Download A Program for the construction of DNA sequences

DNASequenceGenerator: A Program for
the construction of DNA sequences
Udo Feldkamp, Sam Saghafi,
Wolfgang Banzhaf, Hilmar Rauhe
DNA7 pp. 179-188
Summarized by Dongmin Kim
Introduction

The main purpose for designing DNA sequences:
 Find a set of sequences as dissimilar as possible,
include complementary sequences.
 avoid non-specific hybridizations.
 Control the thermodynamic properties of the sequences
 Regard other constraints given by the application.
© 2001 SNU CSE Artificial Intelligence Lab (SCAI)
Theoretical background(1)

The concept of uniqueness
 nb-unique if any subsequence in the pool of length nb if
unique
 Uniqueness 1-(nb-1)/ns, a ratio to measure how much of
a set of sequences of length ns is unique.
 Example
 9mers
these are 6-unique have at most 5 subsequent common
subsequence and a uniqueness of 44%
© 2001 SNU CSE Artificial Intelligence Lab (SCAI)
Theoretical background(2)



The number of base strands of length nb is N bs (nb )  4
The number of base strands that can be used in the generation process
is
N bs (nb )  4nb / 2
N useful (nb ) 
,
nb is even
2
N (n )
N useful (nb )  bs b ,
nb is odd
2
The maximum number of sequences is
nb
 N useful (nb ) 
N seqs (ns , nb )  

n

n

1
b
 s


Further requirements such as GC-ratio, melting temperature, the
exclusion of long guanine subsequences or of start codons decrease the
yield.
© 2001 SNU CSE Artificial Intelligence Lab (SCAI)
DNA Sequence Generator

The user can
 Import or manually add existing or strictly required
sequences
 Import or manually add sequence templates
 Generate sequences de novo
 Use the DNASequenceGenerator as a Tm calculator
 Estimating
the melting temperature can be chosen in Wallace
rule, GC-% formula, nearest-neighbor method
© 2001 SNU CSE Artificial Intelligence Lab (SCAI)
Result

In silico
In vitro
 Generate oligonucleotides for parallel overlap assembly, and tested in
vitro
 Sequences have restriction sites at specified locations, and a GC ratio of
50%
© 2001 SNU CSE Artificial Intelligence Lab (SCAI)
DNASequenceCompiler

Sibling tool of DNASequenceGenerator
 More suited for sticky-end design.
 Designed to translate formal grammars directly into
DNA molecules representing the rules of the grammar
 Provides an interface for the programmable selfassembly of molecules
© 2001 SNU CSE Artificial Intelligence Lab (SCAI)
Conclusion

A software tool for the design of DNA oligomers
useful for DNA computation.
 The design of sophisticated DNA structures, such
as cubes or double- or triple-crossover molecules
will require a more specialized program.
© 2001 SNU CSE Artificial Intelligence Lab (SCAI)