What are the best programs and methods to computationally dock RNA onto proteins?

We have used DOT to dock DNA to proteins but increasingly need to examine computational models for RNA docking onto proteins. Would appreciate advice and examples where this has proven successful.

10 November 2019 7,823 4 View

What is the best way to make antibodies against DNA and DNA-RNA hybrids?

We are examining structures of non-B-DNA such as DNA or DNA-RNA G quadruplex and would like to test if these occur in cells using antibodies. I know some G guadruplex antobides exist but we are...

08 September 2018 6,384 7 View

What are rigorous assays to measure the impact of a given enzyme and its inctivation on mutation rates, patterns, and signatures?

I am intersted in measuring the impact of specific enzymes and their inactivating mutations on genome instability and on the mutation burden in human cells and cancers. I want experiment ways to...

06 July 2018 2,257 0 View

Are scientific meetings a net expense that should be limited or do they save research time and money?

Many institutions are limiting travel and meeting attendance with the idea of saving money. Yet, I think meetings always save research money for me. I find that when I attend meetings the...

10 November 2017 2,132 4 View

What are the best ways to detect dsDNA in the cytoplasm?

re there specific stains and fluorescent methods to detect dsDNA in the cytoplasm of cells? Are these quantitative? What are the best controls and methods to validate dsDNA in cytoplasm?

09 October 2017 5,217 1 View

Given the issues with journal impact factors, would it be helpful to have some type of author-based metrics or impact factors or not?

Since the use of journal impact factors as frequently used to evaluate researh quality has been criticised for many reaons, might it be useful to devise mertics based upon a given author's impact....

11 December 2016 1,925 3 View

'What methods have you found to be effective for increasing your lab's productivity?

07 August 2016 6,071 2 View

What are the best ways to cross-link proteins to DNA?

07 August 2016 1,452 2 View

How can we best teach students to answer questions where they have not learned the answer?

We largely teach students and then ask them questions that we taught them how to answer. In science and many other areas of life, one wishes to address and answer questions where you have not...

06 July 2016 6,509 2 View

What do you see as the major contributions that will come from cry-electron miscopy in the next decade?

11 December 2015 8,615 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

Does anyone know HRM channel in a 2 plex QIAGEN Rotor- Gene Q qPCR can be used as a separate channel?

I am going to have 3 different probes in my qPCR work that I am going to do. But I realized that the machine we have in the lab is a Rotor-Gene Q 2plex HRM Platform, saying it has green, yellow,...

01 March 2021 8,544 1 View

Which cell line should we use to perform biological dosimetry experiments?

We are preparing some experiments based on irradiating cells under different conditions in order to evaluate the effects in terms of DNA damage, genetic expression, etc. As our project is...

01 March 2021 3,355 3 View

Isolates of Hymenoscyphus fraxineus?

Dear Dr. Cai, my name is Simone Prospero and I work in the team of Phytopathology at the Swiss Federal Institute for Forest Snow and Landscape Research (WSL;...

01 March 2021 1,133 1 View

Is it possible for two human neuronal cell lines to have different gene sequence for the same protein?

I am looking at the ATP1A2 (Sodium/Potassium ATPase alpha subunit 2) in two human neuronal cell lines. Expression levels of this protein seems to be almost equal when detected by one antibody....

01 March 2021 3,607 3 View

Is there a deep reason for using the squared modulus of the wave function as the probability density of the existence of the particle?

I think we were all surprised at the first time we got to know quantum mechanics that the squared modulus of the wave function is the probability density of the existence of the particle? The role...

28 February 2021 6,282 9 View

Runs of nucleotides in Sanger sequencing?

I performed site directed mutagenesis, transformation, and then I sent out plasmids for Sanger sequencing and found out that there is extension of DNA just before the stop codon. I am not sure...

27 February 2021 547 3 View

Calculating volume of DNA required from DNA concentration?

Hi I am a bit confused. They are asking me to find out the volume of DNA required in ul (a total of 30-100 ng for genomic DNA) from the DNA concentration in the nanodrop reading which was 404.8...

26 February 2021 5,029 2 View

Has anyone used the Illumina ITS1 primer sets?

Hi everyone, Illumina provides a list of primers to amplify with high taxonomic coverage the ITS1 region for further fungal sequencing, but I cannot find the exact amount necessary of each...

25 February 2021 6,969 3 View

Errors in DNA sequences?

I am trying to better understand the scope of DNA replication and sequencing errors, e.g. 1. I have seen similar error rates of 10e4 to 10e5 for cell & instrumental DNA replication,...

24 February 2021 4,397 3 View