double strand melts open to single stranded DNA and all enzymatic reactions stop, including the extension from the previous cycle.
   
2. Annealing at 50°C: In each sequencing reaction, a specific primer is required. This primer is a short sequence of bases complementary to a region of the plasmid upstream of the target gene. The primer will anneal and stay, we hope, only at one position on the single stranded DNA template. In sequencing reactions there is only one strand copied whereas, in PCR, two primers are used so both strands of the DNA template are copied. The primer jiggles around, caused by the Brownian motion. Ionic bonds are constantly formed and broken between the single stranded primer and the single stranded template. The more stable bonds last a little bit longer (primers that fit exactly) and on that small section of double stranded DNA (template and primer), the polymerase can attach and starts copying the template. Once there are a few bases built in, the ionic bond is so strong between the template and the primer, that it does not break anymore.
   
3. Extension at 60°C: Sixty degrees is the ideal working temperature for polymerase activity in sequencing even though, normally, it is 72 °C. Because the growing strand must incorporate ddNTP's which are chemically modified with a fluorescent label, the temperature is lowered so it has time to incorporate the 'strange' molecules. Well designed primers, where there are a few bases built in, already have a stronger ionic attraction to the template than the forces breaking these attractions. Primers that are on positions with no exact match, come loose again and don't give an extension of the fragment. The bases (complementary to the template) are coupled to the primer on the 3'side (adding dNTP's or ddNTP's from 5' to 3', reading from the template from 3' to 5' side, bases are added complementary to the template). When a ddNTP is incorporated, the extension reaction stops because a ddNTP contains a H-atom on the 3rd carbon atom (dNTP's contain a OH-atom on that position). Since the ddNTP's are fluorescently labeled, it is possible to detect the color of the last base of this fragment on an automated sequencer.
   

Because only one primer is used, only one strand is copied during sequencing, there is a linear (not log as in PCR) increase of the number of copies of one strand of the gene. Therefore, there has to be a large number of copies of the gene in the starting mixture for sequencing. If there are 1000 copies of the wanted gene before the cycling starts, after one cycle there will be 2000 copies: the 1000 original templates and 1000 complementary strands with each one fluorescent label on the last base. After two cycles, there will be 2000 complementary strands, three cycles will result in 3000 complementary strands and so on.

What your instructor did for you:
Due to time restraints your instructor completed the sequencing for you and it is your job to analyze the results of the sequencing reaction.

Steps in sequencing a C. elegans gene:
1. Digest the tough outer cuticle.
          Add worms to a mixture of 10 mM Tris, 50 mM KCl, 1.5 mM MgCl₂, pH 8.3, with 10 mg/ml Proteinase K.
          Freeze the worms at -80°C for 15 minutes
          Incubate at 65°C for 1 hour to digest the cuticle and then at 95°C for 15 minutes to denature the Proteinase K.
2. Amplify the gene of interest by Polymerase Chain Reaction (PCR)
          Add dNTPs to a final concentration of 0.2 mM and primers to a final concentration of 0.4 mM each.
          Add Taq according to manufacturer's instructions.
          Determine the proper reaction conditions for your primers and gene size.
          After amplification check for success via agarose gel electrophoresis.
3. Purify the product and send for sequencing
          Remove all impurities and chemicals from the PCR product using a Qiagen PCR Purification Kit
          following manufacturer's instructions.
          Quantify DNA concentration.
          Send proper concentration of DNA and primers to company for sequencing. We have used Genewiz.

What you need to do:

Assignment

Remember to check the Assignment section of the wiki for instructions about the graded assignment due in the next lab and check the Weekly Calendar for other work to accomplish before the next lab.

Links to Labs& Project Info

Series1:
Worm Info
Lab 1: Worm Boot Camp & Sex-Linked or Autosomal Start
Lab 2: Sex-Linked or Autosomal Finale
Series2:
Background: Classical Forward Genetics and Gene Mapping
Lab 2: Mutant Hunt
Lab 3: Linkage Test Part 1
Lab 4: Linkage Test Part 2, Mapping and Complementation
Lab 5: Mapping Con't
Lab 6: Finish Complementation; Mapping Con't
Lab 7: Complete Mapping: Score
Series3:
Schedule of Reverse Genetics Project
RNAi General Information
Media Recipes
Lab 5: Picking your gene to RNAi
Lab 6: Cloning your gene of interest
Lab 7: Picking your transformant
Lab 8: Plasmid purification and transformation
Lab 9: Induction of bacteria for RNAi
Lab 10: Scoring your worms and RNA purification
Lab 11: RT PCR reactions