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Found 1 Document (0.414 seconds)

BMRB: 18427

2LSC

Solution structure of 2'F-ANA and ANA self-complementary duplex

Authors

Martin-Pintado, N., Yahyaee, M., Campos, R., Noronha, A., Wilds, C., Damha, M., Gonzalez, C.

Assembly

2'F-ANA and ANA self-complementary duplex

Entity

1. 2'F-ANA and ANA self-complementary duplex (polymer, Thiol state: not present), 12 monomers, 3906.236 × 2 Da

Total weight

7812.472 Da

Max. entity weight

3906.236 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chemcal Shifts

¹H: 72, Other nucleus: null assignments Detail

ID	Entity ID	Seq ID	Comp ID	Atom ID	Atom type	Val	Ambig. code
1	1	1	CFL	H1'	H	5.950
2	1	1	CFL	H2'	H	5.360
3	1	1	CFL	H4'	H	4.154
4	1	1	CFL	H5	H	5.961	1
5	1	1	CFL	H5'1	H	3.844
6	1	1	CFL	H5'2	H	3.926	2
7	1	1	CFL	H6	H	7.641	1
8	1	1	CFL	HN41	H	8.201	2
9	1	1	CFL	F	F	-120.488
10	1	2	GFL	H1'	H	5.961
11	1	2	GFL	H2'	H	5.537
12	1	2	GFL	H3'	H	4.993
13	1	2	GFL	H4'	H	4.285
14	1	2	GFL	H8	H	7.624	1
15	1	2	GFL	HN1	H	13.010	1
16	1	2	GFL	F	F	-119.468
17	1	3	CFL	H1'	H	5.802
18	1	3	CFL	H2'	H	5.410
19	1	3	CFL	H4'	H	4.186
20	1	3	CFL	H5	H	5.218	1
21	1	3	CFL	H6	H	7.151	1
22	1	3	CFL	HN41	H	8.599	2
23	1	3	CFL	HN42	H	6.640	2
24	1	3	CFL	F	F	-118.451
25	1	4	GFL	H1'	H	5.835
26	1	4	GFL	H2'	H	5.579
27	1	4	GFL	H3'	H	4.982
28	1	4	GFL	H4'	H	4.239
29	1	4	GFL	H8	H	7.427	1
30	1	4	GFL	HN1	H	12.490	1
31	1	4	GFL	F	F	-119.213
32	1	5	A5O	H1'	H	6.012
33	1	5	A5O	H2	H	7.284	1
34	1	5	A5O	H2'	H	4.805
35	1	5	A5O	H8	H	7.679	1
36	1	6	A5O	H1'	H	5.806
37	1	6	A5O	H2	H	7.402	1
38	1	6	A5O	H2'	H	4.615
39	1	6	A5O	H3'	H	4.452
40	1	6	A5O	H4'	H	4.365
41	1	6	A5O	H8	H	7.327	1
42	1	7	UAR	H1'	H	5.712
43	1	7	UAR	H2'	H	4.409
44	1	7	UAR	H3	H	14.029	1
45	1	7	UAR	H4'	H	4.021
46	1	7	UAR	H5	H	5.419	1
47	1	7	UAR	H6	H	7.171	1
48	1	8	UAR	H1'	H	5.851
49	1	8	UAR	H2'	H	4.437
50	1	8	UAR	H3	H	13.839	1
51	1	8	UAR	H4'	H	4.143
52	1	8	UAR	H5	H	5.123	1
53	1	8	UAR	H6	H	7.321	1
54	1	9	CFL	H1'	H	5.920
55	1	9	CFL	H2'	H	5.481
56	1	9	CFL	H5	H	5.843	1
57	1	9	CFL	H6	H	7.027	1
58	1	9	CFL	HN41	H	8.652	2
59	1	9	CFL	HN42	H	6.942	2
60	1	10	GFL	H1'	H	5.895
61	1	10	GFL	H2'	H	5.570
62	1	10	GFL	H3'	H	5.002
63	1	10	GFL	H4'	H	4.037
64	1	10	GFL	H8	H	7.478	1
65	1	10	GFL	HN1	H	12.865	1
66	1	10	GFL	F	F	-118.578
67	1	11	CFL	H1'	H	5.860
68	1	11	CFL	H2'	H	5.419
69	1	11	CFL	H5	H	5.283	1
70	1	11	CFL	H6	H	7.143	1
71	1	11	CFL	HN41	H	8.663	2
72	1	11	CFL	HN42	H	6.775	2
73	1	11	CFL	F	F	-117.822
74	1	12	GFL	H1'	H	6.147
75	1	12	GFL	H2'	H	5.133
76	1	12	GFL	H3'	H	4.633
77	1	12	GFL	H4'	H	4.034
78	1	12	GFL	H8	H	7.506	1
79	1	12	GFL	F	F	-118.553

Release date

2012-07-15

Citation

The solution structure of double helical arabino nucleic acids (ANA and 2'F-ANA): effect of arabinoses in duplex-hairpin interconversion
Martin-Pintado, N., Yahyaee-Anzahaee, M., Campos-Olivas, R., Noronha, A.M., Wilds, C.J., Damha, M.J., Gonzalez, C.
Nucleic Acids Res. (2012), 40, 9329-9339, PubMed 22798499 , DOI 10.1093/nar/gks672 , Abstract

Experiments performed 9 experiments Detail

1 2D 1H-1H NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	potassium phosphate	natural abundance	25 mM
2	DNA/RNA chain	natural abundance	0.8 mM
3	sodium chloride	natural abundance	100 mM
4	D2O	natural abundance	10 %
5	H2O	natural abundance	90 %

2 2D 1H-1H TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K, pH 7.0

#	Name	Isotope labeling	Concentration
6	potassium phosphate	natural abundance	25 mM
7	sodium chloride	natural abundance	100 mM
8	DNA/RNA chain	natural abundance	0.8 mM
9	D2O	natural abundance	100 %

3 2D DQF-COSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K, pH 7.0

#	Name	Isotope labeling	Concentration
6	potassium phosphate	natural abundance	25 mM
7	sodium chloride	natural abundance	100 mM
8	DNA/RNA chain	natural abundance	0.8 mM
9	D2O	natural abundance	100 %

4 2D 1H-19F HOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K, pH 7.0

#	Name	Isotope labeling	Concentration
6	potassium phosphate	natural abundance	25 mM
7	sodium chloride	natural abundance	100 mM
8	DNA/RNA chain	natural abundance	0.8 mM
9	D2O	natural abundance	100 %

5 2D 1H-1H NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K, pH 7.0

#	Name	Isotope labeling	Concentration
6	potassium phosphate	natural abundance	25 mM
7	sodium chloride	natural abundance	100 mM
8	DNA/RNA chain	natural abundance	0.8 mM
9	D2O	natural abundance	100 %

6 2D 1H-1H TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	potassium phosphate	natural abundance	25 mM
2	DNA/RNA chain	natural abundance	0.8 mM
3	sodium chloride	natural abundance	100 mM
4	D2O	natural abundance	10 %
5	H2O	natural abundance	90 %

7 2D 1H-1H NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	potassium phosphate	natural abundance	25 mM
2	DNA/RNA chain	natural abundance	0.8 mM
3	sodium chloride	natural abundance	100 mM
4	D2O	natural abundance	10 %
5	H2O	natural abundance	90 %

8 2D 1H-1H NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K, pH 7.0

#	Name	Isotope labeling	Concentration
6	potassium phosphate	natural abundance	25 mM
7	sodium chloride	natural abundance	100 mM
8	DNA/RNA chain	natural abundance	0.8 mM
9	D2O	natural abundance	100 %

9 2D 1H-19F HOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K, pH 7.0

#	Name	Isotope labeling	Concentration
6	potassium phosphate	natural abundance	25 mM
7	sodium chloride	natural abundance	100 mM
8	DNA/RNA chain	natural abundance	0.8 mM
9	D2O	natural abundance	100 %

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_18427_2lsc.nef
Input source #2: Coordindates	2lsc.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	True (see coodinates for details)
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)

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
1:7:UAR:O3'	1:8:UAR:P	unknown	unknown	n/a
1:8:UAR:O3'	1:9:CFL:P	unknown	unknown	n/a
2:7:UAR:O3'	2:8:UAR:P	unknown	unknown	n/a
2:8:UAR:O3'	2:9:CFL:P	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
A	1	CFL	4-amino-1-(2-deoxy-2-fluoro-5-O-phosphono-beta-D-arabinofuranosyl)pyrimidin-2(1H)-one	Assigned chemical shifts, Distance restraints, Coordinates
A	2	GFL	2-AMINO-9-(2-DEOXY-2-FLUORO-5-O-PHOSPHONO-BETA-D-ARABINOFURANOSYL)-1,9-DIHYDRO-6H-PURIN-6-ONE	Assigned chemical shifts, Distance restraints, Coordinates
A	3	CFL	4-amino-1-(2-deoxy-2-fluoro-5-O-phosphono-beta-D-arabinofuranosyl)pyrimidin-2(1H)-one	Assigned chemical shifts, Distance restraints, Coordinates
A	4	GFL	2-AMINO-9-(2-DEOXY-2-FLUORO-5-O-PHOSPHONO-BETA-D-ARABINOFURANOSYL)-1,9-DIHYDRO-6H-PURIN-6-ONE	Assigned chemical shifts, Distance restraints, Coordinates
A	5	A5O	ADENINE ARABINOSE-5'-PHOSPHATE	Assigned chemical shifts, Coordinates
A	6	A5O	ADENINE ARABINOSE-5'-PHOSPHATE	Assigned chemical shifts, Coordinates
A	7	UAR	URACIL ARABINOSE-5'-PHOSPHATE	Assigned chemical shifts, Distance restraints, Coordinates
A	8	UAR	URACIL ARABINOSE-5'-PHOSPHATE	Assigned chemical shifts, Distance restraints, Coordinates
A	9	CFL	4-amino-1-(2-deoxy-2-fluoro-5-O-phosphono-beta-D-arabinofuranosyl)pyrimidin-2(1H)-one	Assigned chemical shifts, Distance restraints, Coordinates
A	10	GFL	2-AMINO-9-(2-DEOXY-2-FLUORO-5-O-PHOSPHONO-BETA-D-ARABINOFURANOSYL)-1,9-DIHYDRO-6H-PURIN-6-ONE	Assigned chemical shifts, Distance restraints, Coordinates
A	11	CFL	4-amino-1-(2-deoxy-2-fluoro-5-O-phosphono-beta-D-arabinofuranosyl)pyrimidin-2(1H)-one	Assigned chemical shifts, Distance restraints, Coordinates
A	12	GFL	2-AMINO-9-(2-DEOXY-2-FLUORO-5-O-PHOSPHONO-BETA-D-ARABINOFURANOSYL)-1,9-DIHYDRO-6H-PURIN-6-ONE	Assigned chemical shifts, Distance restraints, Coordinates
B	13	CFL	4-amino-1-(2-deoxy-2-fluoro-5-O-phosphono-beta-D-arabinofuranosyl)pyrimidin-2(1H)-one	Distance restraints, Coordinates
B	14	GFL	2-AMINO-9-(2-DEOXY-2-FLUORO-5-O-PHOSPHONO-BETA-D-ARABINOFURANOSYL)-1,9-DIHYDRO-6H-PURIN-6-ONE	Distance restraints, Coordinates
B	15	CFL	4-amino-1-(2-deoxy-2-fluoro-5-O-phosphono-beta-D-arabinofuranosyl)pyrimidin-2(1H)-one	Distance restraints, Coordinates
B	16	GFL	2-AMINO-9-(2-DEOXY-2-FLUORO-5-O-PHOSPHONO-BETA-D-ARABINOFURANOSYL)-1,9-DIHYDRO-6H-PURIN-6-ONE	Distance restraints, Coordinates
B	17	A5O	ADENINE ARABINOSE-5'-PHOSPHATE	Coordinates
B	18	A5O	ADENINE ARABINOSE-5'-PHOSPHATE	Coordinates
B	19	UAR	URACIL ARABINOSE-5'-PHOSPHATE	Distance restraints, Coordinates
B	20	UAR	URACIL ARABINOSE-5'-PHOSPHATE	Distance restraints, Coordinates
B	21	CFL	4-amino-1-(2-deoxy-2-fluoro-5-O-phosphono-beta-D-arabinofuranosyl)pyrimidin-2(1H)-one	Distance restraints, Coordinates
B	22	GFL	2-AMINO-9-(2-DEOXY-2-FLUORO-5-O-PHOSPHONO-BETA-D-ARABINOFURANOSYL)-1,9-DIHYDRO-6H-PURIN-6-ONE	Distance restraints, Coordinates
B	23	CFL	4-amino-1-(2-deoxy-2-fluoro-5-O-phosphono-beta-D-arabinofuranosyl)pyrimidin-2(1H)-one	Distance restraints, Coordinates
B	24	GFL	2-AMINO-9-(2-DEOXY-2-FLUORO-5-O-PHOSPHONO-BETA-D-ARABINOFURANOSYL)-1,9-DIHYDRO-6H-PURIN-6-ONE	Distance restraints, Coordinates

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

--------10--
XXXXXXXXXXXX
||||||||||||
XXXXXXXXXXXX

Entity_assembly_ID (NMR): B vs Auth_asym_ID (model): B

------20----
XXXXXXXXXXXX
||||||||||||
XXXXXXXXXXXX
--------10--

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	12	0	0	100.0
B	B	12	0	0	100.0

Content subtype: combined_18427_2lsc.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	4		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	79		100.0 (chain: A, length: 12)
1	Distance restraints	AMBER_distance_constraints_2	OK	162 (1)	noe	83.3 (chain: A, length: 12), 83.3 (chain: B, length: 12)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 12, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 72
  - ¹⁹F chemical shifts: 7
- Completeness of assignments
  - Entity_assemble_ID: A
- Histogram of normalized assigned chemical shifts

Comp_index_ID	Comp_ID
1	CFL
2	GFL
3	CFL
4	GFL
5	A5O
6	A5O
7	UAR
8	UAR
9	CFL
10	GFL
11	CFL
12	GFL

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: AMBER_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 12, Sequence coverage: 83.3%
  - Entity_assembly_ID: B, Chain length: 12, Sequence coverage: 83.3%
- Total number of restraints: 162
- Weight of restraints: 1.0 (162)
- Potential type of restraints: square-well-parabolic (162)
- Range of distance target values: 2.5, 6.75 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
- Distance restraints on contact map

Keywords 2'F-ANA, ANA, NMR, nucleic acids

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Found 1 Document (0.414 seconds)

BMRB: 18427

Experiments performed 9 experiments Detail

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NMR combined restraints 3 contents Detail