Question: How Can I Detect If A Protein Can Bind A Segment Of Dna Sequence In Vivo?
1
gravatar for Ct586
8.2 years ago by
Ct586540
China
Ct586540 wrote:

Hi, all,

I want to detect if a protein can bind single strand DNA sequence in vivo, which experimental methods should I use? And I do not know whether this protein has binding ability, is there any in silico method can predict this binding?

I prefer fluorescent label technique like FISH.

Thank you!

binding dna • 2.6k views
ADD COMMENTlink modified 8.2 years ago by Alex Reynolds29k • written 8.2 years ago by Ct586540
2

I would like to ask that question: why, given this question was posed on on a site dedicated to bioinformatics, do the first answers given feature the experimental part and not the computational prediction? Could it be that they have impression that the prediction tools have a terrible performance? From what I know, the accuracy of most the de-novo prediction methods is very low (this 2005 review states a correlation-coefficient of 0.2 http://www.ncbi.nlm.nih.gov/pubmed/15637633). Could somebody, link one or two more recent reviews to answer this?

ADD REPLYlink written 8.2 years ago by Michael Dondrup47k
1

This is a bioinformatics Q&A site, so we can help you with the in silico part - but ask elsewhere for experimental details.

ADD REPLYlink written 8.2 years ago by Neilfws48k
1

Though I agree that this question does border on the edge of bioinformatics, I think it is still valid since it is about experimental design relevant to bioinformatics analysis. Similar questions about advice on experimental design/technology have been regarded as valid previously...e.g. Access Array (Platform From Fluidigm) For 454 Library Preparation Paired End Sequencing With Barcodes

ADD REPLYlink modified 7 weeks ago by RamRS25k • written 8.2 years ago by Casey Bergman18k

Amazingly, the answers which you got up to now are about the experiments, not the in silico analysis.

ADD REPLYlink written 8.2 years ago by Michael Dondrup47k

Yes :) Can I ask that people restrain themselves, even when they know the answer, where questions are off-topic.

ADD REPLYlink written 8.2 years ago by Neilfws48k

I would not expect this question can evoke this debate. :)

ADD REPLYlink written 8.2 years ago by Ct586540
3
gravatar for Chris
8.2 years ago by
Chris190
Munich
Chris190 wrote:

Our group develops sequence-based structure/functions predictors. We also provide a DNA-binding predictor: DISIS

ADD COMMENTlink written 8.2 years ago by Chris190

Thank you! It is a great predictor.

ADD REPLYlink written 8.2 years ago by Ct586540
1
gravatar for Casey Bergman
8.2 years ago by
Casey Bergman18k
Athens, GA, USA
Casey Bergman18k wrote:

Chromatin Immunoprecipitation followed by microarray analysis (ChIP-chip), high-throughput sequencing (ChIP-seq) or Real Time PCR (CHiP-PCR) are the industry standard for demonstrating protein-DNA interactions in vivo. All three techniques require in silico processing of the data. You can start your reading with the wikipedia entries on these topics:

ADD COMMENTlink modified 4 months ago by RamRS25k • written 8.2 years ago by Casey Bergman18k

Thank you! Chip analysis is one of the best methods to detect this interaction. Also It supposed to reflect in vivo interaction. But are there any other methods which can do this, too? Such as FISH like http://www.piercenet.com/browse.cfm?fldID=B7A23C70-5056-8A76-4E39-B7DB24C3742C#fish?

ADD REPLYlink modified 4 months ago by RamRS25k • written 8.2 years ago by Ct586540
1
gravatar for Asaf
8.2 years ago by
Asaf6.8k
Israel
Asaf6.8k wrote:

You could try the various servers for TFBS prediction but according to http://www.ncbi.nlm.nih.gov/pubmed/21304941 you won't get the answers you want unless you have DNase I digestion data.

ADD COMMENTlink written 8.2 years ago by Asaf6.8k

Great suggestions! Prediction is only the first step and only gives a concept that this protein may have the binding ability. Experimental results can give strong evidence.

ADD REPLYlink written 8.2 years ago by Ct586540
0
gravatar for Alex Reynolds
8.2 years ago by
Alex Reynolds29k
Seattle, WA USA
Alex Reynolds29k wrote:

For motif binding instances, take a look at the FIMO tool, part of the MEME suite.

ADD COMMENTlink written 8.2 years ago by Alex Reynolds29k

Thank you! I will try to learn it.

ADD REPLYlink written 8.2 years ago by Ct586540
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