BMRB Entry 18427

Name: Solution structure of 2'F-ANA and ANA self-complementary duplex
Published: 2012-07-16

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PDB ID: 2lsc
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR18427
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title: Solution structure of 2'F-ANA and ANA self-complementary duplex PubMed: 22798499

Deposition date: 2012-04-26 Original release date: 2012-07-16

Authors: Martin-Pintado, Nerea; Yahyaee, Maryam; Campos, Ramon; Noronha, Anne; Wilds, Cristopher; Damha, Masad; Gonzalez, Carlos

Citation: Martin-Pintado, Nerea; Yahyaee-Anzahaee, Maryam; Campos-Olivas, Ramon; Noronha, Anne; Wilds, Christopher; Damha, Masad; Gonzalez, Carlos. "The solution structure of double helical arabino nucleic acids (ANA and 2'F-ANA): effect of arabinoses in duplex-hairpin interconversion." Nucleic Acids Res. 40, 9329-9339 (2012).

Assembly members:
DNA/RNA_(5'-D(*(CFL)P*(GFL)P*(CFL)P*(GFL))-R(P*(A5O)P*(A5O)P*(UAR)P*(UAR))-D(P*(CFL)P*(GFL)P*(CFL)P*(GFL))-3')_, polymer, 12 residues, 3843.290 Da.

Natural source: Common Name: Human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):
DNA/RNA_(5'-D(*(CFL)P*(GFL)P*(CFL)P*(GFL))-R(P*(A5O)P*(A5O)P*(UAR)P*(UAR))-D(P*(CFL)P*(GFL)P*(CFL)P*(GFL))-3')_: XXXXXXXXXXXX

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
19F chemical shifts	7
1H chemical shifts	72

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	DNA/RNA_chain_A	1
2	DNA/RNA_chain_B	1

Entities:

Entity 1, DNA/RNA_chain_A 12 residues - 3843.290 Da.

1

CFL

GFL

CFL

GFL

A5O

UAR

CFL

GFL

2

CFL

GFL

Samples:

sample_1: potassium phosphate 25 mM; DNA/RNA chain 0.8 mM; sodium chloride 100 mM; D2O 10%; H2O 90%

sample_2: potassium phosphate 25 mM; sodium chloride 100 mM; DNA/RNA chain 0.8 mM; D2O 100%

sample_conditions_1: ionic strength: 100 mM; pH: 7.0; pressure: 1 atm; temperature: 273 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_2	isotropic	sample_conditions_1
2D DQF-COSY	sample_2	isotropic	sample_conditions_1
2D 1H-19F HOESY	sample_2	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_1
2D 1H-19F HOESY	sample_2	isotropic	sample_conditions_1

Software:

AMBER, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman - structure solution

Molmol, Koradi, Billeter and Wuthrich - data analysis

SPARKY, Goddard - peak picking

NMR spectrometers:

Bruker Avance 600 MHz
Bruker Avance 800 MHz