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BMRB: 17535

2LAR

DNA / RNA Hybrid containing a central stereo specific Rp borano phosphate linkage

Authors

Johnson, C.N., Spring, A.M., Shaw, B.R., Germann, M.W.

Assembly

DNA/RNA hybrid

Entity

1. DNA (5'-D(*AP*TP*GP*GP*TP*BGR*CP*TP*C)-3') (polymer, Thiol state: not present), 9 monomers, 2806.609 Da Detail

ATGGTXCTC

2. RNA (5'-R(*GP*AP*GP*CP*AP*CP*CP*AP*U)-3') (polymer, Thiol state: not present), 9 monomers, 2917.755 Da Detail

GAGCACCAU

Total weight

5724.364 Da

Max. entity weight

2917.755 Da

Exptl. method

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 94.4 %, Completeness: 62.3 %, Completeness (bb): 58.1 % Detail

Polymer type: polydeoxyribonucleotide polyribonucleotide

	Total	¹H	¹³C	³¹P
All	62.3 % (147 of 236)	72.2 % (114 of 158)	29.5 % (18 of 61)	88.2 % (15 of 17)
Suger, PO4	58.1 % (100 of 172)	69.1 % (76 of 110)	20.0 % (9 of 45)	88.2 % (15 of 17)
Nucleobase	73.4 % (47 of 64)	79.2 % (38 of 48)	56.3 % (9 of 16)
Aromatic	86.3 % (44 of 51)	100.0 % (35 of 35)	56.3 % (9 of 16)
Methyl	100.0 % (3 of 3)	100.0 % (3 of 3)

1. DNA (5'-D(*AP*TP*GP*GP*TP*BGR*CP*TP*C)-3')

ATGGTXCTC

2. RNA (5'-R(*GP*AP*GP*CP*AP*CP*CP*AP*U)-3')

GAGCACCAU

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	DNA_chain_A	natural abundance		1.0 mM
2	RNA_chain_B	natural abundance		1.0 mM
3	sodium chloride	natural abundance		50 mM
4	sodium phosphate	natural abundance		10 mM
5	EDTA	natural abundance		0.5 mM
6	DSS	natural abundance		0.3 uM
7	D2O	natural abundance		10 %
8	H2O	natural abundance		90 %

Sample #2

Solvent system 99.999 % D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
9	DNA_chain_A	natural abundance		1.0 mM
10	RNA_chain_B	natural abundance		1.0 mM
11	sodium chloride	natural abundance		50 mM
12	sodium phosphate	natural abundance		10 mM
13	EDTA	natural abundance		0.5 mM
14	DSS	natural abundance		0.3 uM
15	D2O	natural abundance		99.999 %

Release date

2011-05-11

Citation

Structural basis of the RNase H1 activity on stereo regular borano phosphonate DNA/RNA hybrids
Johnson, C.N., Spring, A.M., Sergueev, D., Shaw, B.R., Germann, M.W.
Biochemistry (2011), 50, 3903-3912, PubMed 21443203 , DOI 10.1021/bi200083d , Abstract

Experiments performed 6 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 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	DNA_chain_A	natural abundance		1.0 mM
2	RNA_chain_B	natural abundance		1.0 mM
3	sodium chloride	natural abundance		50 mM
4	sodium phosphate	natural abundance		10 mM
5	EDTA	natural abundance		0.5 mM
6	DSS	natural abundance		0.3 uM
7	D2O	natural abundance		10 %
8	H2O	natural abundance		90 %

2 2D 1H-13C HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 99.999 % D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
9	DNA_chain_A	natural abundance		1.0 mM
10	RNA_chain_B	natural abundance		1.0 mM
11	sodium chloride	natural abundance		50 mM
12	sodium phosphate	natural abundance		10 mM
13	EDTA	natural abundance		0.5 mM
14	DSS	natural abundance		0.3 uM
15	D2O	natural abundance		99.999 %

3 2D 1H-1H TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 99.999 % D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
9	DNA_chain_A	natural abundance		1.0 mM
10	RNA_chain_B	natural abundance		1.0 mM
11	sodium chloride	natural abundance		50 mM
12	sodium phosphate	natural abundance		10 mM
13	EDTA	natural abundance		0.5 mM
14	DSS	natural abundance		0.3 uM
15	D2O	natural abundance		99.999 %

4 2D DQF-COSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 99.999 % D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
9	DNA_chain_A	natural abundance		1.0 mM
10	RNA_chain_B	natural abundance		1.0 mM
11	sodium chloride	natural abundance		50 mM
12	sodium phosphate	natural abundance		10 mM
13	EDTA	natural abundance		0.5 mM
14	DSS	natural abundance		0.3 uM
15	D2O	natural abundance		99.999 %

5 2D 1H-1H NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 99.999 % D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
9	DNA_chain_A	natural abundance		1.0 mM
10	RNA_chain_B	natural abundance		1.0 mM
11	sodium chloride	natural abundance		50 mM
12	sodium phosphate	natural abundance		10 mM
13	EDTA	natural abundance		0.5 mM
14	DSS	natural abundance		0.3 uM
15	D2O	natural abundance		99.999 %

6 2D 1H-31P CORR

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 99.999 % D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
9	DNA_chain_A	natural abundance		1.0 mM
10	RNA_chain_B	natural abundance		1.0 mM
11	sodium chloride	natural abundance		50 mM
12	sodium phosphate	natural abundance		10 mM
13	EDTA	natural abundance		0.5 mM
14	DSS	natural abundance		0.3 uM
15	D2O	natural abundance		99.999 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_17535_2lar.nef
Input source #2: Coordindates	2lar.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)
1:5:DT:O3'	1:6:BGR:P			n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
A	6	BGR	[[(2R,3S,5R)-5-(2-azanyl-6-oxo-1H-purin-9-yl)-3-hydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]boranuide	Assigned chemical shifts, Distance restraints, Torsion angle restraints, Coordinates

Sequence alignments

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

---------
ATGGTXCTC
|||||||||
ATGGTXCTC

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

10-------
GAGCACCAU
|||||||||
GAGCACCAU
---------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	9	0	0	100.0
B	B	9	0	0	100.0

Content subtype: combined_17535_2lar.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	1		No information
1	Distance restraints	AMBER_distance_constraints_2	OK	211 (1)	noe	100.0 (chain: A, length: 9), 100.0 (chain: B, length: 9)
1	Dihedral angle restraints	AMBER_dihedral_3	OK	80 (80)	.	100.0 (chain: A, length: 9), 100.0 (chain: B, length: 9)

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: 9, Sequence coverage: 100.0%
  - Entity_assembly_ID: B, Chain length: 9, Sequence coverage: 100.0%
- Total number of restraints: 211
- Weight of restraints: 1.0 (211)
- Potential type of restraints: square-well-parabolic (211)
- Range of distance target values: 2.99, 6.51 (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

Dihedral angle restraints

Saveframe: AMBER_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 9, Sequence coverage: 100.0%
  - Entity_assembly_ID: B, Chain length: 9, Sequence coverage: 100.0%
- Total number of restraints: 80
- Total number of restraints per polymer type: 80
- Weight of restraints: 1.0 (80)
- Potential type of restraints: square-well-parabolic (80)
- Dihedral angle restraints per residue
  - Chain_ID: A
  - Chain_ID: B

Keywords DNA, DNA / RNA hybrid, modified ODN, modified oligonucleotides, NMR, Nuclear Magnetic Resonance, nucleic acid conformation, nucleic acid heteroduplex, RNA, RNase H, RNase H1 activity, substrate specificity