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Need Help Desperately!
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optimization
- Posts: 4
- Joined: Sun Dec 10, 2006 6:37 pm
Need Help Desperately!
Hi. I have to design a primer for the sulfiredoxin protein. I am completely lost as to how to do this. I've tried a few tutorials and things online, but I don't know what I'm doing. I was told to try using ensembl.org, but I just don't know how to. Please respond asap. Thank you so much.
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kerrmyau
- Posts: 3
- Joined: Mon Nov 27, 2006 1:05 pm
Primers Design
Dear Optimization,
Before I can help you with your question, I would first need to know the followings:
i. What are the primers for?
ii. How are you going to make them?
iii. A brief description of your project
Hope to hear back from you soon.
Kerrm
Before I can help you with your question, I would first need to know the followings:
i. What are the primers for?
ii. How are you going to make them?
iii. A brief description of your project
Hope to hear back from you soon.
Kerrm
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optimization
- Posts: 4
- Joined: Sun Dec 10, 2006 6:37 pm
Hi. Thank you so much for your reply.
The primers are for typical Polymerase Chain Reaction (PCR). In my project, I will be using PCR to compare the sizes of two proteins, which I believe to have very similar sizes. The reason for this is that they have similar functions. The two proteins, in humans, are Peroxiredoxin II and Sulfiredox.
I do not yet know how to make them, but the proteins and lab equipment will be given to me. I will, also, have help from my mentor in actually making them. I am just supposed to design them, first, which I have yet to be able to do.
The primers are for typical Polymerase Chain Reaction (PCR). In my project, I will be using PCR to compare the sizes of two proteins, which I believe to have very similar sizes. The reason for this is that they have similar functions. The two proteins, in humans, are Peroxiredoxin II and Sulfiredox.
I do not yet know how to make them, but the proteins and lab equipment will be given to me. I will, also, have help from my mentor in actually making them. I am just supposed to design them, first, which I have yet to be able to do.
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carolinethorn
- Former Expert
- Posts: 393
- Joined: Tue Sep 20, 2005 2:40 pm
Hi,
Designing primers can be very challenging. I know graduate students that have trouble with this so don't feel bad that you are having trouble. Its usually much easier to go through the steps along side your mentor, perhaps you can ask them to help walk you through this. We can help you on the board but it might be quite slow going through the steps, especially as you might need to ask questions from your mentor anyway about later stages of how the PCR product will be used.
First off - You will need to have the DNA sequences for the proteins that you want to make. Also it helps to know if you are going to clone them into a plasmid in order to transcribe them to RNA and translate them to proteins. Do you have the sequences or do you need help finding them? Ensembl can be quite hard to find your way around at the beginning but we can help.
Best of luck,
Caroline
Designing primers can be very challenging. I know graduate students that have trouble with this so don't feel bad that you are having trouble. Its usually much easier to go through the steps along side your mentor, perhaps you can ask them to help walk you through this. We can help you on the board but it might be quite slow going through the steps, especially as you might need to ask questions from your mentor anyway about later stages of how the PCR product will be used.
First off - You will need to have the DNA sequences for the proteins that you want to make. Also it helps to know if you are going to clone them into a plasmid in order to transcribe them to RNA and translate them to proteins. Do you have the sequences or do you need help finding them? Ensembl can be quite hard to find your way around at the beginning but we can help.
Best of luck,
Caroline
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kerrmyau
- Posts: 3
- Joined: Mon Nov 27, 2006 1:05 pm
Primers Design
Hi Optimization,
If you try doing some data mining, for example, using the free web-based NCBI Database (http://www.ncbi.nlm.nih.gov/Database), you will find sequences of your proteins of interest. Just enter the name of your protein. They will not only have information on both the protein and nucleotide sequences, but also publications on the work conducted on the particular molecules. Then from those papers, in particular the Methods and Materials section, a lot of time the primers the authors used for the gene cloning would have been described, along with PCR conditions and the source of their template. It will be a good place to start your project.
Come back and let me know if it helps.
Kerrm
If you try doing some data mining, for example, using the free web-based NCBI Database (http://www.ncbi.nlm.nih.gov/Database), you will find sequences of your proteins of interest. Just enter the name of your protein. They will not only have information on both the protein and nucleotide sequences, but also publications on the work conducted on the particular molecules. Then from those papers, in particular the Methods and Materials section, a lot of time the primers the authors used for the gene cloning would have been described, along with PCR conditions and the source of their template. It will be a good place to start your project.
Come back and let me know if it helps.
Kerrm