Can someone suggest how to calculate the base-pair energy in DNA using computational tools over MD trajectory ?

More Arunima Verma's questions See All

Absorption coefficient of methane?

Hello, Can anyone provide me with the absorption coefficient of methane gas at 7.7 um? Any reference?

06 August 2024 980 5 View

How are Large Models Exploring and Outputting Knowledge Understanding in Specific Content Areas, and What Does Academic Research Say About It?

Hello everyone！ I am currently exploring the performance of large models in understanding knowledge in specific domains, and attempting to construct a knowledge framework similar to what...

05 August 2024 5,729 2 View

Regarding a model for simulating battery charge and discharge, what do you consider to be high fidelity?

Regarding a model for simulating battery charge and discharge, what do you consider to be high fidelity? What is the acceptable percentage of error (regardless of the metric)? Could you suggest...

03 August 2024 5,358 0 View

How do i get an account to upload my published papers?

need to open an account to upload my published papers

01 August 2024 9,255 1 View

What is the problem with these tissue culture plants?

All plants are green but some of these plants becomes yellow. I did not found any reason. Please help me to find out the real problem.

01 August 2024 589 4 View

How to correctly use the UTE and ZTE pulse sequences in Bruker's ParaVision software?

I am using a Bruker 600M solid-state NMR spectrometer with a Micro 2.5 microimaging system. The test sample is a tube of 1M LiCl aqueous solution, and the nucleus detected is 1H. I am trying to...

01 August 2024 9,227 1 View

Is artifacts in XPS possible to build high deviation in binding energy larger than 5 eV??

Hello. Thanks for your consideration to see my question. Recently, I conducted XPS anaylsis of g-CN that is prepared from thermal polycondensation of DCDA, so-called conventional bulk-g-CN,...

30 July 2024 9,824 2 View

Which statistical test should we use?

N=6 Comparing pre and post test likert scale responses. Participants are mix of practicing & preservice teachers.

30 July 2024 7,233 4 View

How to build my own lab made four point probe set up?

Hello, I'm trying to measure the conductivity of semiconductor films but since I don't have a commercial four point probe set up I would like to build one on my own in my lab. I have generators,...

30 July 2024 906 2 View

Can the limit of quantification (LOQ) of an analytical method fall outside its linear dynamic range, or must it always be within it?

Can an analytical method's limit of quantification (LOQ) be outside its linear dynamic range, or is it always required to be within it? Please provide a thorough explanation supported by verified...

29 July 2024 7,198 9 View

Can I base on reverse DNA sequences to perform alignment, convert to amino acids and GenBank submission?

I have reverse sequences (AB1 format), can I base on reverse DNA sequences to perform nucleotide alignment, convert nucleotides to amino acids and deposit the sequence in GenBank database?

11 August 2024 5,138 1 View

I can't see the ssDNA band after performing asymmetric PCR. Is there any way to do this?

After performing symmetric PCR, PCR purification was performed. Afterwards, asymmetric PCR was performed using the PCR purification product as a template, but no ssDNA band was confirmed in the...

08 August 2024 1,668 3 View

Does crude extraction using NaOH and Tris work well with Fungi?

I'm trying to find a DNA extraction method for fungi that does not require equipment and heating. Is there anyone who can suggest an alternative option? Thank you

08 August 2024 4,733 2 View

Why after performing site directed mutagenesis ,I don't see any colony after transformation?

I want to introduce a point mutation (change in one nucleotide) into my gene of interest (DNA binding domain) I have designed primers as recommended on the Data sheet of the kit : -Both primers...

05 August 2024 9,059 3 View

Does anyone have issues using Prepman Ultra reagent for MicroSeq ID bacterial, fungal and yeast sample preparation?

I have been attempting to extract DNA from Bacterial, Fungal and Yeast banked samples (>1e7 cells) using Prepman Ultra reagent and I seem to be struggling to obtain a sequence. Although the...

01 August 2024 2,079 0 View

Inquiry on Maximum Nucleic Acid Volume for 2.5 mL Liposome Solution?

I am currently working on a project involving liposomes and need to determine the maximum volume of siRNA that can be added to a 2.5 mL liposome solution with a total lipid concentration of 10...

30 July 2024 6,420 1 View

Are the apoptotic cells is positive for γH2AX ?

It has been documented that apoptotic cells themselves can induce phosphorylation of serine 139 on H2AX (γH2AX) due to DNA fragmentation during apoptosis (doi: 10.1074/jbc.275.13.9390). As γH2AX...

28 July 2024 7,983 2 View

Can anyone help me explain my problem?

Hi, Now I am doing a single-base editing by using HiFi Cas 9, guideRNA, single stranded DNA, HDR Enhancer V2 and my tranfection mehtod is lipofection (RNAiMax). Unfortunately, after gene editing,...

26 July 2024 2,136 0 View

Illustra™ MicroSpin™ G-25 columns what it is used for?

Hello, We found three packages of Illustra™ MicroSpin™ G-25 columns in the cabinet of an unused lab. They are very old but have never been opened. I have never used this kit before, and I couldn't...

25 July 2024 4,927 3 View

Dear fellow researchers studying in molecular biology, are there any tips on how to avoid plasmid dimerization when extracting plasmids?

Using INTRON's DNA-spin Plasmid DNA purification kit to extract plasmids from specific E.Coli strains, my team and I have encountered numerous plasmid dimerizations that lead to over-weighted...

23 July 2024 3,490 6 View

Philip G Penketh

You could calculate the energy (- ΔG0) on paper as there is a relatively simple relationship between the energy of a reaction and the equilibrium constant (keq). However, you'll need to know the equilibrium constant for the base pair associations.

- ΔG0 = RT(lnkeq)

Arunima Verma

Thank you, Philip G Penketh for your suggestion, but from MD simulations, I have the trajectories and the keq is unknown.

Hussein H. Al-Turnachy

Just determine which nucleotide pair and aply any doking software then you will get top 10 configuratios and their binding energy