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visits member for 2 years, 9 months
seen Oct 13 at 21:13

PhD student in chemical engineering


Apr
3
comment E coli cotransformation efficiency
I've always understood for this process to be incredibly low. When you consider how much DNA is added and how many competent cells there are, if you have even 1% transformation efficiency, you'll always get lawns. Since we don't, that gives a rough estimate of the process.
Apr
3
asked How does DNA resolve on size exclusion resin?
Mar
4
comment Does the MS2 RNA binding protein have any translational repression effects?
Probably because I asked this question back in 2012 and was more of a curiosity question rather than an actual experimental question. More specifically, I'm concerned more about generating a tuneable analog type of repression system where you can generate a range of repress rather than perform a complete knockdown using CRISPR.
Mar
3
revised Function of an VEGF inhibitor in the treatment of macular degeneration
adding tags
Mar
3
comment What is the fastest way to build an alanine scanning library?
@GerganaVandova, not really but it might be of interest to the broader community.
Mar
3
comment Does the MS2 RNA binding protein have any translational repression effects?
The idea would actually be to repress translation via the mecahnism that you suggest. Hence, the rationale of putting the MS2 hairpin upstream of the ORF.
Mar
3
comment What implications has the missing 2'-OH on the capability of DNA to form 3D structures?
This answer is incorrect for a variety of reasons. For one, it makes the assessment that RNA is more flexible. It isn't; DNA is. The role described in the Aleadam paper thus is minimal. The comments about degradation has little to do with the ability to adopt 3D structures. It is more of a reflection of the presence of specific defensive mechanisms via DNases and RNases.
Jan
22
awarded  Yearling
Jan
21
comment How straightforward is in vitro compartmentalization?
Thanks! Since it has been awhile since I've asked this question, I now get the impression that certain reactions like transcription and smPCR work well. When concentrations and size become more important or translation is important things go south.
Dec
13
comment Is there a PSI-BLAST for nucleotide sequences?
why not blastn?
Dec
11
comment Finding RNA Loops
As an improvement to what @WYSIWYG mentioned, PARS is fairly low resolution since it is still enzyme based. The newer in vivo SHAPE or DMS-seq methods are much better and more informative.
Dec
10
answered Finding RNA Loops
Nov
16
awarded  Notable Question
Nov
8
awarded  Popular Question
Oct
17
awarded  Popular Question
Oct
11
awarded  Enlightened
Oct
11
awarded  Nice Answer
Sep
8
awarded  Popular Question
Sep
6
comment Does RNA polymerase move around DNA or does DNA rotate benath the polymerase?
I think he is asking a different question. At some point the RNA should be wound around the DNA if the RNAP is spinning around the DNA.
Sep
6
comment Is there any database with RNA classification?
Probably scor.berkeley.edu