BMRB Entry 19441

Name: NMR structure of spermine modified DNA duplex
Published: 2014-01-21

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PDB ID: 2mcj
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR19441
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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

NMR structure of spermine modified DNA duplex

Deposition date:

2013-08-20

Original release date:

2014-01-21

Authors:

Brzezinska, Jolanta; Gdaniec, Zofia; Popenda, Lukasz; Markiewicz, Wojciech

Citation:

Citation: Brzezinska, Jolanta; Gdaniec, Zofia; Popenda, Lukasz; Markiewicz, Wojciech. "Polyaminooligonucleotide: NMR structure of duplex DNA containing a nucleoside with spermine residue, N-[4,9,13-triazatridecan-1-yl]-2'-deoxycytidine" Biochim. Biophys. Acta 1840, 1163-1170 (2014).
PubMed: 24361616

Assembly members:

Assembly members:
DNA_(5'-D(*GP*TP*CP*GP*GP*CP*TP*G)-3'), polymer, 8 residues, 2458.635 Da.
DNA_(5'-D(*CP*AP*GP*(N4S)P*CP*GP*AP*C)-3'), polymer, 8 residues, 2107.429 Da.

Natural source:

Natural source: Common Name: not available Taxonomy ID: not available Superkingdom: not available Kingdom: not available Genus/species: not available not available

Experimental source:

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
DNA_(5'-D(*GP*TP*CP*GP*GP*CP*TP*G)-3'): GTCGGCTG
DNA_(5'-D(*CP*AP*GP*(N4S)P*CP*GP*AP*C)-3'): CAGXCGAC

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1
- assigned_chem_shift_list_2

Data type	Count
1H chemical shifts	164
31P chemical shifts	14

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	DNA (5'-D(GPTPCPGPGPCPTPG)-3')	1
2	DNA (5'-D(CPAPGP(N4S)PCPGPAPC)-3')	2

Entities:

Entity 1, DNA (5'-D(*GP*TP*CP*GP*GP*CP*TP*G)-3') 8 residues - 2458.635 Da.

1

DG

DT

DC

DG

DC

DT

DG

Entity 2, DNA (5'-D(*CP*AP*GP*(N4S)P*CP*GP*AP*C)-3') 8 residues - 2107.429 Da.

1

DC

DA

DG

N4S

DC

DG

DA

DC

Samples:

sample_1: DNA (5'-D(*CP*AP*GP*(N4S)P*CP*GP*AP*C)-3') 0.5 mM; DNA (5'-D(*GP*TP*CP*GP*GP*CP*TP*G)-3') 0.5 mM; D2O, [U-100% 2H], 100%; sodium chloride 50 mM; sodium phosphate 10 mM; EDTA 0.1 mM

sample_2: DNA (5'-D(*CP*AP*GP*(N4S)P*CP*GP*AP*C)-3') 0.5 mM; DNA (5'-D(*GP*TP*CP*GP*GP*CP*TP*G)-3') 0.5 mM; D2O, [U-100% 2H], 10%; H2O 90%; sodium chloride 50 mM; sodium phosphate 10 mM; EDTA 0.1 mM

sample_conditions_1: ionic strength: 60 mM; pH: 7.0; pressure: 1 atm; temperature: 298 K

sample_conditions_2: ionic strength: 60 mM; pH: 7.0; pressure: 1 atm; temperature: 283 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-1H COSY	sample_1	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-31P HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_2

Software:

X-PLOR NIH vv2.22, Schwieters, Kuszewski, Tjandra and Clore - refinement, structure solution

TOPSPIN vv2.0, Bruker Biospin - collection, processing

FELIX vv2002, Accelrys Software Inc. - chemical shift assignment, data analysis, peak picking

NMR spectrometers:

Bruker Avance 600 MHz