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Documentation => FAQs => Topic started by: xiangjun on October 26, 2012, 01:23:14 pm

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Title: How can I mutate cytosine to 5-methylcytosine
Post by: xiangjun on October 26, 2012, 01:23:14 pm
Methylation of cytosines (http://en.wikipedia.org/wiki/5-Methylcytosine) in DNA is a crucial epigenetic modification that regulate expression of many genes. Chemically, it is the addition of a methyl group to the 5 position of cytosine (C).

The mutate_bases (http://forum.x3dna.org/programs/mutate_bases/) program in 3DNA v2.x performs in silico base mutations given a nucleic acid structure in PDB format. It is not a problem to mutate any C to a 5-methylcytosine (5CM) provided that users set a 5CM in its standard base reference frame. Given the importance of 5CM in epigenetics and the increasing simulation studies to understand its effects, I have included Atomic_5CM.pdb in the 3DNA v2.1 distribution as of 2012oct26.

According to PDB, the three-letter nucleotide name for 5-methylcytosine is 5CM instead of 5MC -- see for example PDB entries 4mht (http://www.rcsb.org/pdb/explore/explore.do?structureId=4mht) and 2uz4 (http://www.rcsb.org/pdb/explore/explore.do?structureId=2uz4). The methyl carbon is named " C5A" instead of " C5M" or " C7 ". Thus, the content of the Atomic_5CM.pdb file is:

Code: [Select]
REMARK    3DNA by Dr. Xiang-Jun Lu [2012-10-26] (xiangjun@x3dna.org)
ATOM      1  C1' 5CM A   1      -2.477   5.402   0.000  1.00  0.00           C 
ATOM      2  N1  5CM A   1      -1.285   4.542   0.000  1.00  0.00           N 
ATOM      3  C2  5CM A   1      -1.472   3.158   0.000  1.00  0.00           C 
ATOM      4  O2  5CM A   1      -2.628   2.709   0.001  1.00  0.00           O 
ATOM      5  N3  5CM A   1      -0.391   2.344   0.000  1.00  0.00           N 
ATOM      6  C4  5CM A   1       0.837   2.868   0.000  1.00  0.00           C 
ATOM      7  N4  5CM A   1       1.875   2.027   0.001  1.00  0.00           N 
ATOM      8  C5  5CM A   1       1.056   4.275   0.000  1.00  0.00           C 
ATOM      9  C5A 5CM A   1       2.466   4.961   0.001  1.00  0.00           C 
ATOM     10  C6  5CM A   1      -0.023   5.068   0.000  1.00  0.00           C 
END

With this new addition, it is now very straightforward to mutate Cs to 5CMs with mutate_bases (http://forum.x3dna.org/programs/mutate_bases/), as illustrated by the following two examples:


The mutated files 355d_AC1BC23_5CM.pdb and 6tna_C2_5CM.pdb are attached for your verification. For comparison, shown below are the original atomic coordinates of the above tRNA 6tna (http://www.rcsb.org/pdb/explore/explore.do?structureId=6tna) cytosine and coordinates of its 5CM mutant in red. Note that the coordinates of the backbone atoms are the same, and coordinates of common base atoms are very close.

Created and maintained by Dr. Xiang-Jun Lu [律祥俊], Principal Investigator of the NIH grant R01GM096889
Dr. Lu is currently affiliated with the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.