Table 6

Balancing cross hybridization, sliding and hairpins
No. ΔG SHINet al. ΔG FELDKAMP
<a onClick="popup('http://www.biomedcentral.com/1471-2105/13/138/mathml/M15','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/13/138/mathml/M15">View MathML</a> 5’ → 3’ <a onClick="popup('http://www.biomedcentral.com/1471-2105/13/138/mathml/M16','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/13/138/mathml/M16">View MathML</a> 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
#
Lc 6 5
Lhp 6 4
Lsc 6 6
Lsl 7 4
No. ΔG EGNAS ΔG EGNAS
<a onClick="popup('http://www.biomedcentral.com/1471-2105/13/138/mathml/M17','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/13/138/mathml/M17">View MathML</a> First set <a onClick="popup('http://www.biomedcentral.com/1471-2105/13/138/mathml/M18','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/13/138/mathml/M18">View MathML</a> 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
# #
Lc 5 4
Lhp 2 3
Lsc 4 4
Lsl 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}.

Kick et al.

Kick et al. BMC Bioinformatics 2012 13:138   doi:10.1186/1471-2105-13-138

Open Data