Recently I have referred a journal in which 1,8 Naphthalimide derived drugs were active on the HeLa cell lines. I am doing simulation work of DNA-anticancer drug interaction. I want to know how to get the DNA sequence from a specific cell line. Can you please suggest me regarding this.
If that specific drug is GG specific then can I choose any DNA sequence which is having GG in its center. eg: CCTGGTCC to do ONIOM calculation (Drug and GG as high and others are in low).
Or we should consider about the whole sequence eg: the particular cell line should be converted into the DNA sequence.
I am not sure you can get sequences from different cell lines, however you can assess the hg19 assembly for chromatin accessibility (ENCODE data) with tissue specificity from the UCSC genome browser.
The genome of the HeLa cell line has been sequenced. I believe the sequence can only be accessed by permission:
https://dbgap.ncbi.nlm.nih.gov/aa/wga.cgi?view_pdf&stacc=phs000640.v1.p1
Hi Radhika,
I'm not clear why is important that we know the exact HeLa genome sequence. Assembling your own HeLa reference sequence (assuming it hasn't been done already) from short reads or deriving the sequence from a list of variants will require some serious bioinformatics.
Surely HeLa's response to your drug is more likely to do with metabolism, transport and chromatin state than the actual DNA sequence. Why not use the human reference to find all CCTGGTCC sites and assume most are also in HeLa?
Dear Dr. Scott Newman,
Thanks for the valuable suggestion. But the sequence which I extracted is already in the Protein Data Bank ( Cisplatinated sequence ).I want to find the structural properties of 1,8 Naphthalimide derived drug. Though both drugs cisplatin & 1,8 Naphthalimide are completely different from each other, both of the drugs are GC specific. So in this case can I use the same sequence (CCTGGTCC)?
Dear Dr. Adam B Shapiro and Mr.Adolfo Flores Saiffe,
Thanks for your suggestions.
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