Sequence-dependent DNA helical rise and nucleosome stability

Pedone, Francesco; Santoni, Daniele

doi:10.1186/1471-2199-10-105

BMC Molecular Biology

Table 1 Helical rise values of the 136 possible tetranucleotides.

From: Sequence-dependent DNA helical rise and nucleosome stability

N°	Tetranuc	h r (Å)	rmsd (Å)	Origin of data	N°	Tetranuc	h r (Å)	rmsd (Å)	Origin of data
1	AAAA\TTTT	3.21	0.19	1fzx.1nev	69	TCCC\GGGA	4.20	----	1kbd
2	AAAG\CTTT	3.17	0.09	1cs2,1kbd,3kbd	70	CCCC\GGGG	4.37	----	1kbd
3	AAAC\GTTT	3.05	0.22	1fzx,1g14,1nev	71	GCCC\GGGC	2.81	0.51	ad0002, ad0003, ad0004, adh008
4	AAAT\ATTT	3.38	----	bdl038	72	ACCC\GGGT	3.32	----	mean CC/GG
5	TTTC\GAAA	3.07	0.01	1g14,1kbd,3kbd	73	CGGA\TCCG	3.15	0.20	1agh,1la1
6	CTTC\GAAG	3.04	0.05	1agh,1axp	74	CCCG\CGGG	3.03	0.26	adh008, adh0102, adh0103, adh0105
7	GAAC\GTTC	3.12	----	mean AA/TT	75	CGGC\GCCG	2.91	----	1uqf
8	ATTC\GAAT	3.36	0.12	1bn9,1bwt,1gip,2dau	76	ACCG\CGGT	3.23	0.04	1 d20,1la1
9	CAAA\TTTG	2.89	0.01	1fzx,1nev	77	TCCA\TGGA	3.33	0.28	1kbd,3kbd
10	CAAG\CTTG	2.98	0.12	140d,141d,142d,1agh,1g14	78	CCCA\TGGG	3.48	----	1kbd
11	CAAC\GTTG	3.03	----	1bdz,	79	TGGC\GCCA	2.94	----	1but
12	ATTG\CAAT	3.27	----	1buf,	80	ACCA\TGGT	3.37	----	1afz
13	TAAA\TTTA	3.08	----	1cs2	81	ACAA\TTGT	2.89	0.58	1agh,1bdz
14	CTTA\TAAG	3.12	----	mean AA/TT	82	ACAG\CTGT	2.99	----	mean CA/TG
15	TAAC\GTTA	3.27	----	1cqo,	83	ACAC\GTGT	3.19	----	1la1
16	ATTA\TAAT	2.88	----	1 d70	84	ACAT\ATGT	2.61	0.39	1bn9,1saa,
17	AAGA\TCTT	3.17	0.11	1agh,1axp,1g14	85	TTGC\GCAA	2.74	0.09	140d,141d,142d,1fzx,1g14,1nev
18	AAGG\CCTT	2.97	0.03	140d,141d,142d	86	CTGC\GCAG	3.73	0.58	1afz,1bdz,1cs2,1opq,3kbd
19	AAGC\GCTT	3.20	0.07	140d,141d,142d,1axp,1cs2	87	GCAC\GTGC	2.86	0.14	adh047, adj075
20	AAGT\ACTT	3.77	0.41	1kbd,3kbd	88	ATGC\GCAT	3.10	0.33	1 d18,1skp
21	TCTC\GAGA	3.19	0.19	1axp,1opq	89	CCAA\TTGG	3.78	0.05	1g5d.1g5e,1giz,1gj0
22	CCTC\GAGG	3.24	----	mean CT/AG	90	CCAG\CTGG	3.19	0.32	1kbd,3kbd
23	GAGC\GCTC	2.80	0.44	1k9h,1k9l,3kbd	91	CCAC\GTGG	2.86	1.00	1afz,1kkv
24	ACTC\GAGT	2.95	----	1dk9	92	ATGG\CCAT	2.85	----	1but
25	CAGA\TCTG	3.92	----	1opq	93	TCAA\TTGA	2.66	0.12	140d,141d,142d
26	CAGG\CCTG	3.09	0.13	1afz,1kbd,3kbd	94	CTGA\TCAG	3.06	----	1bn9
27	CAGC\GCTG	3.39	----	1uqb	95	TCAC\GTGA	3.01	0.09	1 d20,1k9h,1saa,3kbd
28	ACTG\CAGT	3.40	0.17	1bdz,1cs2	96	ATGA\TCAT	2.36	0.26	1dk9,1k9l,1skp
29	TAGA\TCTA	3.21	0.33	1bn9,1 d20	97	AATA\TATT	3.23	----	mean AT/AT
30	CCTA\TAGG	3.26	----	1bn9	98	AATG\CATT	3.34	0.01	1bn9,1d70
31	TAGC\GCTA	2.96	----	1g7z	99	AATC\GATT	3.23	----	mean AT/AT
32	ACTA\TAGT	3.29	----	bdj061	100	AATT	3.43	0.14	1buf,1bwt,1gip,2dau
33	AACA\TGTT	3.41	----	mean AC/GT	101	TATC\GATA	3.16	0.19	1 d20,1skp
34	AACG\CGTT	3.42	0.31	1cqo,1fzx,1g14,1nev	102	CATC\GATG	3.23	----	mean AT/AT
35	AACC\GGTT	3.41	----	mean AC/GT	103	GATC	3.22	0.16	1opq,1uqd
36	AACT\AGTT	3.56	----	1bdz	104	CATA\TATG	3.31	0.24	1k9l,1skp,1uqa
37	TGTC\GACA	3.22	0.06	1agh,1la1	105	CATG	3.20	0.23	1but,1d18,1dk9,1saa
38	CGTC\GACG	3.90	----	1saa	106	TATA	2.94	0.12	1d42,1d70
39	GACC\GGTC	3.57	----	1bn9	107	AGCA\TGCT	3.53	0.05	1cs2,3kbd
40	AGTC\GACT	3.66	----	1kbd	108	AGCG\CGCT	3.42	0.09	1q7z,1k9h,1k9l
41	CACA\TGTG	3.30	0.17	1k9h,1saa	109	AGCC\GGCT	3.44	----	214d
42	CACG\CGTG	3.46	0.10	1kkv,1uqc	110	AGCT	3.29	0.07	140d,141d,142d,1uqb
43	CACC\GGTG	3.00	0.24	1afz,1 d20,1la1	111	TGCC\GGCA	3.08	0.20	140d,141d,142d,1afz,1fzx,1g14,1nev
44	AGTG\CACT	3.58	----	3kbd	112	CGCC\GGCG	3.16	0.18	1a9g,1a9h
45	TACA\TGTA	3.14	----	1bn9	113	GGCC	3.40	0.25	1but,1uqf
46	CGTA\TACG	3.25	0.19	1 d19,1 d68,1g80.1uqe	114	CGCA\TGCG	4.46	----	1opq
47	TACC\GGTA	3.26	0.21	1axu,1bw7	115	CGCG	3.35	0.36	1gip,1kkv,1la1,1uqq,1dau
48	AGTA\TACT	3.42	0.05	1cs2,1dk9	116	TGCA	3.63	0.20	1bdz,1d18
49	AGAA\TTCT	3.15	0.12	xp,1bn9,1g14	117	ACGA\TCGT	3.12	0.07	1onm,1sot
50	AGAG\CTCT	3.01	0.25	1axp1agh,1a	118	ACGG\CCGT	2.81	0.49	1fzx,1g14,1nev
51	AGAC\GTCT	3.08	----	adh041	119	ACGC\GCGT	2.48	0.36	1cqo,1d68,1q80,1kkv
52	ATCT\AGAT	3.02	----	1opq	120	ACGT	4.02	1.35	1d19,1saa,1uqc
53.	TTCC\GGAA	3.38	0.19	1kbd,3kbd	121	TCGC\GCGA	3.36	0.16	1bwt,1gip,1opq,2dau
54	CTCC\GGAG	3.24	----	mean AG/TC	122	CCGC\GCGG	2.83	----	1la1
55	GTCC\GGAC	3.46	0.04	1agh,1kbd,1la1	123	GCGC	2.61	0.22	1k9h,1k9l,1uqq
56	ATCC\GGAT	3.24	----	mean GA/TC	124	CCGA\TCGG	3.33	----	bd0001
57	CGAA\TTCG	3.15	0.31	1bwt,1gip,2dau	125	CCGG	2.85	0.33	adh008, adj022
58	CTCG\CGAG	3.98	----	1opq	126	TCGA	3.44	0.19	bdj025, bdj060
59	CGAC\GTCG	3.34	0.16	1onm,1rn9,1s74,1sot	127	ATAA\TTAT	2.69	----	1 d70
60	ATCG\CGAT	3.29	----	1uqd,	128	ATAG/CTAT	2.63	0.65	1 d20,1skp
61	TTCA\TGAA	3.24	0.11	1hm1,1onm	129	ATAC\GTAT	2.72	0.19	1d42,1d68,1d70
62	CTCA\TGAG	3.03	0.17	140d,141d,142d,1dk9,1k9h,1k9l,3kbd	130	ATAT	2.47	0.80	1d42,1skp,1uqa
63	TGAC\GTCA	3.10	0.18	1bn9,1saa	131	TTAC\GTAA	2.62	0.35	1bid,1bw7
64	ATCA\TGAT	3.18	0.08	1 d20,1skp,	132	CTAC\GTAG	2.86	0.09	1bn9,1cs2,
65	AGGA\TCCT	3.32	----	mean CC/GG	133	GTAC	2.90	0.27	1d19,1dk9,1g80,1uqe
66	AGGG\CCCT	2.96	0.12	ad0003, ad0004, adh078	134	CTAA\TTAG	2.60	----	1cs2
67	AGGC\GCCT	2.92	0.07	140d,141d,142d	135	CTAG	2.94	----	1g7z
68	ACCT\AGGT	3.82	0.30	1afz,1bn9	136	TTAA	3.21	----	1cqo

Columns report from the left to the right: sample number, sequence/reverse complement of the tetranucleotide, helical rise in angstrom units, root mean square deviation of the helical rise, name of samples used to retrieve data from Nucleic Acid Database at http://ndbserver.rutgers.edu/atlas. Names in normal characters are from NMR database of DNA duplexes, names in boldface are from NMR database for DNA duplexes accommodating a modified base and names in italics are from X-ray database.

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