Does a restriction site downstream of a promoter serve as an enough factor for a gene to be expressed at +1 of that promoter?

More Mahbobeh zamani babgohari's questions See All

What are your alternative data collection methods during the pandemic? What are the pros and cons?

Dear colleagues We are exploring possible data collection methods for environment and behavior research in the context of architectural environments. Have you conducted any Post Occupancy...

16 February 2021 2,575 4 View

Quantification of GC-MS data, issue with Masshunter, Any ideas?

Hi, I am using the Masshunter software to quantify my GC-MS data. So, did the integration using MassHunter. but the data (area) are weird. I have a lot of peaks in one chromatogram, therefore,...

09 November 2020 2,181 5 View

How to apply cyclic loading to a discrete model of a masonry wall in 3DEC software?

It is possible to apply a monotonic load to a URM wall in 3DEC code but I am wondering is it possible to apply a cyclic load there like FEM softwares?

10 February 2020 3,237 3 View

Can pET expression vectors get used for sequencing and storage?

I was wondering if we could skip one step in cloning process from sequencing vector to expression vector? Meaning that start cloning the gene directly into expression vector such as pET 28b and do...

04 February 2020 9,742 2 View

Do you recommend ligation free cloning system?

I plan to clone some terpene synthase genes into a sequencing vector and later do the heterologous expression using an expression vector. I was wondering if anyone has experience with free...

28 January 2020 7,751 3 View

Why R studio deletes some rows from the heatmap/ doesn't show all genes?

I am using Rstudio to create heatmap for some expression data; My file includes 38 genes, therefore, 38 rows and 20 columns as samples. The output heatmap shows only 19 of my genes!!! Any idea how...

10 December 2019 7,530 3 View

What software/program you recommend to convert fasta file to Nexus.nxs?

I need to convert my fasta format alignment file to "Nexus.nxs" to be able to use it in Mybeys. What is your suggestion? So far the files I created using Mega x as well as an online database...

09 October 2019 4,362 2 View

Problem with trimAL installation?

Is anyone can help in how to install trimAL on windows 10? I am gonna use the software for trimming of my aligned sequences. It seems the software does not get installed in my system! Any idea...

15 September 2019 6,068 3 View

What will be the programming language of future Computational Codes? Good old FORTRAN evolves or will be removed from heavy duty computational world?

I know there are great reliable libraries on Fortran for Computational PDE/ODE, Computational Statistics and Numerical Linear Algebra. Also almost all the legacy software packages of Civil...

30 August 2018 5,424 4 View

Do I need to design a specific antibody for purification of my small recombinant peptides?

I am fusing small peptides around 10 to 30 a.a into the C-terminus of a larger protein. The question is if I need to design specific antibodies against those small epitopes? I actually have two...

10 May 2018 1,091 1 View

MD MOE RMSD

How to calculate the RMSD values for a MD simulation using MOE?

07 August 2021 0 0 View

MD MOE RMSD

How to calculate the RMSD values for a MD simulation using MOE?

07 August 2021 0 0 View

fatal error

When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.

16 June 2021 0 0 View

fatal error

16 June 2021 0 0 View

fatal error

16 June 2021 0 0 View

fatal error

16 June 2021 0 0 View

Enhanced Yellow Fluorescent Protein (Aequorea victoria) DNA sequence?

I am on the lookout for the Enhanced Yellow Fluorescent Protein (Aequorea victoria) DNA sequence. Does anyone know where I can find it? Thank you in advance

03 March 2021 3,568 1 View

What kind of fluid could I use for a pitfall trap that also does not invalidate molecular testing?

Hi, I want to start testing pitfall trap to obtain ants samples, but I need to conduct molecular analysis on those insects. So, what kind of fluid can I use? Ethanol expires too early and I need...

03 March 2021 5,978 5 View

Can linear DNA be used as template for site-directed mutagenesis?

Is it possible to induce site-directed substitution mutation by quick-change method on linear dsDNA? or it has to be cloned in some vector? If yes, should it be treated with the Dpn1 enzyme...

03 March 2021 401 4 View

How to repeat an operation on an atom selection for multiple times in PyMol?

Hi, I am trying to construct a multi-layer fibril structure from a single layer in PyMol by translating the layer along the fibril axis. For now, I am able to use the Translate command in PyMol...

02 March 2021 4,569 4 View

Abel Tan

So you plan to overlap the CDS with the +1 promoter? That is not recommended, the ribosome would need to scan some distance from the 5 mg cap to find a kozak sequence.If the ATG is the end of the mRNA, then you cant fit the ribosome binding site.

Mahbobeh zamani babgohari

dear Abel, i dont need to make that overlap. Imgine if i consider some space for RBS, then may i use any restriction site further? I mean downstream of 35S promoter?

Thanks in advance.

yes you may put the rbs directly behind the promoter. But ideally you would like to leave like a few tens of bp at least.

So,should i definitely add RBS? Just to make sure i understand it correctly, because I need my gene to start at +1 of the promoter, i need to put RBS around tens bp behind (upstream) of the promoter. Right?

Thanks a lot.

no, you put the RBS tens of bp infront the +1. So for example, +10 .

ThanksvAbel!