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BMRB: 34882

A quadruplex-duplex hybrid with a three-layered hybrid-2 G-quadruplex topology complexed with Phen-DC3

Authors

Vianney, Y.M., Weisz, K.

Assembly

DNA (34-MER)

Entity

1. DNA (34-MER), entity 1 (polymer, Thiol state: not present), 33 monomers, 10451.61 Da Detail

GGGCGCGAAG CATTCGCGGG GTTAGGGTTA GGG

2. DNA (34-MER), entity PQ3 (non-polymer), 550.609 Da

Total weight

11002.22 Da

Max. entity weight

10451.61 Da

Source organism

synthetic construct

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chemcal Shifts

¹H: 249, ¹³C: 38 assignments Detail

ID	Entity ID	Seq ID	Comp ID	Atom ID	Atom type	Val	Val err	Ambig. code
1	1	1	DG	H1	H	11.679	0.001	1
2	1	1	DG	H1'	H	6.012	0.002	1
3	1	1	DG	H2'	H	2.732	0.009	1
4	1	1	DG	H2''	H	3.070	0.004	1
5	1	1	DG	H3'	H	4.905	0.003	1
6	1	1	DG	H8	H	7.370	0.001	1
7	1	1	DG	C8	C	141.726		1
8	1	2	DG	H1	H	11.526	0.003	1
9	1	2	DG	H1'	H	5.738	0.002	1
10	1	2	DG	H2'	H	2.414	0.003	1
11	1	2	DG	H2''	H	2.757	0.002	1
12	1	2	DG	H3'	H	5.075	0.001	1
13	1	2	DG	H8	H	7.823	0.002	1
14	1	2	DG	C8	C	138.695		1
15	1	3	DG	H1	H	10.300	0.003	1
16	1	3	DG	H1'	H	5.945	0.002	1
17	1	3	DG	H2'	H	2.853	0.005	1
18	1	3	DG	H2''	H	2.841	0.004	1
19	1	3	DG	H3'	H	5.186	0.001	1
20	1	3	DG	H8	H	7.940	0.003	1
21	1	3	DG	C8	C	138.235		1
22	1	4	DC	H1'	H	5.214	0.003	1
23	1	4	DC	H2'	H	2.259	0.004	1
24	1	4	DC	H2''	H	2.317	0.003	1
25	1	4	DC	H3'	H	4.827	0.003	1
26	1	4	DC	H5	H	5.453	0.002	1
27	1	4	DC	H6	H	7.505	0.002	1
28	1	4	DC	H41	H	7.579	0.004	1
29	1	4	DC	H42	H	6.282	0.003	1
30	1	4	DC	C6	C	143.295		1
31	1	5	DG	H1	H	12.447	0.002	1
32	1	5	DG	H1'	H	5.796	0.001	1
33	1	5	DG	H2'	H	2.552	0.004	1
34	1	5	DG	H2''	H	2.638	0.003	1
35	1	5	DG	H3'	H	4.967	0.001	1
36	1	5	DG	H8	H	7.764	0.003	1
37	1	5	DG	C8	C	137.924		1
38	1	6	DC	H1'	H	5.462	0.002	1
39	1	6	DC	H2'	H	1.783	0.003	1
40	1	6	DC	H2''	H	2.196	0.006	1
41	1	6	DC	H3'	H	4.744	0.003	1
42	1	6	DC	H5	H	5.250	0.003	1
43	1	6	DC	H6	H	7.145	0.002	1
44	1	6	DC	H41	H	8.147	0.002	1
45	1	6	DC	H42	H	6.226	0.002	1
46	1	6	DC	C6	C	142.212		1
47	1	7	DG	H1	H	12.637	0.003	1
48	1	7	DG	H1'	H	5.310	0.003	1
49	1	7	DG	H2'	H	2.555	0.007	1
50	1	7	DG	H2''	H	2.632	0.003	1
51	1	7	DG	H3'	H	4.894	0.003	1
52	1	7	DG	H8	H	7.769	0.002	1
53	1	7	DG	C8	C	138.181		1
54	1	8	DA	H1'	H	5.817	0.004	1
55	1	8	DA	H2	H	7.490	0.003	1
56	1	8	DA	H2'	H	2.232	0.002	1
57	1	8	DA	H2''	H	2.552	0.005	1
58	1	8	DA	H3'	H	4.898	0.001	1
59	1	8	DA	H8	H	7.837	0.002	1
60	1	8	DA	C2	C	154.423		1
61	1	8	DA	C8	C	140.943		1
62	1	9	DA	H1'	H	5.821	0.002	1
63	1	9	DA	H2	H	7.632	0.002	1
64	1	9	DA	H2'	H	2.003	0.003	1
65	1	9	DA	H2''	H	2.369	0.002	1
66	1	9	DA	H3'	H	4.823	0.001	1
67	1	9	DA	H8	H	7.398	0.001	1
68	1	9	DA	C2	C	154.956		1
69	1	9	DA	C8	C	139.854		1
70	1	10	DG	H1'	H	5.331	0.002	1
71	1	10	DG	H2'	H	2.587	0.005	1
72	1	10	DG	H2''	H	2.296	0.002	1
73	1	10	DG	H3'	H	4.754	0.004	1
74	1	10	DG	H8	H	8.003	0.002	1
75	1	10	DG	C8	C	138.946		1
76	1	11	DC	H1'	H	5.655	0.003	1
77	1	11	DC	H2'	H	1.547	0.005	1
78	1	11	DC	H2''	H	1.994	0.0	1
79	1	11	DC	H3'	H	4.372	0.002	1
80	1	11	DC	H5	H	5.166	0.003	1
81	1	11	DC	H6	H	7.150	0.002	1
82	1	11	DC	C6	C	143.471		1
83	1	12	DA	H1'	H	6.259	0.003	1
84	1	12	DA	H2	H	7.982	0.002	1
85	1	12	DA	H2'	H	2.963	0.002	1
86	1	12	DA	H2''	H	2.892	0.0	1
87	1	12	DA	H3'	H	4.788	0.002	1
88	1	12	DA	H8	H	8.030	0.002	1
89	1	12	DA	C2	C	155.417		1
90	1	12	DA	C8	C	143.105		1
91	1	13	DT	H1'	H	5.620	0.004	1
92	1	13	DT	H2'	H	2.054	0.004	1
93	1	13	DT	H2''	H	2.429	0.003	1
94	1	13	DT	H3	H	13.251	0.002	1
95	1	13	DT	H3'	H	4.699	0.002	1
96	1	13	DT	H6	H	7.350	0.002	1
97	1	13	DT	H71	H	1.780	0.001	1
98	1	13	DT	H72	H	1.780	0.001	1
99	1	13	DT	H73	H	1.780	0.001	1
100	1	13	DT	C6	C	139.327		1
101	1	14	DT	H1'	H	5.961	0.002	1
102	1	14	DT	H2'	H	2.091	0.004	1
103	1	14	DT	H2''	H	2.375	0.002	1
104	1	14	DT	H3	H	13.799	0.005	1
105	1	14	DT	H3'	H	4.785	0.003	1
106	1	14	DT	H6	H	7.337	0.002	1
107	1	14	DT	H71	H	1.548	0.004	1
108	1	14	DT	H72	H	1.548	0.004	1
109	1	14	DT	H73	H	1.548	0.004	1
110	1	14	DT	C6	C	139.804		1
111	1	15	DC	H1'	H	5.449	0.004	1
112	1	15	DC	H2'	H	1.872	0.003	1
113	1	15	DC	H2''	H	2.162	0.004	1
114	1	15	DC	H3'	H	4.678	0.002	1
115	1	15	DC	H5	H	5.524	0.002	1
116	1	15	DC	H6	H	7.329	0.003	1
117	1	15	DC	H41	H	8.408	0.002	1
118	1	15	DC	H42	H	6.769	0.003	1
119	1	15	DC	C6	C	143.448		1
120	1	16	DG	H1	H	12.651	0.002	1
121	1	16	DG	H1'	H	5.456	0.002	1
122	1	16	DG	H2'	H	2.262	0.003	1
123	1	16	DG	H2''	H	2.263	0.003	1
124	1	16	DG	H3'	H	4.681	0.001	1
125	1	16	DG	H8	H	7.564	0.002	1
126	1	16	DG	C8	C	137.927		1
127	1	17	DC	H1'	H	5.455	0.004	1
128	1	17	DC	H2'	H	1.147	0.004	1
129	1	17	DC	H2''	H	1.892	0.002	1
130	1	17	DC	H3'	H	4.435	0.002	1
131	1	17	DC	H5	H	4.791	0.002	1
132	1	17	DC	H6	H	6.644	0.003	1
133	1	17	DC	H41	H	7.690	0.003	1
134	1	17	DC	H42	H	5.934	0.003	1
135	1	17	DC	C6	C	141.854		1
136	1	18	DG	H1	H	11.454	0.002	1
137	1	18	DG	H1'	H	5.582	0.003	1
138	1	18	DG	H2'	H	2.730	0.005	1
139	1	18	DG	H2''	H	2.963	0.003	1
140	1	18	DG	H3'	H	5.095	0.001	1
141	1	18	DG	H8	H	7.430	0.001	1
142	1	18	DG	C8	C	138.023		1
143	1	19	DG	H1	H	10.976	0.004	1
144	1	19	DG	H1'	H	5.867	0.003	1
145	1	19	DG	H2'	H	3.473	0.003	1
146	1	19	DG	H2''	H	2.977	0.002	1
147	1	19	DG	H3'	H	4.901	0.001	1
148	1	19	DG	H8	H	6.539	0.002	1
149	1	19	DG	C8	C	141.872		1
150	1	20	DG	H1	H	10.757	0.003	1
151	1	20	DG	H1'	H	5.519	0.003	1
152	1	20	DG	H2'	H	2.370	0.004	1
153	1	20	DG	H2''	H	2.250	0.006	1
154	1	20	DG	H3'	H	4.914	0.002	1
155	1	20	DG	H8	H	6.973	0.002	1
156	1	20	DG	C8	C	140.373		1
157	1	21	DG	H1	H	11.104	0.003	1
158	1	21	DG	H1'	H	5.783	0.001	1
159	1	21	DG	H2'	H	2.535	0.004	1
160	1	21	DG	H2''	H	2.426	0.004	1
161	1	21	DG	H3'	H	5.065	0.001	1
162	1	21	DG	H8	H	7.621	0.001	1
163	1	21	DG	C8	C	137.795		1
164	1	22	DT	H1'	H	6.253	0.002	1
165	1	22	DT	H2'	H	2.237	0.004	1
166	1	22	DT	H2''	H	2.438	0.002	1
167	1	22	DT	H3'	H	4.831	0.002	1
168	1	22	DT	H6	H	7.841	0.001	1
169	1	22	DT	H71	H	1.952	0.003	1
170	1	22	DT	H72	H	1.952	0.003	1
171	1	22	DT	H73	H	1.952	0.003	1
172	1	22	DT	C6	C	139.892		1
173	1	23	DT	H1'	H	5.731	0.002	1
174	1	23	DT	H2'	H	1.162	0.003	1
175	1	23	DT	H2''	H	1.840	0.003	1
176	1	23	DT	H3'	H	4.615	0.003	1
177	1	23	DT	H6	H	7.206	0.002	1
178	1	23	DT	H71	H	1.575	0.002	1
179	1	23	DT	H72	H	1.575	0.002	1
180	1	23	DT	H73	H	1.575	0.002	1
181	1	23	DT	C6	C	138.529		1
182	1	24	DA	H1'	H	5.885	0.003	1
183	1	24	DA	H2	H	7.812	0.004	1
184	1	24	DA	H2'	H	2.675	0.004	1
185	1	24	DA	H2''	H	2.680	0.005	1
186	1	24	DA	H3'	H	4.921	0.001	1
187	1	24	DA	H8	H	7.891	0.001	1
188	1	24	DA	C2	C	155.890		1
189	1	24	DA	C8	C	141.202		1
190	1	25	DG	H1	H	10.939	0.002	1
191	1	25	DG	H1'	H	5.990	0.003	1
192	1	25	DG	H2'	H	3.300	0.003	1
193	1	25	DG	H2''	H	2.895	0.002	1
194	1	25	DG	H3'	H	4.898	0.005	1
195	1	25	DG	H8	H	7.131	0.001	1
196	1	25	DG	C8	C	141.781		1
197	1	26	DG	H1	H	11.282	0.002	1
198	1	26	DG	H1'	H	5.767	0.005	1
199	1	26	DG	H2'	H	2.361	0.001	1
200	1	26	DG	H2''	H	2.757	0.006	1
201	1	26	DG	H3'	H	4.979	0.004	1
202	1	26	DG	H8	H	7.604	0.001	1
203	1	26	DG	C8	C	137.826		1
204	1	27	DG	H1	H	10.682	0.002	1
205	1	27	DG	H1'	H	6.091	0.002	1
206	1	27	DG	H2'	H	2.696	0.003	1
207	1	27	DG	H2''	H	2.797	0.002	1
208	1	27	DG	H3'	H	5.086	0.001	1
209	1	27	DG	H4'	H	4.111		1
210	1	27	DG	H8	H	7.562	0.001	1
211	1	27	DG	C8	C	137.918		1
212	1	28	DT	H1'	H	6.408	0.001	1
213	1	28	DT	H2'	H	2.438	0.003	1
214	1	28	DT	H2''	H	2.565	0.002	1
215	1	28	DT	H3'	H	4.814	0.0	1
216	1	28	DT	H4'	H	4.457		1
217	1	28	DT	H6	H	7.810	0.003	1
218	1	28	DT	H71	H	1.990	0.004	1
219	1	28	DT	H72	H	1.990	0.004	1
220	1	28	DT	H73	H	1.990	0.004	1
221	1	28	DT	C6	C	140.290		1
222	1	29	DT	H1'	H	6.310	0.002	1
223	1	29	DT	H2'	H	2.387	0.002	1
224	1	29	DT	H2''	H	2.549	0.003	1
225	1	29	DT	H3'	H	4.944	0.003	1
226	1	29	DT	H4'	H	4.339	0.0	1
227	1	29	DT	H6	H	7.818	0.004	1
228	1	29	DT	H71	H	2.070	0.003	1
229	1	29	DT	H72	H	2.070	0.003	1
230	1	29	DT	H73	H	2.070	0.003	1
231	1	29	DT	C6	C	140.054		1
232	1	30	DA	H1'	H	6.341	0.003	1
233	1	30	DA	H2	H	7.845	0.002	1
234	1	30	DA	H2'	H	2.619	0.002	1
235	1	30	DA	H2''	H	2.620	0.006	1
236	1	30	DA	H3'	H	4.948	0.002	1
237	1	30	DA	H4'	H	4.405	0.001	1
238	1	30	DA	H8	H	8.245	0.002	1
239	1	30	DA	C2	C	155.178		1
240	1	30	DA	C8	C	141.370		1
241	1	31	DG	H1	H	11.780	0.001	1
242	1	31	DG	H1'	H	5.991	0.002	1
243	1	31	DG	H2'	H	3.228	0.005	1
244	1	31	DG	H2''	H	3.010	0.004	1
245	1	31	DG	H3'	H	4.900	0.002	1
246	1	31	DG	H8	H	7.371	0.002	1
247	1	31	DG	C8	C	142.379		1
248	1	32	DG	H1	H	11.369	0.001	1
249	1	32	DG	H1'	H	5.818	0.002	1
250	1	32	DG	H2'	H	2.521	0.002	1
251	1	32	DG	H2''	H	2.766	0.002	1
252	1	32	DG	H3'	H	5.067	0.001	1
253	1	32	DG	H8	H	7.896	0.002	1
254	1	32	DG	C8	C	138.514		1
255	1	33	DG	H1	H	10.502	0.004	1
256	1	33	DG	H1'	H	6.127	0.002	1
257	1	33	DG	H2'	H	2.754	0.003	1
258	1	33	DG	H2''	H	2.626	0.002	1
259	1	33	DG	H3'	H	4.823	0.002	1
260	1	33	DG	H8	H	7.787	0.002	1
261	1	33	DG	C8	C	137.901		1
262	2	1	PQ3	HK	H	7.830		1
263	2	1	PQ3	HK'	H	7.830		1
264	2	1	PQ3	HD	H	7.660		1
265	2	1	PQ3	HD'	H	7.690		1
266	2	1	PQ3	HB	H	8.820		1
267	2	1	PQ3	HB'	H	8.950		1
268	2	1	PQ3	HJ	H	8.260		1
269	2	1	PQ3	HJ'	H	8.250		1
270	2	1	PQ3	HH	H	7.610		1
271	2	1	PQ3	HH'	H	7.630		1
272	2	1	PQ3	HA	H	11.740		1
273	2	1	PQ3	HA'	H	12.170		1
274	2	1	PQ3	HC	H	10.190		1
275	2	1	PQ3	HC'	H	10.210		1
276	2	1	PQ3	HI1	H	4.530		1
277	2	1	PQ3	HI1'	H	4.700		1
278	2	1	PQ3	HI2	H	4.530		1
279	2	1	PQ3	HI2'	H	4.700		1
280	2	1	PQ3	HI3	H	4.530		1
281	2	1	PQ3	HI3'	H	4.700		1
282	2	1	PQ3	HG	H	7.960		1
283	2	1	PQ3	HG'	H	8.110		1
284	2	1	PQ3	HF	H	7.960		1
285	2	1	PQ3	HF'	H	7.880		1
286	2	1	PQ3	HE	H	7.710		1
287	2	1	PQ3	HE'	H	7.690		1

Release date

2024-01-10

Citation

Structural Differences at Quadruplex-Duplex Interfaces Enable Ligand-Induced Topological Transitions
Vianney, Y.M., Dierks, D., Weisz, K.
Adv. Sci (Weinh). (2024), e2309891-e2309891, PubMed 38477454 , DOI 10.1002/advs.202309891 , Abstract

Experiments performed 4 experiments Detail

#	Name	Isotope labeling	Type	Concentration
1	DNA (34-MER)	natural abundance		0.92 mM

#	Name	Isotope labeling	Type	Concentration
1	DNA (34-MER)	natural abundance		0.92 mM

#	Name	Isotope labeling	Type	Concentration
1	DNA (34-MER)	natural abundance		0.92 mM

#	Name	Isotope labeling	Type	Concentration
2	DNA (34-MER)	[U-10% 15N]dG		0.22 mM

Chemical shift validation 4 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr34882_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	Assigned chemical shifts

Content subtype: bmr34882_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	287		100.0 (chain: 1, length: 33), 100.0 (chain: 2, length: 1)
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: 33, Sequence coverage: 100.0%
- Entity_assembly_ID: 2, Chain length: 1, Sequence coverage: 100.0%
Total number of assignments
- ¹H chemical shifts: 249
- ¹³C chemical shifts: 38

Completeness of assignments

Entity_assemble_ID: 1

Excluded Atom_ID in statistics

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
1	DG	C8	141.726
2	DG	C8	138.695
3	DG	C8	138.235
4	DC	C6	143.295
5	DG	C8	137.924
6	DC	C6	142.212
7	DG	C8	138.181
8	DA	C2	154.423
8	DA	C8	140.943
9	DA	C2	154.956
9	DA	C8	139.854
10	DG	C8	138.946
11	DC	C6	143.471
12	DA	C2	155.417
12	DA	C8	143.105
13	DT	C6	139.327
14	DT	C6	139.804
15	DC	C6	143.448
16	DG	C8	137.927
17	DC	C6	141.854
18	DG	C8	138.023
19	DG	C8	141.872
20	DG	C8	140.373
21	DG	C8	137.795
22	DT	C6	139.892
23	DT	C6	138.529
24	DA	C2	155.89
24	DA	C8	141.202
25	DG	C8	141.781
26	DG	C8	137.826
27	DG	C8	137.918
28	DT	C6	140.29
29	DT	C6	140.054
30	DA	C2	155.178
30	DA	C8	141.37
31	DG	C8	142.379
32	DG	C8	138.514
33	DG	C8	137.901

All atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	313	211	67.4

Backbone atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	231	136	58.9

Side chain atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	82	75	91.5

Methyl group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	6	6	100.0
¹³C chemical shifts	6	0	0.0

Aromatic group atoms

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

Entity_assemble_ID: 2

Histogram of normalized assigned chemical shifts

Comp_index_ID	Comp_ID
1	PQ3

Keywords (3+1) hybrid, DNA, Phen-DC3, Quadruplex-duplex hybrid, intercalation

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BMRB: 34882

Experiments performed 4 experiments Detail

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Chemical shift validation 4 contents Detail