Please give the principles in detail. For example, in odder to avoid the formation of hair-pin structure etc.
Your question needs to be refined before anyone can provide a constructive answer.
Design of a particular DNA sequence depends on the end use. What do you want the sequence to do? What is it's intended function?
If you want a DNA sequence to be used as a PCR primer then you design to a specific set of criteria. If you want a sequence that will fold into a specific secondary structure, then you design to a completely different set of criteria.
Designing of sequences that adopt a given secondary structure (as pointed above) has been explored by Dr. Niles Pierce's lab. Their publications have been included below.
http://web.caltech.edu/~niles/papers/jcc11b.pdf
http://web.caltech.edu/~niles/papers/jcc11a.pdf
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