BMRB: 36326

NMR solution structure of a DNA minidumbbell containing an abasic bulge between two CCTG repeats

Authors

Wan, L., Lam, S.L., Guo, P.

Assembly

DNA (5'-CCTGXCCTG)

Entity

1. DNA (5'-CCTGXCCTG), entity 1 (polymer, Thiol state: not present), 9 monomers, 2621.635 Da Detail

CCTGXCCTG

2. SODIUM ION (non-polymer), 22.990 × 8 Da

Total weight

2805.555 Da

Max. entity weight

2621.635 Da

Entity Connection

metal coordination 17 Detail

---

ID	Type	Value order	Atom ID 1	Atom ID 2
1	metal coordination	sing	1:DC2:O2	2:NA1:NA
2	metal coordination	sing	1:DC2:OP1	2:NA1:NA
3	metal coordination	sing	1:DC2:OP2	2:NA1:NA
4	metal coordination	sing	1:DT3:OP1	2:NA1:NA
5	metal coordination	sing	1:DG4:OP1	2:NA1:NA
6	metal coordination	sing	1:DG4:OP2	2:NA1:NA
7	metal coordination	sing	1:3DR5:OP1	2:NA1:NA
8	metal coordination	sing	1:3DR5:OP2	2:NA1:NA
9	metal coordination	sing	1:DC6:OP1	2:NA1:NA
10	metal coordination	sing	1:DC6:O2	2:NA1:NA
11	metal coordination	sing	1:DC6:OP2	2:NA1:NA
12	metal coordination	sing	1:DC7:O2	2:NA1:NA
13	metal coordination	sing	1:DC7:OP1	2:NA1:NA
14	metal coordination	sing	1:DC7:O4'	2:NA1:NA
15	metal coordination	sing	1:DC7:OP2	2:NA1:NA
16	metal coordination	sing	1:DT8:OP1	2:NA1:NA
17	metal coordination	sing	1:DG9:OP1	2:NA1:NA

Source organism

Homo sapiens

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chemcal Shifts

¹H: 92 assignments Detail

Download

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ID	Entity ID	Seq ID	Comp ID	Atom ID	Atom type	Val	Val err	Ambig. code
1	1	1	DC	H1'	H	6.07	0.02	1
2	1	1	DC	H2'	H	1.93	0.02	1
3	1	1	DC	H2''	H	2.40	0.02	1
4	1	1	DC	H3'	H	4.76	0.02	1
5	1	1	DC	H4'	H	4.32	0.02	1
6	1	1	DC	H5	H	5.53	0.02	1
7	1	1	DC	H5'	H	3.88	0.02	1
8	1	1	DC	H5''	H	3.88	0.02	1
9	1	1	DC	H6	H	7.58	0.02	1
10	1	1	DC	H41	H	8.45	0.02	1
11	1	1	DC	H42	H	6.83	0.02	1
12	1	2	DC	H1'	H	6.50	0.02	1
13	1	2	DC	H2'	H	2.11	0.02	1
14	1	2	DC	H2''	H	2.53	0.02	1
15	1	2	DC	H3'	H	4.85	0.02	1
16	1	2	DC	H4'	H	4.46	0.02	1
17	1	2	DC	H5	H	6.23	0.02	1
18	1	2	DC	H5'	H	4.26	0.02	1
19	1	2	DC	H5''	H	4.11	0.02	1
20	1	2	DC	H6	H	8.19	0.02	1
21	1	3	DT	H1'	H	5.63	0.02	1
22	1	3	DT	H2'	H	1.86	0.02	1
23	1	3	DT	H2''	H	2.14	0.02	1
24	1	3	DT	H3'	H	4.69	0.02	1
25	1	3	DT	H4'	H	3.80	0.02	1
26	1	3	DT	H5'	H	3.95	0.02	1
27	1	3	DT	H5''	H	4.09	0.02	1
28	1	3	DT	H6	H	7.71	0.02	1
29	1	3	DT	H71	H	1.40	0.02	1
30	1	3	DT	H72	H	1.40	0.02	1
31	1	3	DT	H73	H	1.40	0.02	1
32	1	4	DG	H1	H	13.24	0.02	1
33	1	4	DG	H1'	H	6.02	0.02	1
34	1	4	DG	H2'	H	2.86	0.02	1
35	1	4	DG	H2''	H	2.86	0.02	1
36	1	4	DG	H3'	H	5.02	0.02	1
37	1	4	DG	H4'	H	4.3	0.02	1
38	1	4	DG	H5'	H	4.06	0.02	1
39	1	4	DG	H5''	H	3.61	0.02	1
40	1	4	DG	H8	H	7.82	0.02	1
41	1	4	DG	H21	H	8.93	0.02	1
42	1	4	DG	H22	H	5.82	0.02	1
43	1	5	3DR	H1'1	H	4.14	0.02	1
44	1	5	3DR	H1'2	H	4.07	0.02	1
45	1	5	3DR	H2'	H	2.29	0.02	1
46	1	5	3DR	H2''	H	2.19	0.02	1
47	1	5	3DR	H3'	H	4.67	0.02	1
48	1	5	3DR	H4'1	H	4.19	0.02	1
49	1	5	3DR	H5'	H	4.06	0.02	1
50	1	5	3DR	H5''	H	3.92	0.02	1
51	1	6	DC	H1'	H	6.13	0.02	1
52	1	6	DC	H2'	H	1.94	0.02	1
53	1	6	DC	H2''	H	2.32	0.02	1
54	1	6	DC	H3'	H	4.88	0.02	1
55	1	6	DC	H4'	H	4.48	0.02	1
56	1	6	DC	H5	H	5.57	0.02	1
57	1	6	DC	H5'	H	4.11	0.02	1
58	1	6	DC	H5''	H	4.14	0.02	1
59	1	6	DC	H6	H	7.46	0.02	1
60	1	6	DC	H41	H	8.37	0.02	1
61	1	6	DC	H42	H	6.89	0.02	1
62	1	7	DC	H1'	H	6.51	0.02	1
63	1	7	DC	H2'	H	2.09	0.02	1
64	1	7	DC	H2''	H	2.52	0.02	1
65	1	7	DC	H3'	H	4.88	0.02	1
66	1	7	DC	H4'	H	4.48	0.02	1
67	1	7	DC	H5	H	6.27	0.02	1
68	1	7	DC	H5'	H	4.30	0.02	1
69	1	7	DC	H5''	H	4.12	0.02	1
70	1	7	DC	H6	H	8.25	0.02	1
71	1	8	DT	H1'	H	5.59	0.02	1
72	1	8	DT	H2'	H	1.87	0.02	1
73	1	8	DT	H2''	H	2.13	0.02	1
74	1	8	DT	H3'	H	4.69	0.02	1
75	1	8	DT	H4'	H	3.87	0.02	1
76	1	8	DT	H5'	H	3.94	0.02	1
77	1	8	DT	H5''	H	4.09	0.02	1
78	1	8	DT	H6	H	7.67	0.02	1
79	1	8	DT	H71	H	1.37	0.02	1
80	1	8	DT	H72	H	1.37	0.02	1
81	1	8	DT	H73	H	1.37	0.02	1
82	1	9	DG	H1	H	13.25	0.02	1
83	1	9	DG	H1'	H	5.96	0.02	1
84	1	9	DG	H2'	H	2.86	0.02	1
85	1	9	DG	H2''	H	2.63	0.02	1
86	1	9	DG	H3'	H	4.67	0.02	1
87	1	9	DG	H4'	H	4.12	0.02	1
88	1	9	DG	H5'	H	3.99	0.02	1
89	1	9	DG	H5''	H	3.57	0.02	1
90	1	9	DG	H8	H	7.80	0.02	1
91	1	9	DG	H21	H	8.93	0.02	1
92	1	9	DG	H22	H	5.95	0.02	1

Release date

2020-07-08

Citation

Rational design of a reversible Mg(2+)/EDTA-controlled molecular switch based on a DNA minidumbbell
Wan, L., Lam, S.L., Lee, H.K., Guo, P.
Chem. Commun. (Camb). (2020), 56, 10127-10130, PubMed 32870195 , DOI 10.1039/d0cc03774e , Abstract

Experiments performed 3 experiments Detail