Formaldehyde fixing of nucleosomes resulted in aggregates?

I am trying to fix the nucleosomes by formaldehyde. The idea is to make the nucleosomes stable at high salt concentration and temperature by crosslinking DNA with Histone octamer. We have...

01 February 2019 7,161 4 View

How long can I store nucleosomes at 4degC?

I am imaging nucleosomes using AFM. I purchased nuclesomes from EpiCypher. The storage buffer contains 10mM TrisCl, 1mM EDTA, 25mM NaCl, 2mM DTT, pH 7.5. I have the stock solution (2ug/ul) kept at...

06 July 2018 7,193 3 View

Why does my observation differ from the literature in RBC stiffness measurement?

I am trying to measure stiffness of red blood cells in RPMI using AFM force spectroscopy method. In literature, the typical indentation of RBC at a force of 500pN is 500nm. But in my case I see...

06 July 2018 8,868 6 View

Does APTES react with acetone?

We use APTES for silanization of glass surface. We observed that 4% APTES prepared in acetone turns yellow within 24hours. But the new batch of APTES (Sigma) in acetone is not turning yellow with...

05 June 2018 1,094 3 View

Why does RBC crenate after attaching to glass surface?

I am performing AFM force spectroscopy on red blood cells by immobilizing them on glass surface. I clean the glass coverslips by sonication in soap solution, Milli Q, ethanol, acetone, ethanol for...

02 March 2018 1,161 3 View

How to obtain better images of DNA using AFM?

I am using tapping mode AFM in MilliQ to image a plasmid PGEM3Z which is ~1um long circular DNA. I prepare the sample in the following way. I take 15mm x 15mm mica sheet and cleave it using scotch...

31 December 2017 1,621 4 View

Can we perform PCR with a primer which is thiolated?

I would like to prepared a DNA sample that has -SH or thiol group at one of its end so that I can covalently immobilize it on a surface. The -SH modified primers are commercially available. I am...

11 December 2017 7,204 8 View

Can we image DNA using scanning electron microscope?

I would like to attach DNA to AFM tip and image it using SEM to check if coating was done properly. I couldn't find any papers that show SEM images of DNA. I would like to know the protocol to do...

10 November 2017 6,580 3 View

How do I check if core histones are present in octameric form?

I have purchased human histone octamers from Sigma (SRP0408) for nucleosome reconstitution experiments. I would like to check the protein complex in octameric form. Running it on SDS-PAGE will...

09 October 2017 7,296 7 View

Why do I get negative values in Nanodrop measurements?

I am measuring a sample of histone octamer which is in buffer containing 20mM Tris-HCl, 1mM EDTA, 2M KCl, 10mM DTT, 0.5mM Benzamidine and MilliQ water. I have prepared 1M Benzamidine in Ethanol...

08 September 2017 5,856 8 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

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

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

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

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

No title

02 March 2021 3,060 3 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