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Table 3 Avoiding hairpin formation in 20 bases long sequences

From: EGNAS: an exhaustive DNA sequence design algorithm

No.

ΔG

Tanaka et al.

ΔG

Feldkamp

ΔG

EGNAS

 

kcal mol

5’ → 3’

kcal mol

5’ → 3’

kcal mol

5’ → 3’

1

1.1

ATGTACGTGAGATGCAGCAG

1.0

TAGTCGCGTGATTTGGAAGG

*

GAGAAGGAACACGATACAGC

2

1.1

ATCACTACTCGCTCGTCACT

0.9

GCTGTCTTTCGTCAATACCG

*

CCTTACACATTTCTTCCGCC

3

0.6

AGATGATCAGCAGCGACACT

0.3

CTGAACGGAATCTAGTAGCG

*

CACAATCAACTCTACCGCTC

4

0.5

TCTGTACTGCTGACTCGAGT

-0.1

GTCTACGGTTCTCTTACGCT

2.4

CCTGTCCTATCTTTCGCTTC

5

0.3

ACATCGACACTACTACGCAC

-0.2

AAAGCCGTCGTTTAAGGAGC

2.1

CTGGCTATGGAAACTGAACG

6

-0.2

GCTGACATAGAGTGCGATAC

-0.2

AATCGCAGTACAGATGGTGG

1.8

CTCGGTCTAAATCTGCTCTC

7

-0.5

TGTGCTCGTCTCTGCATACT

-0.2

GGATGACCAGAGCACTTCAA

1.8

GCCGTTATCCTCTGTTTGTC

8

-0.5

TCAGAGATACTCACGTCACG

-0.6

TACGTCTCGAACTGATAGCC

1.8

GGTTTATTGAGGTTGCGAGG

9

-0.8

CGAGTAGTCACACGATGAGA

-0.8

TGATCTTGTAAAGGCCAGGC

1.8

CCTCCGTATTTGCCTTGTTG

10

-0.9

CGAGACATCGTGCATATCGT

-0.8

TACGATACTTGGCGAGCCAT

1.5

GTTGTAGTTCGTTGGTGGTC

11

-1.2

AGACGAGTCGTACAGTACAG

-0.9

TGCAGAAAAACTATGCCGCC

1.5

CTTCGGCTGGTTCTATTCTG

12

-1.8

TATAGCACGAGTGCGCGTAT

-1.1

GCGCGGACAATTCATTGGTT

1.4

GGCTCACTCATCACACTAAC

13

-2.2

GATCTACGATCATGAGAGCG

-1.7

CCGCAATCCGGTGAAATTAG

1.4

CCTTTACGCCTGACTTTGAC

14

-2.3

GACAGAGCTATCAGCTACTG

-3.0

CTTAGGCAGGTGCCACATAT

1.3

CCTGCGTCTTATGTCTCTTG

15

    

0.9

GCGTGAATGAAGTGGAGTAG

16

    

0.9

GGATTACTTGCTTGGACTGG

      

GC ends

    

#

 

§

L c

 

9

 

5

 

5

L hp

 

5

 

5

 

2

L sc

 

10

 

6

 

4

L sl

 

7

 

5

 

5

  1. Comparison with Tanaka et al.[17]Feldkamp et al.[20]. Comparison of 20 bases long sequences generated by Tanaka et al.[17], Feldkamp et al.[20] and EGNAS. Molar free enthalpies of the most stable hairpins.
  2. *No hairpin structure possible.
  3. #Without {GGG;CCC}.
  4. §Without {GGG;CCC;AAAA;TTTT}.