BMRB: 34741

Solution structure of a phenyl-indoloquinoline intercalating into a quadruplex-duplex hybrid

Authors

Vianney, Y.M., Weisz, K.

Assembly

DNA (27-MER)

Entity

1. DNA (27-MER), entity 1 (polymer, Thiol state: not present), 27 monomers, 8508.375 Da Detail

GGTTGGCGCG AAGCATTCGC GGGTTGG

2. DNA (27-MER), entity LNF (non-polymer), 493.662 Da

Total weight

9002.037 Da

Max. entity weight

8508.375 Da

Source organism

synthetic construct

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chemcal Shifts

¹H: 220, ¹³C: 30 assignments Detail

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• BMRB/XML (partial)
• CSV
• TSV

ID	Entity ID	Seq ID	Comp ID	Atom ID	Atom type	Val	Val err	Ambig. code
1	1	1	DG	H1	H	12.139	0.004	1
2	1	1	DG	H1'	H	6.009	0.001	1
3	1	1	DG	H2'	H	2.795	0.001	1
4	1	1	DG	H2''	H	2.943	0.01	1
5	1	1	DG	H3'	H	4.980		1
6	1	1	DG	H8	H	7.432	0.003	1
7	1	1	DG	C8	C	141.397		1
8	1	2	DG	H1	H	12.159	0.004	1
9	1	2	DG	H1'	H	5.988	0.002	1
10	1	2	DG	H2'	H	2.966	0.003	1
11	1	2	DG	H2''	H	2.288	0.002	1
12	1	2	DG	H3'	H	5.098	0.001	1
13	1	2	DG	H8	H	8.107	0.001	1
14	1	2	DG	C8	C	137.843		1
15	1	3	DT	H1'	H	6.133	0.002	1
16	1	3	DT	H2'	H	2.144	0.003	1
17	1	3	DT	H2''	H	2.501	0.002	1
18	1	3	DT	H3'	H	4.831	0.004	1
19	1	3	DT	H6	H	7.799	0.001	1
20	1	3	DT	H71	H	1.920	0.001	1
21	1	3	DT	H72	H	1.920	0.001	1
22	1	3	DT	H73	H	1.920	0.001	1
23	1	3	DT	C6	C	139.324		1
24	1	4	DT	H1'	H	5.909	0.003	1
25	1	4	DT	H2'	H	1.967	0.004	1
26	1	4	DT	H2''	H	2.519	0.002	1
27	1	4	DT	H3'	H	4.816	0.008	1
28	1	4	DT	H6	H	7.036	0.002	1
29	1	4	DT	H71	H	0.977	0.002	1
30	1	4	DT	H72	H	0.977	0.002	1
31	1	4	DT	H73	H	0.977	0.002	1
32	1	4	DT	C6	C	137.622		1
33	1	5	DG	H1	H	12.175	0.002	1
34	1	5	DG	H1'	H	5.886	0.002	1
35	1	5	DG	H2'	H	3.364	0.002	1
36	1	5	DG	H2''	H	2.841	0.003	1
37	1	5	DG	H3'	H	4.820	0.002	1
38	1	5	DG	H8	H	7.250	0.002	1
39	1	5	DG	C8	C	142.696		1
40	1	6	DG	H1	H	11.092	0.005	1
41	1	6	DG	H1'	H	5.507	0.001	1
42	1	6	DG	H2'	H	2.691	0.008	1
43	1	6	DG	H2''	H	2.252		1
44	1	6	DG	H3'	H	5.060	0.002	1
45	1	6	DG	H8	H	7.849	0.001	1
46	1	6	DG	C8	C	137.856		1
47	1	7	DC	H1'	H	5.090	0.001	1
48	1	7	DC	H2'	H	2.294	0.004	2
49	1	7	DC	H2''	H	2.289		2
50	1	7	DC	H3'	H	4.799	0.0	1
51	1	7	DC	H5	H	5.168	0.001	1
52	1	7	DC	H6	H	7.296	0.002	1
53	1	7	DC	H41	H	7.070	0.002	1
54	1	7	DC	H42	H	6.087	0.005	1
55	1	7	DC	C6	C	143.311		1
56	1	8	DG	H1	H	12.625	0.002	1
57	1	8	DG	H1'	H	5.895	0.002	1
58	1	8	DG	H2'	H	2.605	0.001	1
59	1	8	DG	H2''	H	2.686	0.01	1
60	1	8	DG	H3'	H	4.980	0.002	1
61	1	8	DG	H8	H	7.830	0.003	1
62	1	8	DG	C8	C	138.192		1
63	1	9	DC	H1'	H	5.528	0.002	1
64	1	9	DC	H2'	H	1.817	0.005	1
65	1	9	DC	H2''	H	2.230	0.003	1
66	1	9	DC	H3'	H	4.748	0.005	1
67	1	9	DC	H5	H	5.276	0.002	1
68	1	9	DC	H6	H	7.171	0.003	1
69	1	9	DC	H41	H	8.207	0.001	1
70	1	9	DC	H42	H	6.252	0.001	1
71	1	9	DC	C6	C	143.514		1
72	1	10	DG	H1	H	12.660	0.004	1
73	1	10	DG	H1'	H	5.351	0.004	1
74	1	10	DG	H2'	H	2.555	0.003	1
75	1	10	DG	H2''	H	2.644	0.004	1
76	1	10	DG	H3'	H	4.906	0.001	1
77	1	10	DG	H8	H	7.783	0.002	1
78	1	10	DG	C8	C	138.200		1
79	1	11	DA	H1'	H	5.836	0.002	1
80	1	11	DA	H2	H	7.521	0.006	1
81	1	11	DA	H2'	H	2.244	0.002	1
82	1	11	DA	H2''	H	2.560	0.002	1
83	1	11	DA	H3'	H	4.910	0.001	1
84	1	11	DA	H8	H	7.851	0.001	1
85	1	11	DA	C2	C	154.459		1
86	1	11	DA	C8	C	140.931		1
87	1	12	DA	H1'	H	5.835	0.003	1
88	1	12	DA	H2	H	7.651	0.007	1
89	1	12	DA	H2'	H	2.010	0.002	1
90	1	12	DA	H2''	H	2.380	0.003	1
91	1	12	DA	H3'	H	4.831	0.004	1
92	1	12	DA	H8	H	7.410	0.002	1
93	1	12	DA	C2	C	154.931		1
94	1	12	DA	C8	C	139.881		1
95	1	13	DG	H1'	H	5.340	0.003	1
96	1	13	DG	H2'	H	2.584	0.003	1
97	1	13	DG	H2''	H	2.303	0.001	1
98	1	13	DG	H3'	H	4.765	0.004	1
99	1	13	DG	H8	H	7.998	0.003	1
100	1	13	DG	C8	C	138.969		1
101	1	14	DC	H1'	H	5.658	0.003	1
102	1	14	DC	H2'	H	1.550	0.004	1
103	1	14	DC	H2''	H	2.002	0.003	1
104	1	14	DC	H3'	H	4.374	0.002	1
105	1	14	DC	H5	H	5.174	0.002	1
106	1	14	DC	H6	H	7.157	0.001	1
107	1	14	DC	C6	C	143.501		1
108	1	15	DA	H1'	H	6.263	0.003	1
109	1	15	DA	H2	H	7.996		1
110	1	15	DA	H2'	H	2.950	0.005	1
111	1	15	DA	H2''	H	2.889	0.003	1
112	1	15	DA	H3'	H	4.772	0.001	1
113	1	15	DA	H8	H	8.037	0.003	1
114	1	15	DA	C2	C	155.388		1
115	1	15	DA	C8	C	143.049		1
116	1	16	DT	H1'	H	5.630	0.001	1
117	1	16	DT	H2'	H	2.059	0.006	1
118	1	16	DT	H2''	H	2.442	0.005	1
119	1	16	DT	H3	H	13.228	0.0	1
120	1	16	DT	H3'	H	4.691	0.003	1
121	1	16	DT	H6	H	7.350	0.001	1
122	1	16	DT	H71	H	1.784	0.001	1
123	1	16	DT	H72	H	1.784	0.001	1
124	1	16	DT	H73	H	1.784	0.001	1
125	1	16	DT	C6	C	139.348		1
126	1	17	DT	H1'	H	5.981	0.004	1
127	1	17	DT	H2'	H	2.119	0.003	1
128	1	17	DT	H2''	H	2.407	0.003	1
129	1	17	DT	H3	H	13.807	0.002	1
130	1	17	DT	H3'	H	4.804	0.006	1
131	1	17	DT	H6	H	7.353	0.002	1
132	1	17	DT	H71	H	1.561	0.0	1
133	1	17	DT	H72	H	1.561	0.0	1
134	1	17	DT	H73	H	1.561	0.0	1
135	1	17	DT	C6	C	139.348		1
136	1	18	DC	H1'	H	5.519	0.003	1
137	1	18	DC	H2'	H	1.952	0.004	1
138	1	18	DC	H2''	H	2.258	0.007	1
139	1	18	DC	H3'	H	4.743	0.004	1
140	1	18	DC	H5	H	5.565	0.002	1
141	1	18	DC	H6	H	7.381	0.001	1
142	1	18	DC	H41	H	8.439	0.001	1
143	1	18	DC	H42	H	6.779	0.003	1
144	1	18	DC	C6	C	143.501		1
145	1	19	DG	H1	H	12.727	0.001	1
146	1	19	DG	H1'	H	5.623	0.005	1
147	1	19	DG	H2'	H	2.435	0.001	1
148	1	19	DG	H2''	H	2.487	0.003	1
149	1	19	DG	H3'	H	4.813	0.004	1
150	1	19	DG	H8	H	7.708	0.002	1
151	1	19	DG	C8	C	138.127		1
152	1	20	DC	H1'	H	5.605	0.002	1
153	1	20	DC	H2'	H	1.278	0.003	1
154	1	20	DC	H2''	H	1.990	0.004	1
155	1	20	DC	H3'	H	4.667	0.001	1
156	1	20	DC	H5	H	4.956	0.002	1
157	1	20	DC	H6	H	6.885	0.003	1
158	1	20	DC	H41	H	7.859	0.0	1
159	1	20	DC	H42	H	5.994	0.001	1
160	1	20	DC	C6	C	142.045		1
161	1	21	DG	H1	H	12.028	0.003	1
162	1	21	DG	H1'	H	5.289	0.002	1
163	1	21	DG	H2'	H	2.557	0.005	1
164	1	21	DG	H2''	H	2.612	0.002	1
165	1	21	DG	H3'	H	4.988	0.002	1
166	1	21	DG	H8	H	7.665	0.001	1
167	1	21	DG	C8	C	138.282		1
168	1	22	DG	H1	H	10.817	0.003	1
169	1	22	DG	H1'	H	5.828	0.001	1
170	1	22	DG	H2'	H	3.242	0.003	1
171	1	22	DG	H2''	H	2.658	0.003	1
172	1	22	DG	H3'	H	4.891	0.0	1
173	1	22	DG	H8	H	7.172	0.002	1
174	1	22	DG	C8	C	142.208		1
175	1	23	DG	H1	H	11.531	0.002	1
176	1	23	DG	H1'	H	5.853	0.004	1
177	1	23	DG	H2'	H	2.870	0.005	1
178	1	23	DG	H2''	H	2.207	0.004	1
179	1	23	DG	H3'	H	5.022	0.001	1
180	1	23	DG	H8	H	8.039	0.002	1
181	1	23	DG	C8	C	137.741		1
182	1	24	DT	H1'	H	6.108	0.001	1
183	1	24	DT	H2'	H	2.101	0.003	1
184	1	24	DT	H2''	H	2.470	0.005	1
185	1	24	DT	H3'	H	4.798	0.002	1
186	1	24	DT	H6	H	7.740	0.002	1
187	1	24	DT	H71	H	1.857	0.002	1
188	1	24	DT	H72	H	1.857	0.002	1
189	1	24	DT	H73	H	1.857	0.002	1
190	1	24	DT	C6	C	139.272		1
191	1	25	DT	H1'	H	5.903	0.001	1
192	1	25	DT	H2'	H	1.911	0.001	1
193	1	25	DT	H2''	H	2.513	0.002	1
194	1	25	DT	H3'	H	4.795		1
195	1	25	DT	H6	H	6.987	0.001	1
196	1	25	DT	H71	H	0.865	0.004	1
197	1	25	DT	H72	H	0.865	0.004	1
198	1	25	DT	H73	H	0.865	0.004	1
199	1	25	DT	C6	C	137.622		1
200	1	26	DG	H1	H	11.718	0.003	1
201	1	26	DG	H1'	H	5.962	0.001	1
202	1	26	DG	H2'	H	3.303	0.003	1
203	1	26	DG	H2''	H	2.799	0.002	1
204	1	26	DG	H3'	H	4.816	0.001	1
205	1	26	DG	H8	H	7.393	0.002	1
206	1	26	DG	C8	C	142.190		1
207	1	27	DG	H1	H	11.849	0.005	1
208	1	27	DG	H1'	H	6.056	0.007	1
209	1	27	DG	H2'	H	2.711	0.002	1
210	1	27	DG	H2''	H	2.337	0.002	1
211	1	27	DG	H3'	H	4.756	0.004	1
212	1	27	DG	H8	H	8.043	0.002	1
213	1	27	DG	C8	C	137.742		1
214	2	1	LNF	H1	H	7.01	0.0	1
215	2	1	LNF	H2	H	6.90	0.0	1
216	2	1	LNF	H3	H	7.38	0.0	1
217	2	1	LNF	H4A1	H	2.61	0.0	1
218	2	1	LNF	H4A2	H	2.61	0.0	1
219	2	1	LNF	H4A3	H	2.61	0.0	1
220	2	1	LNF	H5A1	H	4.73	0.0	1
221	2	1	LNF	H5A2	H	4.73	0.0	1
222	2	1	LNF	H5A3	H	4.73	0.0	1
223	2	1	LNF	H6	H	7.76	0.0	1
224	2	1	LNF	H7	H	6.80	0.0	1
225	2	1	LNF	H8	H	7.00	0.0	1
226	2	1	LNF	H9A1	H	1.96	0.0	1
227	2	1	LNF	H9A2	H	1.96	0.0	1
228	2	1	LNF	H9A3	H	1.96	0.0	1
229	2	1	LNF	H10	H	10.33	0.0	1
230	2	1	LNF	H12	H	7.48	0.0	1
231	2	1	LNF	H13	H	7.59	0.0	1
232	2	1	LNF	H14	H	8.03	0.0	1
233	2	1	LNF	H15	H	8.03	0.0	1
234	2	1	LNF	H16	H	8.30	0.0	1
235	2	1	LNF	H171	H	3.38	0.0	1
236	2	1	LNF	H172	H	3.01	0.0	1
237	2	1	LNF	H181	H	1.87	0.0	1
238	2	1	LNF	H182	H	1.87	0.0	1
239	2	1	LNF	H191	H	3.06	0.0	1
240	2	1	LNF	H192	H	3.06	0.0	1
241	2	1	LNF	H201	H	3.13	0.0	1
242	2	1	LNF	H202	H	3.13	0.0	1
243	2	1	LNF	H221	H	3.13	0.0	1
244	2	1	LNF	H222	H	3.13	0.0	1
245	2	1	LNF	H211	H	1.19	0.0	1
246	2	1	LNF	H212	H	1.19	0.0	1
247	2	1	LNF	H213	H	1.19	0.0	1
248	2	1	LNF	H231	H	1.19	0.0	1
249	2	1	LNF	H232	H	1.19	0.0	1
250	2	1	LNF	H233	H	1.19	0.0	1

Release date

2022-07-12

Citation

High-affinity binding at quadruplex-duplex junctions: rather the rule than the exception
Vianney, Y.M., Weisz, K.
Nucleic Acids Res. (2022), 50, 11948-11964, PubMed 36416262 , DOI 10.1093/nar/gkac1088 , Abstract

Experiments performed 4 experiments Detail

Chemical shift validation 4 contents Detail