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BMRB: 17409

2L8I

A biocompatible backbone modification? - Structure and dynamics of a triazole-linked DNA duplex

Authors

El-Sagheer, A., Brown, T., Ernsting, N., Dehmel, L., Griesinger, C., M gge, C.

Assembly

triazole-linked DNA duplex

Entity

1. DNA strand I (polymer, Thiol state: not present), 13 monomers, 4039.571 Da Detail

GCTGCAAACG TCG

2. DNA strand II (polymer, Thiol state: not present), 13 monomers, 3988.629 Da Detail

CGACGTXTGC AGC

Total weight

8028.2 Da

Max. entity weight

4039.571 Da

Exptl. method

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 96.2 %, Completeness: 78.0 %, Completeness (bb): 71.4 % Detail

Polymer type: polydeoxyribonucleotide

	Total	¹H
All	78.0 % (191 of 245)	78.0 % (191 of 245)
Suger, PO4	71.4 % (125 of 175)	71.4 % (125 of 175)
Nucleobase	94.3 % (66 of 70)	94.3 % (66 of 70)
Aromatic	96.0 % (48 of 50)	96.0 % (48 of 50)
Methyl	100.0 % (4 of 4)	100.0 % (4 of 4)

1. DNA strand I

GCTGCAAACG TCG

2. DNA strand II

CGACGTXTGC AGC

Show sample condition

Sample #1

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	DNA strand I	natural abundance		3 mM
2	DNA strand II	natural abundance		3 mM
3	D2O	[U-100% 2H]		99.98 %
4	sodium chloride	natural abundance		150 mM
5	sodium phosphate	natural abundance		10 mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
6	DNA strand I	natural abundance		3 mM
7	DNA strand II	natural abundance		3 mM
8	D2O	[U-99% 2H]		10 %
9	H2O	natural abundance		90 %
10	sodium chloride	natural abundance		150 mM
11	sodium phosphate	natural abundance		10 mM

Sample #3

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
12	DNA strand I	natural abundance		3 mM
13	DNA strand II	natural abundance		3 mM
14	D2O	[U-100% 2H]		99.98 %
15	Pf1 phage	natural abundance		20 mg/mL
16	sodium chloride	natural abundance		150 mM
17	sodium phosphate	natural abundance		10 mM

Release date

2012-01-04

Citation

Structure and dynamics of triazole-linked DNA: biocompatibility explained
Dallmann, A., El-Sagheer, A.H., Dehmel, L., Muegge, C., Griesinger, C., Ernsting, N.P., Brown, T.
Chemistry (2011), 17, 14714-14717, PubMed 22131102 , DOI 10.1002/chem.201102979 , Abstract

Experiments performed 6 experiments Detail

1 2D DQF-COSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	DNA strand I	natural abundance		3 mM
2	DNA strand II	natural abundance		3 mM
3	D2O	[U-100% 2H]		99.98 %
4	sodium chloride	natural abundance		150 mM
5	sodium phosphate	natural abundance		10 mM

2 2D 1H-1H NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	DNA strand I	natural abundance		3 mM
2	DNA strand II	natural abundance		3 mM
3	D2O	[U-100% 2H]		99.98 %
4	sodium chloride	natural abundance		150 mM
5	sodium phosphate	natural abundance		10 mM

3 2D 1H-1H TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	DNA strand I	natural abundance		3 mM
2	DNA strand II	natural abundance		3 mM
3	D2O	[U-100% 2H]		99.98 %
4	sodium chloride	natural abundance		150 mM
5	sodium phosphate	natural abundance		10 mM

4 2D 1H-13C HMQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	DNA strand I	natural abundance		3 mM
2	DNA strand II	natural abundance		3 mM
3	D2O	[U-100% 2H]		99.98 %
4	sodium chloride	natural abundance		150 mM
5	sodium phosphate	natural abundance		10 mM

5 2D 1H-13C HMQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
12	DNA strand I	natural abundance		3 mM
13	DNA strand II	natural abundance		3 mM
14	D2O	[U-100% 2H]		99.98 %
15	Pf1 phage	natural abundance		20 mg/mL
16	sodium chloride	natural abundance		150 mM
17	sodium phosphate	natural abundance		10 mM

6 2D 1H-1H NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
6	DNA strand I	natural abundance		3 mM
7	DNA strand II	natural abundance		3 mM
8	D2O	[U-99% 2H]		10 %
9	H2O	natural abundance		90 %
10	sodium chloride	natural abundance		150 mM
11	sodium phosphate	natural abundance		10 mM

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints, RDC restraints	combined_17409_2l8i.nef
Input source #2: Coordindates	2l8i.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	Error

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)
2:5:DG:O3'	2:6:2L8:P1	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	19	2L8	[(2R,3S,5R)-3-[(1-{[(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)tetrahydrofuran-2-yl]methyl}-1H-1,2,3-triazol-4-yl)methoxy]-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)tetrahydrofuran-2-yl]methyl dihydrogen phosphate	Distance restraints, RDC restraints, Coordinates

Sequence alignments

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

--------10---
GCTGCAAACGTCG
|||||||||||||
GCTGCAAACGTCG

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

-----20-----
CGACGXTGCAGC
||||||||||||
CGACGXTGCAGC
--------10--

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	13	0	0	100.0
B	B	12	0	0	100.0

Content subtype: combined_17409_2l8i.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	1		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Error	287		No information
1	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	250 (1)	noe	100.0 (chain: A, length: 13), 83.3 (chain: B, length: 12)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	53 (1)	hbond	92.3 (chain: A, length: 13), 100.0 (chain: B, length: 12)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	OK	125 (125)	.	100.0 (chain: A, length: 13), 91.7 (chain: B, length: 12)
1	RDC restraints	CNS/XPLOR_dipolar_coupling_6	OK	30 (30)	.	61.5 (chain: A, length: 13), 66.7 (chain: B, length: 12)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Error

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_4
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 13, Sequence coverage: 100.0%
  - Entity_assembly_ID: B, Chain length: 12, Sequence coverage: 83.3%
- Total number of restraints: 250
- Weight of restraints: 1.0 (250)
- Potential type of restraints: square-well-parabolic (250)
- Range of distance target values: 2.16, 4.97 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_3
  - Status: Warning
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 13, Sequence coverage: 92.3%
    - Entity_assembly_ID: B, Chain length: 12, Sequence coverage: 100.0%
  - Total number of restraints: 53
  - Weight of restraints: 1.0 (53)
  - Potential type of restraints: square-well-parabolic (53)
  - Range of distance target values: 1.81, 3.69 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 13, Sequence coverage: 100.0%
  - Entity_assembly_ID: B, Chain length: 12, Sequence coverage: 91.7%
- Total number of restraints: 125
- Total number of restraints per polymer type: 125
- Weight of restraints: 1.0 (125)
- Potential type of restraints: square-well-parabolic (125)
- Dihedral angle restraints per residue
  - Chain_ID: A
  - Chain_ID: B

RDC restraints

Saveframe: CNS/XPLOR_dipolar_coupling_6
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 13, Sequence coverage: 61.5%
  - Entity_assembly_ID: B, Chain length: 12, Sequence coverage: 66.7%
- Total number of restraints: 30
- Potential type of restraints: square-well-parabolic (30)
- Range of observed RDC values: -15.6, 38.4 (Hz)
- Histogram of observed RDC values
- RDC restraints per residue
  - Chain_ID: A
    None
  - Chain_ID: B
    None

Keywords 13merTAL