EGNAS: an exhaustive DNA sequence design algorithm

BMC Bioinformatics

Table 6 Balancing cross hybridization, sliding and hairpins

No.	ΔG	Shin et al.	ΔG	Feldkamp
	$[\frac{kcal}{mol}]$	5’ → 3’	$[\frac{kcal}{mol}]$	5’ → 3’
1	0.8	AGGCGAGTATGGGGTATATC	1.0	TAGTCGCGTGATTTGGAAGG
2	0.8	TTATGATTCCACTGGCGCTC	0.6	TTACACTTGAAGCTGGCTCG
3	0.3	CTTCGCTGCTGATAACCTCA	0.3	CTTCGTGTCGGCCATCATAT
4	0.2	CGCTCCATCCTTGATCGTTT	-0.2	AAAGCCGTCGTTTAAGGAGC
5	0.1	ATCGTACTCATGGTCCCTAC	-0.3	GGTTCTTACGCTCTACTGCA
6	-0.3	GAGTTAGATGTCACGTCACG	-0.6	TACGTCTCGAACTGATAGCG
7	-2.3	CCTGTCAACATTGACGCTCA	-2.4	TCATGTTGGCACCGTATGCA
				#
L _c		6		5
L _hp		6		4
L _sc		6		6
L _sl		7		4
No.	Δ G	EGNAS	Δ G	EGNAS
	$[\frac{kcal}{mol}]$	First set	$[\frac{kcal}{mol}]$	Second set
		5’ → 3’		5’ → 3’
1	*	CAAAGAACCGACATAGCCAC	*	CCAACCAAACCACCAATCTC
2	*	GAACGGCAGGAGACAAATAC	1.4	CTGTCGTCGTGTCTTCTTCA
3	*	CATAAGAGGAAACAGCACGG	1.3	GCAGGCAGGTCAAGGTAAAT
4	2.1	GTTCGTCCTATTGCTCTGTG	1.0	ATCCGCCATAATAAGTCCGC
5	1.5	GTCGTGTTGCCTTTCTATCC	0.9	CTTTCGGCTCCTAACATTCG
6	1.3	GGTTTATTCTCGGCTTGTGG	0.7	GAGTGAGTTCCAGAGTATCG
7	1.3	GGCTCGTTTGGTGTATCTTC	0.5	TTGTAGCATCATCAGCGAGG
		GC ends
		#		#
L _c		5		4
L _hp		2		3
L _sc		4		4
L _sl		3		6

Comparison of 20 bases long sequences generated by Shin et al.[16], Feldkamp et al.[20] and EGNAS. Molar free enthalpies of the most stable hairpins.
^*No hairpin structure possible.
^#Without {GGG;CCC;AAAA;TTTT}.

ISSN: 1471-2105