- Hanh Nguyen added an answer:Is 1500 nucleotides RNA too big to do a RNA -protein binding gel shift?
It is the first time I do a gel shift for RNA. I feel kind of lost. I need to do several RNA protein binding gel shifts. My purify protein is 10 KDa and my RNAs is 200, 600, 1500, 1600 nucleotides. Do you think I can see the shift on the gel without using radioactive? Are those RNA sizes too big for RNA gel shift? I really appreciate any responses from you.
Thank you very much!
Dear Craig A Gelfand and Prescott Deininger ,
Thank you very much for your responses. Those help me a lot. I'll cut my sequences down to around 200 nucleotides instead. I hope this should work. I forgot to mention both of my protein and RNAs are purified ones. In the active form, the protein stays in hexamer form around 60 Kda. I'll labelled my rna with biotin for Lishtshift chemiluminescent. That case I can switch to a pool down if it is necessary.
- Arjen Boender added an answer:Any experts on post-transcriptional modulation of mRNAs?
I am interested in the expressional regulation of an mRNA that has three different isoforms: one with almost no 3'-UTR and two with 3'-UTRs of about 6000 nucleotides. I am wondering what I can deduce from this fact? For example, is it possible that the mRNA lacking the 3'-UTR is constitutively expressed, while the others are under regulation of post-transcriptional mechanisms? If anybody knows some good reviews about this topic, please share!
Thanks Francesco! If am working in glial cells, but I think this should also go for glial mRNAsFollowing
- Srinivas Penumutchu asked a question:How do I define RNA boundary conditions ?
I am characterizing Protein-RNA interactions. I would like to construct the RNA to check the protein interactions. I know binding region on the RNA, but i guess three dimensional structure of RNA the playing a role to recognizing the Protein. So I want to define the boundary conditions for RNA construct.
Please let us know that what are the parameters to keep in mind while define the RNA boundary conditions ?Following
- Man Liu added an answer:How can I reduce non-specific binding of proteins on my streptavidin beads?
Dear all, I'm doing RNA pulldown experiments to identify RNA-binding proteins which interact with my RNA. I biotinylated my RNA using biotin RNA labeling mix (roche) and PAGE purified the RNA. For binding, I overnight incubated 5 ug (~80 pmoles) of biotinylated RNA with 1.6 mg of Hela nuclear extract in the presence of 0.1 ug/ul tRNA and 1U/ul RNasin. For pulldown, I added 30 ul of streptavidin agarose beads (Thermo) to the binding reaction and incubated for 1 hr. After extensitve washing, I eluted captured proteins in SDS sample buffer and performed SDS-PAGE. Following coomassie staining, I could observe several bands specifically enriched in the RNA(+) sample, but the problem is that there are too many non-specific proteins appearing in both beads-only and RNA(+) samples to precisely excise out bands of interest without contamination. I tried pre-clearing my extract by incubating it with 60 ul of streptavidin beads before binding, but this did not significantly improve specificity. Can anybody help me reduce non-specific protein binding on beads? Any comments would be greatly appreciated.
I encounter the same problem as you did and I'm wondering whether you sovled it or not and how. Thanks a lot!Following
- Ag Muhammad Sagaf Abu Bakar added an answer:Has anyone expressed a recombinant double stranded RNA binding protein?
I am trying to clone the mentioned gene into a pET vector, preferably with no fusion partner. Each time I try, I get no transformants. Could this gene be toxic to the host?
Thanks for your input. I am transforming the ligation mixture into TOP10 E. coli (DH5-alpha strain), as directly transforming it into a BL21 might cause basal expression and can cause toxicity.Following
- Xiaoquan Sun added an answer:Are you familiar with RNA-Protein docking?
I would like to docking the LNA (locked nucleic acid) with a protein so that the ligand (LNA) should be flexible. Which docking server or software can help me for this job? The LNA is about 80mer. Best regards.
Autodock is also fine. You can find video tutorial on Youtube and many many relative literatures.Following
- Brent Passer added an answer:Where do I start screening for RNA-protein interactions?
I want to identify the host proteins that interact with the non-coding RNA of virus. Is it possible to do the screening on the similar lines as done in protein-protein interactions using Y2H.
We offer RNA-protein screening platform at Hybrigenics. Here is the link.
- Arjen Boender added an answer:How do I determine which specific RNAs are bound to a RNA-binding protein at different timepoints?
I just want to know if it possible to profile differences in the type and amounts of RNA that RNA-binding proteins bind during a behavioral task. I expect that this would change during different learning stages, but I would like to test if this is really true. I know about CLIP-IP etc, but I was wondering if it is possible with these methods to compare the amount of binding of a specific mRNA to an RNA-binding protein throughout different learning stages and for example say that mRNA A is more bound to protein in B in the later stages of learning
- Shuba Varshini Alampalli added an answer:What is the best strategy to catch a regulatory non-coding RNA in action ?
I am a studying a long ncRNA in S. aureus. This ncRNA is important for virulence but no molecular mechanism or interaction studies have been performed yet. This could have possible post-transcriptional control in virulence regulation.
I want to know what other possible RNA species or even proteins, does this ncRNA interact with or regulates. For this I need a good strategy to investigate interacting RNAs or proteins from the bacterium ( would be nice to know it on a genome-wide scale)
What are the constraints?
Do I need an overexpression ? do I have to used non-chaotropic conditions and what are the associated points to be considered?
I would be much obliged in someone could help me out with designing a strategy.
Thank you Sudip for putting up this query. I was also having trouble finding ncRNA targets in malaria parasite. And now I have few strategies to dwell on.Following
- Gabrielle Haas added an answer:How to design the RNA oligos for RNA/Protein pull down assay?
I have to do a Biotinylated RNA pull-down assay to verify the ability of two RNA binding proteins to bind RNA of interest. I’m working on designing the oligos. I wonder it is better to add biotin at 3’ end or at 5’end, and whether a sequence spacer is needed between the two binding sites and what composition it should have (random?).
Thanks in advance
In my opinion, the orientation doesn't matter as soon as your choice is not interfering biologically with your system. To explain, in my case my bait was carrying the biotin in 3' because I wanted to reduce the steric hindrance with the 3' of my prey. So, I made a choice knowing it would be the best orientation.
So I guess that if you don't know if the orientation might influence or not, maybe try both separately. It might be an option. In any case, I would highly recommend a spacer between the oligo and the biotin.Following
- Marco Mazzorana added an answer:How can I inhibit prokaryotic RNases?
I would like to use biotin-RNA to fish RNA binding proteins from E. coli extracts. Do you have any idea how to prevent RNases from chopping off RNA?
If metal-binding is not required for the interaction between your protein/s and RNA, I assume you can just use EDTA to chelate the catalytic Mg2+ in RNAse thereby blocking the enzyme activity.
Biotin/Streptavidin bindind is not affected by EDTA, as far as I know.
- Pradip Kumar Biswas added an answer:How can I remove RNase A from my Ni column-purified protein?
My protein is an RNA binding protein which necessitates removal of RNA for its activity.
I assumed by affinity chromatography that RNase A would be removed as it is an affinity-based separation, but I still have residual RNase A activity which is hurting my assay.
Dear Adam, Paco and Anna thank you so much for all the suggestions!!!! I did pass my crude extract on DEAE in presence of 200mM NaCl as I know my protein will not bind to DEAE at that [NaCl] while the RNA and DNA should bind to the resin. The flow through was charged on Ni column and am yet to see the results. Thanks for all the suggestions. I will try out Anna's way if things do not work out. Thanks a ton guysFollowing
- Maria Letizia Di Martino added an answer:In which volume should I dissolve tRNA-fMet from Sigma (10U) to obtain a 10uM solution?
Hi! I will perform toeprint assays. I got the tRNA-fMet from Sigma (10U). The only indication from sigma is that 1U will have acceptor activity of 1000 pmoles /A260 unit. In my protocol I should use 10 uM solution of tRNA-fMet, but no MW is indicated. Can anyone help me?
Ok...è il calcolo che avevo fatto. Il dubbio era che le pmoli sono riferite all' attività e non alla concentrazione. GrazieFollowing
- Maria Wiktoria Górna added an answer:Why am I seeing a Subshift in the RNA-protein after running EMSA?
I've run a number of RNA-protein and RNA-peptide EMSAs but this is my first sub-shift (complex running below free) result. I'm wondering if others have seen before? Google and literature have been little help and my labmates/PI are a bit shocked also. Is this suggesting a major structure change upon binding? (this would be cool) Should I be more worried about aggregation?
I've ruled out RNAse contamination after running denaturing gel of RNA-Protein complex, also have 3 controls of different binding and non-binding RNAs of same size on same gel with same protein sample added. The RNA showing the sub-shift is a 34mer stem loop with 2x1 internal loop and 18nt single strand region. The protein is 80AA with single RNA binding site.
Maybe run DLS to confirm not aggregation related problem? Maybe fluorecence anisotropy? Or DOSY-NMR?
I've tried different gel %'s (from 8-15%), different buffering systems, different bis/acrylamide ratios, adding detergents, tRNAs, different running temps, and voltages, gel thickness. All have helped sharpen the bands but the subshift is still there.
- beulah mae ann villalobos Solivio added an answer:What is the best program for determining the minimization energy of a protein structure bound to a nucleotide?
I am trying to find the minimization energy of an RNA binding protein when bound to a specific nucleotide. I tried CHARMMING but it seems like it only allows protein-protein interaction. So far, Arguslab worked for me but I'm hoping to try other programs, too. Any suggestions will be really helpful. Thank you!
Thank you so much. This really helpsFollowing
- Alexander Rohe added an answer:How sensitive is FITC to heat and pH changes for the purposes of fluorescence anisotropy?I have recently tried using fluorescence anisotropy to measure FITC-tagged shRNA binding to an RNA binding protein. My questions are:
1.) Will running an annealing program with high temperatures to properly fold the RNA will cause the FITC tag to dissociate from the RNA?
Annealing program :
95C 3 min
Ramp cool -0.1% 10 sec
repeat 700X (brings temp to 25C)
Hold 25C 5 min
4C hold forever
This particular program takes about 2 hours to complete.
2.) Is the buffer type and pH very important for making sure FITC stays "happy"?
Our buffer we are using is a Phophate based buffer containging: 20 mM NaPO4, 50 mM NaCl, 1mM EDTA pH6.8.
Should we change the buffer base to something like HEPES or Tris?
Our experiment parameters were a stable 10 nM shRNA and variable protein concentrations:
.5, 1, 2, 4, 6, 8, 10, 15, 20, 25, 30, 35, 40, 45, 50, 60, 70, 80, 90, 100, 250, 500, 750, 1000 nM
Any help would be greatly appreciated! We just aren't sure why we are not seeing binding of the RNA to the protein which has been shown to bind to this protein in published studies.
Just a general note towards fluorescence anisotropy: Sinve it is quantified via the emission ratio of both measured intensities (parallel and perpendicular to the exciting plane), fluorescence anisotropy does not depend on the overall fluorescence intensity.
Therefore, as along as your total fluorescence intensity is high enough to ensure an adequate measurement error, your anisotropy results won't be negatively influenced by photobleaching.
However, since anisotropy is an additive entity, fluorescein-derivatives derived from your labelled shRNA (e.g. breaking of the covalent linker) will definitely interfere with your measurements by narrowing the assay window. Depending on the extent of "free" fluorophore, it may even cause an assay window of zero...Following
- Sneha Singh added an answer:How do you design a primer for an RNA target?We are trying to develop a biosensor to detect the Dengue virus (DENV) in field condition. Since DENV is an RNA virus, I need to design primers that can specifically bind to RNA. These primers are not for the purpose of any form of PCR but only to capture DENV.Hi Shishir.............. I believe you can use the same primers as we use for RT PCR to detect RNA in the field since DENV RNA lacks a poly A tail, we use its specific reverse primer for preparing the cDNA. You can take help from Anoop M et al., 2010; 2012.Following
- Heide Marie Resch added an answer:Does anyone have any suggestions on how to solve some problem with EMSA for Detecting RNA-Protein complexes?I am having problem with my proteins that have ~10 and ~11 pI and 17kD and 14kDa respectively. They do not get into the gel because of their charge. I tried purifying them even with a maltose binding protein tag to reduce the pI, however they are still too basic to migrate into the gel. My RNA is 130 nt long. I see the unbound RNA and decreasing concentration of unbound RNA with increasing protein concentration but the bands corresponding to RNA-protein complex are not very clear. Proteins alone are not showing up at all. I am using 5% Native PAGE. I am staining the RNA with Sybr Green and Protein with Sypro Red. Since I don't see clear complex bands, I cannot estimate the Kd. Any ideas on how to improve the quality of the bands and how to get the proteins to migrate into the gel instead of moving backwards? I tried non-ionic detergents such as Triton etc. but this did not help.MicroScale Thermophoresis (MST) is a powerful method to determine binding affinities. There are lot of publications available where this method has been employed to investigate protein-RNA interactions. The measurements are taking place free in solution, so you do not have to worry about the protein migrating into gels anymore!
Please also feel free to contact me directly for any further questions on this technique or if I can assist you with your MST experiments!Following
- Emmanuel Po-Shun Wang added an answer:What's the best way to prove direct binding between protein(s) and RNA?How to prove PROTEIN-RNA binding is direct or indirect?RIP assays can be performed using the EZ-Magna RIP™ RNA-Binding Protein Immunoprecipitation Kit.Following
- Deepak Kumar asked a question:Protein-RNA simulation - can anyone help?I am looking to do :
a) free energy calculations (linear interaction energy) in order to analyze the contributions of the protein residues to the binding of RNA.
b) analyze the specificity by running computational alanine scanning.
Can anyone tell me what simulation tool/software could be used to accomplish these tasks?Following
- Christof Lenz added an answer:What kind of method can help me find RNA binding proteins interacting with certain mRNA or pre-mRNA?There are many kinds of RIP methods. With no experiences of this experiment, I don't know which is more efficient and more specific. I would appreciate any advice.Qingyu, how complex, specific and stable is your protein/RNA set? Our group in Göttingen has long-standing experience in isolating and purifying protein/RNA complexes e.g. ribonucleoprotein particles. Crosslinks are then "fixated" via UV crosslinking, purified from non-crosslinked protein and RNA by sequential digestion and separation steps, and finally identified by nLC/MS/MS. Look for corresponding papers by the Reinhard Lührmann and Henning Urlaub groups. The approach still requires a good deal of manual interpretation of results and will usually not produce long global lists of proteins, however it does in many cases allow for pinpointing the actual sites of contact between protein and RNA which can be used as constraints e.g. for molecular modeling of complex structures. Methods Mol Biol. 2008;488:221-45. doi: 10.1007/978-1-60327-475-3_16.Following
- Cong Ren added an answer:No shift in RNA-EMSA ?I have been doing RNA-EMSA for three months but I did not get any shift. Hfq is a known RNA binding protein.You can just add GST tag to your protein to decrease the pI of your protein.Following
- Ali McCorkindale asked a question:Why is KCl necessary in conventional RNA-IP (RIP) buffers? Does it preserve the nucleic acid:protein complex? Why can't you use RIPA buffer?Refer to: http://www.abcam.com/index.html?pageconfig=resource&rid=14913 for recipe for typical RIP bufferFollowing
- Rick van Nuland added an answer:Protein binding too tightly to the beads.I have been trying to elute protein of my interest tagged to GST using a protocol containing 10mM reduced glutathione buffered at pH 8.0. However, contrary to the proposed protocol for this elution to take place, I am having much less success as more than 95% of the fused protein is remaining bound to the beads (beads for binding to GST). I even tried to supplement the protocol by adding 2-mercaptoethanol so that glutathione would be kept at the reduced form. Still, the protein is not getting eluted. Can anyone please suggest the reason for this and any modifications that need to be done for proper elution from the beads?I generally use 50mM. In some cases the elution peak will tilt a bit. This is generally solved by using 60mM.Following
- Guosheng qu added an answer:Ribosome digestion with RNase A giving RNA fragment with very low mobility in gel.I am digesting ribosome with RNase A to remove rRNA and release the ribosomal proteins. When I run a 1% agarose gel after reaction, compared to my control (without digestion), in the experiment lane a smear of RNA is showing at the extreme top of the gel. What might be the reason? There are degraded RNA products at the bottom of the gel, but what are those at the top?I completely agree to Anna's analysis. I guess it 's very possible that the stained band-like stuffs contain fragmented RNAs that are in complex with proteins.Following
- Barbara Ridolfi added an answer:Does the speed of translation possibly influence the configuration of a protein?The number of tRNA varies among different cells, which I think might cause a different speed of translation. I'm curious as to whether the speed will possibly have an impact on the configuration of a translated protein? Are there any other factors that may contribute to the change of configuration?Following
- Knut-Jan Andersen added an answer:Sucrose centrifugation.I am trying to separate RNA binding sequences to virus particles from non-binders through sucrose centrifugation. I am layering the RNA virus particle mix onto 20% sucrose and taking the pellet out, which should have the virus particle with the bound RNA, whereas the supernatant should have the unbound RNA. I was wondering whether RNA ever enters the sucrose or if it continues to sit at the top and never gets into the sucrose layer. I would really like to clear my concept here, any thoughts would be really appreciated.I suggest that you switch to RNase free sucrose. Regular p.a. sucrose can be treated with charcoal to be essential RNase free.Following
- Xu Zhang asked a question:What kind of buffer should I use for the SA-PMPs (Promega) binding?Biotin or RNA aptamer binding of SA-PMPsFollowing
- Emanuel A Devers added an answer:How can I isolate Protein-RNA complex and count small amount of RNAs?I have protein (GFP) tagged miRNA, and want to isolate the complex from whole cell lysate.
My target is miRNA, not protein. Since there's only small amount of miRNA expressed in my system, I was planning to use qPCR, but failed on RNA isolation.
I used Trizol, and all my RNAs were trashed with GFP-protein. Can anyone help me fix the problem?Following