Hi,
I found that my protein bound ethidium bromide in an agarose gel. I tested that
by treating my protein with protease and DNAse in two different tubes and
running a gel. The band in the agarose gel disappeared only when the
protein was treated with protease. It is worth trying.
I hope that helps,
Chiara
Pramod,
You already got good suggestions on how to handle DNA contamination in
protein preparations.
Let me point out briefly that you haven't demonstrated yet that your
contamination is DNA.
I had the same observation when purifying UvsX. A very persistent and strong
contamination in all my preps at ~500kb. To test weather it was DNA or RNA I
boiled the protein 30 minutes and incubated it with DNAase and RNAse and
result was the same. I concluded it was neither RNA nor DNA and continued as
if nothing had happened.
This publication is reporting the same observation:
Formosa and Alberts (1986) Purification and characterization of the T4
bacteriophage uvsX protein. J Biol Chem. 1986 May 5;261(13):6107-18.
If you ever find out what it is that runs like 500kb DNA on Agarose, please
let me know.
S.
--
Date:Sat, 27 Jun 2015 04:39:45 +0100
From:Stefan Gajewski sgajew...@gmail.com mailto:sgajew...@gmail.com
Subject: Re: Interesting DNA contamination
Correction,
I meant to say 0.5kb, not 500kb
sorry for that.
S.
--
Date:Sat, 27 Jun 2015 16:52:06 +
From:Rose, Peter pwr...@ucsd.edu mailto:pwr...@ucsd.edu
Subject: Postdoctoral Fellows in Big Data/Structural Bioinformatics at
University of California, San Diego
Summary: We are looking for two highly motivated post-docs as part of our new
project “Compressive Structural Bioinformatics” funded by the US National
Institutes of Health (NIH) Big Data to Knowledge (BD2K) initiative.
The Challenge: To enable efficient research on the rapidly growing number of
3D molecular structures of ever increasing size and complexity. Develop
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visualization tools.
Qualifications: Ph.D. in structural bioinformatics, structural biology,
bioinformatics, computational biology or chemistry, computer science, or
related discipline. Experience with scientific software development as
demonstrated by publications or participation in open source software
projects. Experience with several programming languages, including Java,
JavaScript, C++, or Python, and software development tools. Strong skills in
applied mathematics and algorithm design are required. Experience with
distributed parallel computing or 3D visualization applications are a plus.
Excellent interpersonal, written, and oral presentation skills are essential.
Note, this position is reviewed annually on the basis of performance and can
be renewed for a maximum of three years.
Our Environment:
The Structural Bioinformatics Group
(http://bioinformatics.sdsc.eduhttp://bioinformatics.sdsc.edu/
http://bioinformatics.sdsc.eduhttp://bioinformatics.sdsc.edu/) at the San
Diego Supercomputer Center (SDSC) (http://www.sdsc.eduhttp://www.sdsc.edu/
http://www.sdsc.eduhttp://www.sdsc.edu/) is involved in research and
development activities centered around 3D structures of proteins and nucleic
acids, the integration of structural data with other domains such as
Medicine, Genomics, Biology, Drug Discovery, and the development of scalable
solution to Big Data problems in Structural Bioinformatics. Our group leads
the RCSB Protein Data Bank (PDB) west-coast operations. The RCSB PDB
(http://www.rcsb.orghttp://www.rcsb.org/
http://www.rcsb.orghttp://www.rcsb.org/) represents the preeminent source
of experimentally determined macromolecular structure information for
research and teaching in biology, biological chemistry, and medicine. With
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PDB is one of the leading worldwide Biological Databases. Our group is
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As an Organized Research Unit of UC San Diego, SDSC is a world leader in
data-intensive computing and cyber infrastructure, providing resources,
services, and expertise to the national research community, including
industry and academia.
To apply, please send cover letter and resume to Dr. Peter Rose
(pwr...@ucsd.edu mailto:pwr...@ucsd.edu).
--
Peter Rose, Ph.D.
Site Head, RCSB Protein Data Bank West
(http://www.rcsb.orghttp://www.rcsb.org/
http://www.rcsb.orghttp://www.rcsb.org/)
Principal Investigator, Structural Bioinformatics Laboratory
(http://bioinformatics.sdsc.eduhttp://bioinformatics.sdsc.edu/
http://bioinformatics.sdsc.eduhttp://bioinformatics.sdsc.edu/)
San Diego Supercomputer Center (http://www.sdsc.eduhttp://www.sdsc.edu/
