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BMRB: 34740

Solution structure of Phen-DC3 intercalating into a quadruplex-duplex hybrid

Authors

Vianney, Y.M., Weisz, K.

Assembly

DNA (36-MER)

Entity

1. DNA (36-MER), entity 1 (polymer, Thiol state: not present), 36 monomers, 11273.22 Da Detail

XTAGGTGGGT AGGGTGGGCT AGTCATTTTG ACTAGG

2. DNA (36-MER), entity PQ3 (non-polymer), 550.609 Da

Total weight

11823.829 Da

Max. entity weight

11273.22 Da

Source organism

synthetic construct

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chemcal Shifts

¹H: 249, ¹³C: 41 assignments Detail

ID	Entity ID	Seq ID	Comp ID	Atom ID	Atom type	Val	Val err	Ambig. code
1	1	1	THM	H1'	H	5.623	0.004	1
2	1	1	THM	H2'	H	1.954	0.002	1
3	1	1	THM	H2''	H	2.139	0.003	1
4	1	1	THM	H3'	H	4.326	0.003	1
5	1	1	THM	H6	H	7.330	0.002	1
6	1	1	THM	H71	H	1.551	0.004	1
7	1	1	THM	H72	H	1.551	0.004	1
8	1	1	THM	H73	H	1.551	0.004	1
9	1	1	THM	C6	C	139.428		1
10	1	2	DT	H1'	H	5.628	0.007	1
11	1	2	DT	H2'	H	1.579	0.003	1
12	1	2	DT	H2''	H	2.012	0.005	1
13	1	2	DT	H3'	H	4.439	0.001	1
14	1	2	DT	H6	H	7.107	0.002	1
15	1	2	DT	H71	H	1.443	0.003	1
16	1	2	DT	H72	H	1.443	0.003	1
17	1	2	DT	H73	H	1.443	0.003	1
18	1	2	DT	C6	C	139.351		1
19	1	3	DA	H1'	H	5.677	0.006	1
20	1	3	DA	H2	H	7.795	0.003	1
21	1	3	DA	H2'	H	2.537	0.003	1
22	1	3	DA	H2''	H	2.579	0.004	1
23	1	3	DA	H3'	H	4.773	0.004	1
24	1	3	DA	H8	H	7.956	0.002	1
25	1	3	DA	C8	C	142.541		1
26	1	4	DG	H1	H	11.240	0.003	1
27	1	4	DG	H1'	H	5.988	0.004	1
28	1	4	DG	H2'	H	2.488	0.01	1
29	1	4	DG	H2''	H	2.869	0.005	1
30	1	4	DG	H3'	H	4.875	0.002	1
31	1	4	DG	H8	H	7.847	0.002	1
32	1	4	DG	C8	C	137.874		1
33	1	5	DG	H1	H	11.158	0.001	1
34	1	5	DG	H1'	H	5.982	0.004	1
35	1	5	DG	H2'	H	2.451	0.002	1
36	1	5	DG	H2''	H	2.365	0.005	1
37	1	5	DG	H3'	H	4.966	0.003	1
38	1	5	DG	H8	H	7.355	0.002	1
39	1	5	DG	C8	C	137.601		1
40	1	6	DT	H1'	H	6.395	0.003	1
41	1	6	DT	H2'	H	2.404	0.003	1
42	1	6	DT	H2''	H	2.607	0.001	1
43	1	6	DT	H3'	H	4.977	0.001	1
44	1	6	DT	H6	H	7.808	0.001	1
45	1	6	DT	H71	H	1.942	0.0	1
46	1	6	DT	H72	H	1.942	0.0	1
47	1	6	DT	H73	H	1.942	0.0	1
48	1	6	DT	C6	C	140.208		1
49	1	7	DG	H1	H	11.502	0.001	1
50	1	7	DG	H1'	H	6.010	0.003	1
51	1	7	DG	H2'	H	2.619	0.005	1
52	1	7	DG	H2''	H	2.828	0.003	1
53	1	7	DG	H3'	H	4.856	0.001	1
54	1	7	DG	H8	H	8.091	0.002	1
55	1	7	DG	C8	C	138.524		1
56	1	8	DG	H1	H	11.100	0.003	1
57	1	8	DG	H1'	H	6.052	0.003	1
58	1	8	DG	H2'	H	2.590	0.01	1
59	1	8	DG	H2''	H	2.842	0.009	1
60	1	8	DG	H3'	H	5.008	0.002	1
61	1	8	DG	H8	H	7.718	0.002	1
62	1	8	DG	C8	C	138.041		1
63	1	9	DG	H1	H	10.741	0.002	1
64	1	9	DG	H1'	H	6.105	0.003	1
65	1	9	DG	H2'	H	2.823	0.004	1
66	1	9	DG	H2''	H	2.787	0.007	1
67	1	9	DG	H3'	H	5.100	0.001	1
68	1	9	DG	H8	H	7.680	0.001	1
69	1	9	DG	C8	C	137.768		1
70	1	10	DT	H1'	H	6.268	0.002	1
71	1	10	DT	H2'	H	2.273	0.003	1
72	1	10	DT	H2''	H	2.478	0.004	1
73	1	10	DT	H3'	H	4.765	0.001	1
74	1	10	DT	H6	H	7.703	0.005	1
75	1	10	DT	H71	H	1.976		1
76	1	10	DT	H72	H	1.976		1
77	1	10	DT	H73	H	1.976		1
78	1	10	DT	C6	C	140.171		1
79	1	11	DA	H1'	H	6.617	0.005	1
80	1	11	DA	H2	H	8.371	0.005	1
81	1	11	DA	H2'	H	2.985	0.001	1
82	1	11	DA	H2''	H	2.897	0.003	1
83	1	11	DA	H3'	H	5.070	0.002	1
84	1	11	DA	H8	H	8.559	0.004	1
85	1	11	DA	C2	C	154.373		1
86	1	11	DA	C8	C	143.504		1
87	1	12	DG	H1	H	11.658	0.005	1
88	1	12	DG	H1'	H	6.049	0.003	1
89	1	12	DG	H2'	H	2.549	0.003	1
90	1	12	DG	H2''	H	2.854	0.002	1
91	1	12	DG	H3'	H	4.901	0.004	1
92	1	12	DG	H8	H	7.924	0.001	1
93	1	12	DG	C8	C	138.269		1
94	1	13	DG	H1	H	11.079	0.002	1
95	1	13	DG	H1'	H	6.121	0.004	1
96	1	13	DG	H2'	H	2.546	0.004	1
97	1	13	DG	H2''	H	2.910	0.004	1
98	1	13	DG	H3'	H	4.998	0.002	1
99	1	13	DG	H8	H	7.662	0.003	1
100	1	13	DG	C8	C	138.011		1
101	1	14	DG	H1	H	10.459	0.002	1
102	1	14	DG	H1'	H	6.101	0.002	1
103	1	14	DG	H2'	H	2.815	0.004	1
104	1	14	DG	H2''	H	2.758	0.004	1
105	1	14	DG	H3'	H	5.215	0.001	1
106	1	14	DG	H8	H	7.668	0.003	1
107	1	14	DG	C8	C	138.006		1
108	1	15	DT	H1'	H	6.478	0.002	1
109	1	15	DT	H2'	H	2.471	0.003	1
110	1	15	DT	H2''	H	2.638	0.002	1
111	1	15	DT	H3'	H	5.034	0.002	1
112	1	15	DT	H6	H	7.843	0.001	1
113	1	15	DT	H71	H	1.998	0.001	1
114	1	15	DT	H72	H	1.998	0.001	1
115	1	15	DT	H73	H	1.998	0.001	1
116	1	15	DT	C6	C	139.937		1
117	1	16	DG	H1	H	11.083	0.003	1
118	1	16	DG	H1'	H	5.953	0.004	1
119	1	16	DG	H2'	H	2.322	0.004	1
120	1	16	DG	H2''	H	2.729	0.004	1
121	1	16	DG	H3'	H	4.959	0.004	1
122	1	16	DG	H8	H	7.786	0.002	1
123	1	16	DG	C8	C	137.803		1
124	1	17	DG	H1	H	11.000	0.003	1
125	1	17	DG	H1'	H	5.963	0.002	1
126	1	17	DG	H2'	H	2.566	0.003	1
127	1	17	DG	H2''	H	2.848	0.001	1
128	1	17	DG	H3'	H	5.055	0.001	1
129	1	17	DG	H8	H	7.656	0.001	1
130	1	17	DG	C8	C	138.023	0.018	1
131	1	18	DG	H1	H	10.406	0.001	1
132	1	18	DG	H1'	H	5.936	0.002	1
133	1	18	DG	H2'	H	2.850	0.001	1
134	1	18	DG	H2''	H	2.796	0.003	1
135	1	18	DG	H3'	H	5.191	0.002	1
136	1	18	DG	H8	H	7.772	0.002	1
137	1	18	DG	C8	C	138.128	0.015	1
138	1	19	DC	H1'	H	5.709	0.004	1
139	1	19	DC	H2'	H	2.203	0.003	1
140	1	19	DC	H2''	H	2.247	0.003	1
141	1	19	DC	H3'	H	4.798	0.002	1
142	1	19	DC	H5	H	5.582	0.002	1
143	1	19	DC	H6	H	7.618	0.001	1
144	1	19	DC	H41	H	6.493	0.003	1
145	1	19	DC	H42	H	7.289	0.002	1
146	1	19	DC	C6	C	143.242		1
147	1	20	DT	H1'	H	5.312	0.004	1
148	1	20	DT	H2'	H	2.026	0.002	1
149	1	20	DT	H2''	H	2.254	0.001	1
150	1	20	DT	H3	H	13.252	0.003	1
151	1	20	DT	H3'	H	4.798	0.001	1
152	1	20	DT	H6	H	7.214	0.002	1
153	1	20	DT	H71	H	1.524	0.002	1
154	1	20	DT	H72	H	1.524	0.002	1
155	1	20	DT	H73	H	1.524	0.002	1
156	1	20	DT	C6	C	139.458		1
157	1	21	DA	H1'	H	5.942	0.004	1
158	1	21	DA	H2	H	7.139	0.002	1
159	1	21	DA	H2'	H	2.739	0.004	1
160	1	21	DA	H2''	H	2.822	0.005	1
161	1	21	DA	H3'	H	4.977	0.001	1
162	1	21	DA	H8	H	8.159	0.002	1
163	1	21	DA	C2	C	153.841		1
164	1	21	DA	C8	C	141.809		1
165	1	22	DG	H1	H	12.938	0.004	1
166	1	22	DG	H1'	H	5.694	0.004	1
167	1	22	DG	H2'	H	2.361	0.004	1
168	1	22	DG	H2''	H	2.581	0.002	1
169	1	22	DG	H3'	H	4.750	0.001	1
170	1	22	DG	H8	H	7.495	0.001	1
171	1	22	DG	C8	C	137.115		1
172	1	23	DT	H1'	H	5.826	0.003	1
173	1	23	DT	H2'	H	1.906	0.002	1
174	1	23	DT	H2''	H	2.312	0.002	1
175	1	23	DT	H3	H	13.524	0.002	1
176	1	23	DT	H3'	H	4.695	0.0	1
177	1	23	DT	H6	H	7.091	0.002	1
178	1	23	DT	H71	H	1.186	0.003	1
179	1	23	DT	H72	H	1.186	0.003	1
180	1	23	DT	H73	H	1.186	0.003	1
181	1	23	DT	C6	C	139.041		1
182	1	24	DC	H1'	H	5.576	0.005	1
183	1	24	DC	H2'	H	1.707	0.002	1
184	1	24	DC	H2''	H	2.176	0.002	1
185	1	24	DC	H3'	H	4.697	0.003	1
186	1	24	DC	H5	H	5.565	0.002	1
187	1	24	DC	H6	H	7.284	0.003	1
188	1	24	DC	H41	H	6.889	0.002	1
189	1	24	DC	H42	H	8.454	0.001	1
190	1	24	DC	C6	C	143.552		1
191	1	25	DA	H1'	H	6.140	0.002	1
192	1	25	DA	H2	H	7.862	0.001	1
193	1	25	DA	H2'	H	2.665	0.001	1
194	1	25	DA	H2''	H	2.507	0.002	1
195	1	25	DA	H3'	H	4.927	0.003	1
196	1	25	DA	H8	H	8.131	0.002	1
197	1	25	DA	C2	C	154.893		1
198	1	25	DA	C8	C	142.205		1
199	1	26	DT	H1'	H	5.986	0.003	1
200	1	26	DT	H2'	H	2.033	0.003	1
201	1	26	DT	H2''	H	2.292	0.002	1
202	1	26	DT	H3'	H	4.967	0.002	1
203	1	26	DT	H6	H	7.494	0.002	1
204	1	26	DT	H71	H	1.738	0.002	1
205	1	26	DT	H72	H	1.738	0.002	1
206	1	26	DT	H73	H	1.738	0.002	1
207	1	26	DT	C6	C	139.358		1
208	1	27	DT	H1'	H	5.712	0.003	1
209	1	27	DT	H2'	H	1.913	0.004	1
210	1	27	DT	H2''	H	2.165	0.001	1
211	1	27	DT	H3'	H	4.577	0.002	1
212	1	27	DT	H6	H	7.307	0.002	1
213	1	27	DT	H71	H	1.568	0.002	1
214	1	27	DT	H72	H	1.568	0.002	1
215	1	27	DT	H73	H	1.568	0.002	1
216	1	27	DT	C6	C	139.416		1
217	1	28	DT	H1'	H	5.945	0.003	1
218	1	28	DT	H2'	H	2.135	0.002	1
219	1	28	DT	H2''	H	2.346	0.002	1
220	1	28	DT	H3'	H	4.671		1
221	1	28	DT	H6	H	7.372	0.001	1
222	1	28	DT	H71	H	1.592	0.001	1
223	1	28	DT	H72	H	1.592	0.001	1
224	1	28	DT	H73	H	1.592	0.001	1
225	1	28	DT	C6	C	139.565		1
226	1	29	DT	H1'	H	5.699	0.004	1
227	1	29	DT	H2'	H	2.051	0.005	1
228	1	29	DT	H2''	H	2.365	0.004	1
229	1	29	DT	H3'	H	4.657	0.004	1
230	1	29	DT	H6	H	7.333	0.001	1
231	1	29	DT	H71	H	1.771	0.002	1
232	1	29	DT	H72	H	1.771	0.002	1
233	1	29	DT	H73	H	1.771	0.002	1
234	1	29	DT	C6	C	139.479		1
235	1	30	DG	H1	H	12.553	0.007	1
236	1	30	DG	H1'	H	5.504	0.001	1
237	1	30	DG	H2'	H	2.614	0.006	1
238	1	30	DG	H2''	H	2.701	0.002	1
239	1	30	DG	H3'	H	4.909	0.001	1
240	1	30	DG	H8	H	7.871	0.001	1
241	1	30	DG	C8	C	138.374		1
242	1	31	DA	H1'	H	6.145	0.003	1
243	1	31	DA	H2	H	7.722	0.002	1
244	1	31	DA	H2'	H	2.591	0.003	1
245	1	31	DA	H2''	H	2.774	0.002	1
246	1	31	DA	H3'	H	4.925	0.001	1
247	1	31	DA	H8	H	8.119	0.003	1
248	1	31	DA	C2	C	155.026		1
249	1	31	DA	C8	C	142.161		1
250	1	32	DC	H1'	H	5.616	0.003	1
251	1	32	DC	H2'	H	1.675	0.005	1
252	1	32	DC	H2''	H	2.176	0.003	1
253	1	32	DC	H3'	H	4.520	0.002	1
254	1	32	DC	H5	H	5.052	0.003	1
255	1	32	DC	H6	H	7.093	0.002	1
256	1	32	DC	H41	H	6.455	0.003	1
257	1	32	DC	H42	H	7.869	0.006	1
258	1	32	DC	C6	C	141.831		1
259	1	33	DT	H1'	H	5.093	0.003	1
260	1	33	DT	H2'	H	1.662	0.003	1
261	1	33	DT	H2''	H	1.831	0.002	1
262	1	33	DT	H3	H	13.456	0.002	1
263	1	33	DT	H3'	H	4.494	0.008	1
264	1	33	DT	H6	H	7.007	0.003	1
265	1	33	DT	H71	H	1.279	0.006	1
266	1	33	DT	H72	H	1.279	0.006	1
267	1	33	DT	H73	H	1.279	0.006	1
268	1	33	DT	C6	C	139.446		1
269	1	34	DA	H1'	H	5.585	0.001	1
270	1	34	DA	H2	H	7.220	0.001	1
271	1	34	DA	H2'	H	2.097	0.005	1
272	1	34	DA	H2''	H	2.297	0.002	1
273	1	34	DA	H3'	H	4.692		1
274	1	34	DA	H8	H	7.514	0.002	1
275	1	34	DA	C2	C	153.926		1
276	1	34	DA	C8	C	141.369		1
277	1	35	DG	H1	H	10.937		1
278	1	35	DG	H1'	H	5.331	0.002	1
279	1	35	DG	H2'	H	2.444	0.003	1
280	1	35	DG	H2''	H	2.795	0.001	1
281	1	35	DG	H3'	H	4.987	0.003	1
282	1	35	DG	H8	H	7.049	0.002	1
283	1	35	DG	C8	C	136.978		1
284	1	36	DG	H1	H	10.699	0.002	1
285	1	36	DG	H1'	H	6.129	0.003	1
286	1	36	DG	H2'	H	3.250	0.003	1
287	1	36	DG	H2''	H	2.548	0.003	1
288	1	36	DG	H3'	H	5.002	0.001	1
289	1	36	DG	H8	H	6.872	0.001	1
290	1	36	DG	C8	C	140.615		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

Entries sharing articles BMRB: 1 entries Detail

BMRB: 34741 released on 2022-07-12
Title Solution structure of a phenyl-indoloquinoline intercalating into a quadruplex-duplex hybrid

Experiments performed 3 experiments Detail

#	Name	Isotope labeling	Type	Concentration
1	DNA (36-MER)	natural abundance		0.5 mM

#	Name	Isotope labeling	Type	Concentration
1	DNA (36-MER)	natural abundance		0.5 mM

#	Name	Isotope labeling	Type	Concentration
1	DNA (36-MER)	natural abundance		0.5 mM

Chemical shift validation 4 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr34740_3.str
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
2	1	PQ3	N2,N9-bis(1-methylquinolin-3-yl)-1,10-phenanthroline-2,9-dicarboxamide	None
1	1	THM	THYMIDINE	Assigned chemical shifts

Content subtype: bmr34740_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	290		100.0 (chain: 1, length: 36)
1	Chemical shift references	chem_shift_reference_1	OK	2		No information

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1

Status: Warning

Sequence coverage of experimental data

Entity_assembly_ID: 1, Chain length: 36, Sequence coverage: 100.0%

--------10--------20--------30------
XTAGGTGGGTAGGGTGGGCTAGTCATTTTGACTAGG
||||||||||||||||||||||||||||||||||||
XTAGGTGGGTAGGGTGGGCTAGTCATTTTGACTAGG

Total number of assignments
- ¹H chemical shifts: 249
- ¹³C chemical shifts: 41

Completeness of assignments

Entity_assemble_ID: 1

Excluded Comp_ID in statistics

Comp_index_ID	Comp_ID
1	THM

Excluded Atom_ID in statistics

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
2	DT	C6	139.351
3	DA	C8	142.541
4	DG	C8	137.874
5	DG	C8	137.601
6	DT	C6	140.208
7	DG	C8	138.524
8	DG	C8	138.041
9	DG	C8	137.768
10	DT	C6	140.171
11	DA	C2	154.373
11	DA	C8	143.504
12	DG	C8	138.269
13	DG	C8	138.011
14	DG	C8	138.006
15	DT	C6	139.937
16	DG	C8	137.803
17	DG	C8	138.023
18	DG	C8	138.128
19	DC	C6	143.242
20	DT	C6	139.458
21	DA	C2	153.841
21	DA	C8	141.809
22	DG	C8	137.115
23	DT	C6	139.041
24	DC	C6	143.552
25	DA	C2	154.893
25	DA	C8	142.205
26	DT	C6	139.358
27	DT	C6	139.416
28	DT	C6	139.565
29	DT	C6	139.479
30	DG	C8	138.374
31	DA	C2	155.026
31	DA	C8	142.161
32	DC	C6	141.831
33	DT	C6	139.446
34	DA	C2	153.926
34	DA	C8	141.369
35	DG	C8	136.978
36	DG	C8	140.615

All atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	332	219	66.0

Backbone atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	245	140	57.1

Side chain atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	87	79	90.8

Methyl group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	11	11	100.0
¹³C chemical shifts	11	0	0.0

Aromatic group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	27	27	100.0

Histogram of normalized assigned chemical shifts

Keywords DNA, Duplex, G-quadruplex, Intercalation, Phen-DC3, Quadruplex-Duplex Junction

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Chemical shift validation 4 contents Detail