MMTSB
Tool Set Documentation

mutateNA.pl

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Usage

usage:   mutateNA.pl [options] [PDBfile]
options: [-seq [chain]index:[complementary:]sequence[=index:sequence]]
         [-rna]
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Description

Allows the mutation of nucleotides in nucleic acids. Mutation of double-stranded DNA maintains better intra-strand hydrogen bonding if base pairs are mutated together (see example below) rather than mutating each strand separately.

For RNA, the option -rna should be used.

Options

-help 
usage information
-seq [chain]index:[complementary:]sequence[=...] 
nucleotide sequence to be mutated to
-rna 
generate RNA instead of DNA

Examples

mutateNA.pl -seq A1:AT 1bna.chainA.pdb
mutate the first two nucleotides to AT in single-stranded DNA

ATOM      5  O5' ADE A   1      18.935  34.195  25.617  1.00 64.35          
ATOM      6  C5' ADE A   1      19.130  33.921  24.219  1.00 44.69          
ATOM      7  C4' ADE A   1      19.961  32.668  24.100  1.00 31.28          
ATOM      8  O4' ADE A   1      19.360  31.583  24.852  1.00 37.45          
ATOM      9  C3' ADE A   1      20.172  32.122  22.694  1.00 46.72          
ATOM     10  O3' ADE A   1      21.350  31.325  22.681  1.00 48.89          
ATOM     11  C2' ADE A   1      18.948  31.223  22.647  1.00 30.88          
ATOM     12  C1' ADE A   1      19.231  30.482  23.944  1.00 36.58          
ATOM     13  N9  ADE A   1      18.054  30.234  24.144  1.00 40.51          
ATOM     13  C5  ADE A   1      16.102  29.236  24.585  1.00 40.51          

...


mutateNA.pl -seq A5:B8:TTAA 1bna.dna.pdb
mutates the central four base pairs (chain A: residues 5 to 8, chain B residues 8 to 5) to (TTAA):(AATT)

ATOM      5  O5' CYT A   1      18.935  34.195  25.617  1.00 64.35          
ATOM      6  C5' CYT A   1      19.130  33.921  24.219  1.00 44.69          
ATOM      7  C4' CYT A   1      19.961  32.668  24.100  1.00 31.28          
ATOM      8  O4' CYT A   1      19.360  31.583  24.852  1.00 37.45          
ATOM      9  C3' CYT A   1      20.172  32.122  22.694  1.00 46.72          
ATOM     10  O3' CYT A   1      21.350  31.325  22.681  1.00 48.89          
ATOM     11  C2' CYT A   1      18.948  31.223  22.647  1.00 30.88          
ATOM     12  C1' CYT A   1      19.231  30.482  23.944  1.00 36.58          
ATOM     13  N1  CYT A   1      18.070  29.661  24.380  1.00 40.51          
ATOM     14  C2  CYT A   1      18.224  28.454  25.015  1.00 16.62          

...