BMRB Entry 19226

Name: Structure of 2'F-RNA/2'F-ANA chimeric duplex
Published: 2013-11-26

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PDB ID: 2m8a
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR19226
MolProbity Validation Chart

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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:

Structure of 2'F-RNA/2'F-ANA chimeric duplex

Deposition date:

2013-05-07

Original release date:

2013-11-26

Authors:

Martin-Pintado, Nerea; Deleavey, Glen; Portella, Guillem; Campos, Ramon; Orozco, Modesto; Damha, Masad; Gonzalez, Carlos

Citation:

Citation: Martin-Pintado, Nerea; Deleavey, Glen; Portella, Guillem; Campos-Olivas, Ramon; Orozco, Modesto; Damha, Masad; Gonzalez, Carlos. "Backbone FC(e)H...O Hydrogen Bonds in 2'F-Substituted Nucleic Acids." Angew. Chem. Int. Ed. Engl. 52, 12065-12068 (2013).
PubMed: 24115468

Assembly members:

Assembly members:
DNA-RNA_(5'-R((CFZ)P*(GFZ)P*(CFZ)P*(GFZ)P*(AF2)P*(AF2)D(P*(TAF)P*(TAF)P*(CFL)P*(GFL)P*(CFL)P*(GFL))-3'), polymer, 12 residues, 1908.162 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-RNA_(5'-R((CFZ)P*(GFZ)P*(CFZ)P*(GFZ)P*(AF2)P*(AF2)D(P*(TAF)P*(TAF)P*(CFL)P*(GFL)P*(CFL)P*(GFL))-3'): XXXXXXXXXXXX

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	1
1H chemical shifts	99

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	2'F-RNA/2'F-ANA chimeric, 1	1
2	2'F-RNA/2'F-ANA chimeric, 2	1

Entities:

Entity 1, 2'F-RNA/2'F-ANA chimeric, 1 12 residues - 1908.162 Da.

1

CFZ

GF2

CFZ

GF2

AF2

TAF

UFT

CFL

GF2

2

CFL

GF2

Samples:

sample_1: DNA/RNA (5'-R((CFZ)P*(GFZ)P*(CFZ)P*(GFZ)P*(AF2)P*(AF2)D(P*(TAF)P*(TAF)P*(CFL)P*(GFL)P*(CFL)P*(GFL))-3') 0.6 mM; sodium chloride 100 mM; sodium phosphate 25 mM

sample_2: DNA/RNA (5'-R((CFZ)P*(GFZ)P*(CFZ)P*(GFZ)P*(AF2)P*(AF2)D(P*(TAF)P*(TAF)P*(CFL)P*(GFL)P*(CFL)P*(GFL))-3') 0.6 mM; sodium chloride 100 mM; sodium phosphate 25 mM

sample_conditions_1: ionic strength: 125 mM; pH: 7.0; pressure: 1 atm; temperature: 283 K

sample_conditions_2: ionic strength: 125 mM; pH: 7.0; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_2
2D DQF-COSY	sample_2	isotropic	sample_conditions_2
2D 1H-1H TOCSY	sample_2	isotropic	sample_conditions_2

Software:

AMBER, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman - geometry optimization

Molmol, Koradi, Billeter and Wuthrich - data analysis

SPARKY, Goddard - peak picking

NMR spectrometers:

Bruker Avance 600 MHz
Bruker Avance 800 MHz
Varian INOVA 800 MHz
Bruker Avance 700 MHz