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6.12 Creating Watson Crick duplexes
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// bdna() - create average B-form duplex
molecule bdna( string seq )
{
molecule m;
string cseq;
cseq = wc_complement( seq, "", "dna" );
m = wc_helix( seq, "", "dna",
cseq, "", "dna",
2.25, -4.96, 36.0, 3.38, "s5a5s3a3" );
return( m );
};
bdna() calls wc_helix() to create the molecule. However, wc_helix() requires both strands of
the duplex so bdna() calls wc_complement() to create a string that represents the Watson/Crick
complement of the sequence contained in its parameter seq. The string "s5a5s3a3" replaces
both the sense and anti 5’ terminal phosphates with hydrogens and adds hydrogens to both the
sense and anti 3’ terminal O3’ oxygens. The finished molecule in m is returned as the function’s
value. If any errors had occurred in creating m, it would have the value NULL, indicating that
bdna() failed.
Note that the simple method used in bdna() for constructing the helix is not very generic,
since it assumes that the internal geometry of the residues in the (default) library are appropriate
for this sort of helix. This is in fact the case for B-DNA, but this method cannot be trivially
generalized to other forms of helices. One could create initial models of other helical forms in
the way described above, and fix up the internal geometry by subsequent energy minimization.
An alternative is to directly use fiber-diffraction models for other types of helices. The fd_helix()
routine does this, reading a database of experimental coordinates from fiber diffraction data, and
constructing a helix of the appropriate form, with the helix axis along z. More details are given
in Section 3.13.
6.12.2 wc_complement()
The function wc_complement() takes three strings. The first is a sequence using the standard
one letter code, the second is the name of an nab residue library, and the third is the nucleic
acid type (RNA or DNA). It returns a string that contains the Watson/Crick complement of the
input sequence in the same one letter code. The input string and the returned complement string
have opposite directions. If the left end of the input string is the 5’ base then the left end of the
returned string will be the 3’ base. The actual direction of the two strings depends on their use.
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// wc_complement() - create a string that is the W/C
// complement of the string seq
string wc_complement( string seq, string rlib, string rlt )
// (note that rlib is unused: included only for backwards compatibility
{
string acbase, base, wcbase, wcseq;
int i, len;
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if( rlt == "dna" )
acbase = "t";
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