Stanford/BIOE44:Module 1:Day5

Introduction

You should define and understand the following vocabularly words.

Open Reading Frame (ORF) Primer Homology Dimer Aneal

Designing Primers

You are probably familiar with the use of PCR reactions to selectively amplify a region of DNA, but you may not have considered what goes into designing a primer set. If you are amplifying a particular region of DNA, you may need to know the regions upstream and downstream of an open reading frame in order to design regions where your primer can "touch down." These regions are called regions of homology, and serve as the template for your primer.

Finding a Target Sequence

Let's use the arsR gene as an example. We may know the sequence of this gene from either a literature search or from researching the registry of standard biological parts description. 'Note that the sequence listed for a std. biological part may be different than the original sequence.(This may be the result of point-mutations added to eliminate a restriction site or could be the product of codon optimization). In the case of the short arsR gene (518 bp), there are no point mutations so we can use the sequence directly as we search.

We can see what organisms might have this sequence or a similar one.

Two tools you may want to use are the

1. Comprehensive Microbial Resource:
2. Basic Local Alignment Search Tool

You can search by gene name or simply a sequence fragment to find what organisms might contain your gene of interest. Use the Comprehensive Microbial Resource to see if the arsR gene is present in a wide range of organisms. There is a "great deal to explore on this site, but you can navigate from the home page, by selecting the "Searches" tab. Select find genes. In the search field type arsR and select "all genomes"

You could design a primer for a wide range of microbes, but you want to make sure the primer you design will work with one of the organism you have readily available to you. We have been using a strand of E.coli named K12-MG1655.

Use either the comprehensive microbial resource or a BLAST search to determine if E.coli MG1655 has the arsR gene.

1. What should be the target of your primer?
2. What sequence do you want to include in your final part?
3. You should open a word file where you can copy and paste the sequences that you view online. This will help you later on.

Regions of Homology

There many ways to do this next step. If you know another good way or database, please feel free to share it with the class and your TAs.

One way to hone in is go to the E.coli MG1655 genome page

Find the coordinate of your gene and associated region by searching for arsR

1. Search by "Gene Sym"
2. type: arsR
3. Record the coordinates of the gene. What do these coordinates reference? Will you need to see more or less sequence to design a primer for the part you wish to "harvest".

1. Go back to Mg1655 genome page and use "Gene Retrieval by Coordinates"
2. Type coordinates you wish to view.
3. Copy this sequence into a word document
4. Identify the beginning of the arsR open reading frame and bold it
5. Identify the end of arsR open reading frame and bold it
6. Identify the arsR operator and sequence where the protein binds to repress transcription
7. In a different colors indicate the regions of homology for your forward primers and reveres primers

Most oligonucleotide primers tend to have a region of homology with the template stand of 18-20 nucleotides in length. You may include an additional overhang on the 5' end of your primer, but you will need to select 18-20 nucleotides that match the genome you are trying to amplify.

1. Select a region of homology in the forward direction
2. Select a region of homology in the backwards direction.

Standard Assembly Parts

On the 5' ends of each of your primers you now need to ad overhangs that will introduce the restriction sites to the arsR part.

Remember a final part will look like this:

5’ --gca GAATTC GCGGCCGC T TCTAGA G--insert--T ACTAGT A GCGGCCG CTGCAG gct--- 3’

3’ --cgt CTTAAG CGCCGGCG A ACATCT C--insert--A TGATCA T CGCCGGC GACGTC cga--- 5’

Record the following in your lab book and in a word document

1. Sketch a diagram of the final part you want to create including the restriction sites
2. Design a forward Primer
3. Design a Reverse Primer
4. Make sure your final primers includes both an overhang and a 18-20bp region of homology with the MG1655 sequence

REMEMBER: WHEN YOU ORDER PRIMERS YOU ALWAYS WRITE THE SEQUENCE IN THE 5' to 3' DIRECTION