BMRB: 34798

Structure of an i-motif domain with the cytosine analog 1,3-diaza-2-oxophenoxacione (tC) at neutral pH

Authors

Mir, B., Serrano-Chacon, I., Terrazas, M., Gandioso, A., Garavis, M., Orozco, M., Escaja, N., Gonzalez, C.

Assembly

DNA (5'-D(*CP*(YCO)P*GP*TP*TP*CP*(DNR)P*GP*TP*TP*TP*TP*TP*CP*CP*GP*TP*TP*CP*(DNR)P*GP*T)-3')

Entity

1. DNA (5'-D(*CP*(YCO)P*GP*TP*TP*CP*(DNR)P*GP*TP*TP*TP*TP*TP*CP*CP*GP*TP*TP*CP*(DNR)P*GP*T)-3') (polymer, Thiol state: not present), 22 monomers, 6782.315 Da Detail

CXGTTCXGTT TTTCCGTTCX GT

Formula weight

6782.315 Da

Source organism

synthetic construct

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chemcal Shifts

¹H: 177 assignments Detail

Download

• NMR-STAR v3.1 (partial)
• BMRB/XML (partial)
• CSV
• TSV

ID	Entity ID	Seq ID	Comp ID	Atom ID	Atom type	Val	Val err	Ambig. code
1	1	1	DC	H1'	H	6.259	0.002
2	1	1	DC	H2'	H	2.510	0.003
3	1	1	DC	H2''	H	2.801	0.002
4	1	1	DC	H3'	H	4.951	0.002
5	1	1	DC	H5	H	6.039	0.000
6	1	1	DC	H6	H	7.850	0.003
7	1	1	DC	H41	H	7.302	0.000
8	1	1	DC	H42	H	8.381	0.000
9	1	2	YCO	H1'	H	6.044	0.000
10	1	2	YCO	H2'	H	1.204	0.001
11	1	2	YCO	H2''	H	1.835	0.003
12	1	2	YCO	H3'	H	4.794	0.002
13	1	2	YCO	H4	H	7.177	0.001
14	1	2	YCO	H6	H	6.072	0.004
15	1	2	YCO	H7	H	6.393	0.001
16	1	2	YCO	H8	H	6.662	0.003
17	1	2	YCO	H9	H	5.919	0.002
18	1	2	YCO	H10	H	9.823	0.001
19	1	3	DG	H1	H	13.934	0.007
20	1	3	DG	H1'	H	6.066	0.002
21	1	3	DG	H2'	H	2.772	0.003
22	1	3	DG	H2''	H	3.056	0.003
23	1	3	DG	H3'	H	5.019	0.004
24	1	3	DG	H8	H	8.108	0.001
25	1	3	DG	H21	H	7.040	0.006
26	1	3	DG	H22	H	8.793	0.005
27	1	4	DT	H1'	H	6.206	0.002
28	1	4	DT	H2'	H	2.071	0.001
29	1	4	DT	H2''	H	2.327	0.002
30	1	4	DT	H3'	H	3.829	0.000
31	1	4	DT	H6	H	7.648	0.002
32	1	4	DT	H71	H	1.779	0.003
33	1	4	DT	H72	H	1.779	0.003
34	1	4	DT	H73	H	1.779	0.003
35	1	5	DT	H1'	H	6.497	0.002
36	1	5	DT	H2'	H	2.324	0.000
37	1	5	DT	H2''	H	2.558	0.003
38	1	5	DT	H3'	H	4.631	0.000
39	1	5	DT	H6	H	7.860	0.000
40	1	5	DT	H71	H	1.936	0.000
41	1	5	DT	H72	H	1.936	0.000
42	1	5	DT	H73	H	1.936	0.000
43	1	6	DC	H1'	H	6.373	0.003
44	1	6	DC	H2'	H	2.462	0.002
45	1	6	DC	H2''	H	2.621	0.008
46	1	6	DC	H3'	H	4.927	0.002
47	1	6	DC	H5	H	6.231	0.001
48	1	6	DC	H6	H	8.024	0.002
49	1	6	DC	H41	H	7.662	0.003
50	1	6	DC	H42	H	8.754	0.001
51	1	7	DNR	H1'	H	6.176	0.007
52	1	7	DNR	H2'	H	1.236	0.001
53	1	7	DNR	H2''	H	2.042	0.002
54	1	7	DNR	H3+	H	15.574	0.005
55	1	7	DNR	H3'	H	4.792	0.002
56	1	7	DNR	H5	H	5.737	0.006
57	1	7	DNR	H6	H	7.644	0.009
58	1	7	DNR	H41	H	8.058	0.000
59	1	7	DNR	H42	H	8.671	0.002
60	1	8	DG	H1	H	13.441	0.003
61	1	8	DG	H1'	H	5.997	0.005
62	1	8	DG	H2'	H	3.030	0.002
63	1	8	DG	H2''	H	2.685	0.002
64	1	8	DG	H3'	H	5.047	0.003
65	1	8	DG	H8	H	8.153	0.002
66	1	8	DG	H21	H	7.188	0.001
67	1	8	DG	H22	H	8.220	0.000
68	1	9	DT	H1'	H	6.008	0.004
69	1	9	DT	H2'	H	2.006	0.003
70	1	9	DT	H2''	H	2.303	0.001
71	1	9	DT	H3'	H	4.781	0.001
72	1	9	DT	H6	H	7.637	0.002
73	1	9	DT	H71	H	1.740	0.002
74	1	9	DT	H72	H	1.740	0.002
75	1	9	DT	H73	H	1.740	0.002
76	1	10	DT	H1'	H	6.136	0.002
77	1	10	DT	H2'	H	2.317	0.003
78	1	10	DT	H2''	H	2.583	0.003
79	1	10	DT	H3'	H	4.910	0.000
80	1	10	DT	H6	H	7.608	0.001
81	1	10	DT	H71	H	1.803	0.000
82	1	10	DT	H72	H	1.803	0.000
83	1	10	DT	H73	H	1.803	0.000
84	1	11	DT	H1'	H	6.414	0.002
85	1	11	DT	H2'	H	2.427	0.001
86	1	11	DT	H2''	H	2.568	0.000
87	1	11	DT	H3'	H	4.932	0.000
88	1	11	DT	H6	H	7.761	0.002
89	1	11	DT	H71	H	1.938	0.000
90	1	11	DT	H72	H	1.938	0.000
91	1	11	DT	H73	H	1.938	0.000
92	1	12	DT	H1'	H	6.352	0.001
93	1	12	DT	H2'	H	2.381	0.003
94	1	12	DT	H2''	H	2.622	0.000
95	1	12	DT	H3'	H	4.953	0.000
96	1	12	DT	H6	H	7.784	0.006
97	1	12	DT	H71	H	1.936	0.000
98	1	12	DT	H72	H	1.936	0.000
99	1	12	DT	H73	H	1.936	0.000
100	1	13	DT	H1'	H	6.449	0.002
101	1	13	DT	H2'	H	2.415	0.004
102	1	13	DT	H2''	H	2.536	0.003
103	1	13	DT	H3'	H	5.057	0.001
104	1	13	DT	H6	H	7.814	0.002
105	1	13	DT	H71	H	2.004	0.003
106	1	13	DT	H72	H	2.004	0.003
107	1	13	DT	H73	H	2.004	0.003
108	1	14	DC	H1'	H	6.327	0.002
109	1	14	DC	H2'	H	2.263	0.004
110	1	14	DC	H2''	H	2.671	0.004
111	1	14	DC	H3'	H	4.934	0.002
112	1	14	DC	H5	H	5.539	0.003
113	1	14	DC	H6	H	7.748	0.002
114	1	14	DC	H41	H	6.371	0.002
115	1	14	DC	H42	H	8.623	0.002
116	1	15	DC	H1'	H	6.025	0.006
117	1	15	DC	H2'	H	0.876	0.002
118	1	15	DC	H2''	H	2.410	0.003
119	1	15	DC	H3'	H	4.437	0.001
120	1	15	DC	H5	H	5.311	0.000
121	1	15	DC	H6	H	7.526	0.004
122	1	15	DC	H42	H	10.830	0.000
123	1	16	DG	H1	H	12.819	0.003
124	1	16	DG	H1'	H	6.110	0.000
125	1	16	DG	H2'	H	2.968	0.000
126	1	16	DG	H2''	H	2.648	0.000
127	1	16	DG	H3'	H	5.039	0.000
128	1	16	DG	H8	H	8.210	0.002
129	1	17	DT	H1'	H	6.114	0.007
130	1	17	DT	H2'	H	1.996	0.001
131	1	17	DT	H2''	H	2.391	0.001
132	1	17	DT	H3'	H	4.772	0.003
133	1	17	DT	H6	H	7.533	0.001
134	1	17	DT	H71	H	1.744	0.007
135	1	17	DT	H72	H	1.744	0.007
136	1	17	DT	H73	H	1.744	0.007
137	1	18	DT	H1'	H	6.429	0.002
138	1	18	DT	H2'	H	2.113	0.001
139	1	18	DT	H2''	H	2.555	0.001
140	1	18	DT	H3'	H	4.702	0.001
141	1	18	DT	H6	H	7.815	0.001
142	1	18	DT	H71	H	1.928	0.000
143	1	18	DT	H72	H	1.928	0.000
144	1	18	DT	H73	H	1.928	0.000
145	1	19	DC	H1'	H	6.436	0.002
146	1	19	DC	H2'	H	2.329	0.002
147	1	19	DC	H2''	H	2.607	0.006
148	1	19	DC	H3'	H	4.881	0.000
149	1	19	DC	H5	H	6.028	0.002
150	1	19	DC	H6	H	7.850	0.004
151	1	19	DC	H41	H	7.219	0.002
152	1	19	DC	H42	H	8.742	0.007
153	1	20	DNR	H1'	H	6.230	0.001
154	1	20	DNR	H2'	H	0.955	0.004
155	1	20	DNR	H2''	H	2.538	0.001
156	1	20	DNR	H3+	H	15.014	0.007
157	1	20	DNR	H3'	H	4.346	0.001
158	1	20	DNR	H5	H	6.024	0.001
159	1	20	DNR	H6	H	7.530	0.002
160	1	20	DNR	H41	H	8.855	0.005
161	1	20	DNR	H42	H	11.344	0.007
162	1	21	DG	H1	H	13.366	0.008
163	1	21	DG	H1'	H	6.116	0.001
164	1	21	DG	H2'	H	2.976	0.006
165	1	21	DG	H2''	H	2.638	0.000
166	1	21	DG	H3'	H	5.029	0.001
167	1	21	DG	H8	H	8.271	0.001
168	1	21	DG	H21	H	7.194	0.001
169	1	21	DG	H22	H	8.218	0.000
170	1	22	DT	H1'	H	5.766	0.001
171	1	22	DT	H2'	H	1.900	0.000
172	1	22	DT	H2''	H	2.103	0.001
173	1	22	DT	H3'	H	4.361	0.001
174	1	22	DT	H6	H	7.566	0.003
175	1	22	DT	H71	H	1.742	0.003
176	1	22	DT	H72	H	1.742	0.003
177	1	22	DT	H73	H	1.742	0.003

Release date

2023-06-15

Citation

Site-specific incorporation of a fluorescent nucleobase analog enhances i-motif stability and allows monitoring of i-motif folding inside cells
Mir, B., Serrano-Chacon, I., Terrazas, M., Gandioso, A., Garavis, M., Orozco, M., Escaja, N., Gonzalez, C.
Nucleic Acids Res. (2024), PubMed 38366792 , DOI 10.1093/nar/gkae106 , Abstract

Experiments performed 6 experiments Detail

Chemical shift validation 3 contents Detail