List of DNA sequences

Molecular Dynamics data for sequences 1-36 and 54-56 below were produced by the ABC consortium. We enhanced the original ABC data set with the oligomers labelled 37-53, which, when considering both the reference and complementary strands, contain all 16 possible end dimers. The MD simulation protocol can be found in:

• R. Lavery, K. Zakrzewska, D. Beveridge, T. Bishop, D. Case, T. Cheatham III, S. Dixit, B. Jayaram, F. Lankas, C. Laughton, J. Maddocks, A. Michon, R. Osman, M. Orozco, A. Perez, T. Singh, N. Spackova, and J. Sponer. A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA. Nucleic Acids Res., 38(1):299-313, 2010.

1	GCTATATATATATATAGC	GCTAGATAGATAGATAGC	29
2	GCATTAATTAATTAATGC	GCGCGGGCGGGCGGGCGC	30
3	GCGCATGCATGCATGCGC	GCGTGGGTGGGTGGGTGC	31
4	GCCTAGCTAGCTAGCTGC	GCACTAACTAACTAACGC	32
5	GCCGCGCGCGCGCGCGGC	GCGCTGGCTGGCTGGCGC	33
6	GCGCCGGCCGGCCGGCGC	GCTATGTATGTATGTAGC	34
7	GCTACGTACGTACGTAGC	GCTGTGTGTGTGTGTGGC	35
8	GCGATCGATCGATCGAGC	GCGTTGGTTGGTTGGTGC	36
9	GCAAAAAAAAAAAAAAGC	AAACAATAAGAA	37
10	GCCGAGCGAGCGAGCGGC	AAAGAACAATAA	38
11	GCGAAGGAAGGAAGGAGC	AAATAACAAGAA	39
12	GCGTAGGTAGGTAGGTGC	GGGAGGTGGCGG	40
13	GCTGAGTGAGTGAGTGGC	GGGCGGAGGTGG	41
14	GCAGCAAGCAAGCAAGGC	GGGCGGTGGAGG	42
15	GCAAGAAAGAAAGAAAGC	GGGTGGAGGCGG	43
16	GCGAGGGAGGGAGGGAGC	GGGTGGCGGAGG	44
17	GCGGGGGGGGGGGGGGGC	AAATAAAAATAAGAACAA	45
18	GCAGTAAGTAAGTAAGGC	AAATAACAATAAGAACAA	46
19	GCGATGGATGGATGGAGC	GGGAGGGGGAGGCGGTGG	47
20	GCTCTGTCTGTCTGTCGC	GACATGGTACAG	48
21	GCACAAACAAACAAACGC	ACGATCCTAGCA	49
22	GCAGAGAGAGAGAGAGGC	ATGCTAATCGTA	50
23	GCGCAGGCAGGCAGGCGC	AGCTGAAGTCGA	51
24	GCTCAGTCAGTCAGTCGC	CGAACTTCAAGC	52
25	GCATCAATCAATCAATGC	GTCTACCATCTG	53
26	GCGTCGGTCGGTCGGTGC	GCATAAATAAATAAATGC	54
27	GCTGCGTGCGTGCGTGGC	GCATGAATGAATGAATGC	55
28	GCACGAACGAACGAACGC	GCGACGGACGGACGGAGC	56

S1_6T	GCTATTTATATATATAGC
S1_6T_13A	GCTATTTATATAAATAGC
S1_9C	GCTATATACATATATAGC