Pallabi Sengupta

12 Questions 14 Answers 0 Followers

Questions related from Pallabi Sengupta

Selective interaction with specific quadruplex in the cells by luciferase assay and in vitro quadruplex-drug interaction are significantly dissimilar?

I am currently working with a compound which is expected to bind G-quadruplex structure in c-MYC promoter. While I observed very poor affinity between c-MYC quadruplex and the compound in vitro in...

06 August 2018 5,935 1 View

Screening of more than 50 lead compounds for in vitro target selectivity?

I have screened more than 50 compounds from a chemical library containing 5 lakh molecules to test its selectivity for specific oncogenic G-quadruplex DNA structures. The in silico study reveals...

26 April 2018 5,731 3 View

How to improve the resolution of DMS footprinting?

I had been trying DMS (Dimethyl sulfate) footprinting experiment to elucidate quadruplex folding topology of the putative quadruplex forming sequences. First time: The oligos were 6-FAM labelled...

02 May 2017 4,321 6 View

Troubleshooting PCR for cloning the promoter?

We are trying to clone a number of gene promoters into a promoter-less luciferase vector and performed PCR reaction using HeLa genomic DNA (250-800 ng). PCR reactions are successful for two gene...

27 January 2017 5,534 10 View

How to label 6-FAM into 5' of DNA?

We are attempting to perform DMS (Dimethyl sulphate) footprinting with 6-FAM labelled oligonucleotide sequence. We are confused about the labelling of the DNA sequence by 6-FAM. Do we need to...

02 November 2016 2,672 4 View

How can we designate the major and/or minor promoter, untranslated regions in a gene using bioinformatic search?

I have loaded the FASTA sequence of the gene. I know the ORF. Using different server for promoter prediction I have come up with multiple predicted promoter sequences in the gene. Is there any...

16 August 2016 5,551 2 View

Determination of the concentration of the PCR product?

I have performed RT (Reverse transcription) PCR and run agarose gel for densitometric analyses. I need to calculate the concentration of the product from the band intensity only. I was considering...

06 August 2016 9,510 3 View

How to estimate negative superhelical density in plasmid DNA?

I am working with ~6000 bp plasmid DNA, which contains the promoter of my interest. This promoter has a cis-element, which forms non-canonical DNA structures in cells, which I have already proved....

01 January 1970 7,835 1 View

How to get better resolution in footprinting gel?

We have recently performed DMS (dimethyl sulphate) footprinting experiment to understand the folding topology of the quadruplex forming sequence (90 nt). The sequence is labelled with 6-FAM at its...

01 January 1970 8,073 3 View

Design of crRNA in putative quadruplex-forming motifs for CRISPR Cas9-mediated gene editing?

I am looking for designing crRNA against the putative G-quadruplex forming motifs. Taking account of the criteria for a good crRNA, web-based design gives crRNA sequences that don't overlap the...

01 January 1970 8,977 1 View

Why does Hydrazine cleave at A and G bases instead of C and T in CT ladder sequencing reaction?

We performed DMS footprinting of a 90 nt sequence. The left most lane is A+G ladder. The 2nd and 3rd lane denote DMS reactions in different conditions which are consistent with our hypotheses. The...

01 January 1970 461 0 View

Fluorescence emission of Crystal Violet is close to baseline and not enhanced upon G-quadruplex DNA titrations

Crystal Violet is a popular DNA binding dye. It is widely known that fluorescence emission of Crystal Violet (CV) is significantly enhanced upon titrations with anti-parallel G-quadruplex DNA....

01 January 1970 6,871 0 View