BMRB Entry 17859

Name: Solution Structure of a DNA duplex Containing an Unnatural, Hydrophobic Base Pair
Published: 2012-06-13

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PDB ID: 2lho
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR17859
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Solution Structure of a DNA duplex Containing an Unnatural, Hydrophobic Base Pair

Deposition date:

2011-08-12

Original release date:

2012-06-13

Authors:

Malyshev, Denis; Pfaff, Danielle; Ippoliti, Shannon; Hwang, Gil; Dwyer, Tammy; Romesberg, Floyd

Citation:

Citation: Malyshev, Denis; Pfaff, Danielle; Ippoliti, Shannon; Hwang, Gil; Dwyer, Tammy; Romesberg, Floyd. "Solution Structure, Mechanism of Replication, and Optimization of an Unnatural Base Pair" Chem. Eur. J. 16, 12650-12659 (2010).
PubMed: 20859962

Assembly members:

Assembly members:
DNA1, polymer, . residues, Formula weight is not available
DNA2, polymer, . residues, Formula weight is not available

Natural source:

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

Experimental source:

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
DNA1: CGTTTCXTTCTC
DNA2: GAGAAXGAAACG

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
1H chemical shifts	155

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	(DC)(DG)(DT)(DT)(DT)(DC)(LHO)(DT)(DT)(DC)(DT)(DC)	1
2	(DG)(DA)(DG)(DA)(DA)(MM7)(DG)(DA)(DA)(DA)(DC)(DG)	2

Entities:

Entity 1, (DC)(DG)(DT)(DT)(DT)(DC)(LHO)(DT)(DT)(DC)(DT)(DC) - Formula weight is not available

SICS is a synthetic non-natural, non-hydrogen bonding nucleoside

1

DC

DG

DT

DC

LHO

DT

DC

2

DT

DC

Entity 2, (DG)(DA)(DG)(DA)(DA)(MM7)(DG)(DA)(DA)(DA)(DC)(DG) - Formula weight is not available

MMO2 is a synthetic non-natural, non-hydrogen bonding nucleoside

1

DG

DA

DG

DA

MM7

DG

DA

2

DC

DG

Samples:

sample_1: DNA1 1 mM; DNA2 1 mM; sodium phosphate 10 mM; sodium chloride 100 mM

sample_conditions_1: ionic strength: 0.1 M; 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 DQF-COSY	sample_1	isotropic	sample_conditions_1

Software:

AMBER v11, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm - structure solution

NMR spectrometers:

Varian INOVA 500 MHz