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- PDB-1n14: Structure and Dynamics of Thioguanine-modified Duplex DNA in Comp... -

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Basic information

Entry
Database: PDB / ID: 1n14
TitleStructure and Dynamics of Thioguanine-modified Duplex DNA in Comparison with Unmodified DNA; Structure of Unmodified Duplex DNA
Components
  • 5'-D(*GP*CP*TP*AP*AP*GP*GP*AP*AP*AP*GP*CP*C)-3'
  • 5'-D(*GP*GP*CP*TP*TP*TP*CP*CP*TP*TP*AP*GP*C)-3'
KeywordsDNA / mercaptopurine / thioguanine / anti-cancer therapy
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / restrained molecular dynamics, relaxation matrix analysis
AuthorsSomerville, L. / Krynetski, E.Y. / Krynetskaia, N.F. / Beger, R.D. / Zhang, W. / Marhefka, C.A. / Evans, W.E. / Kriwacki, R.W.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Structure and dynamics of thioguanine-modified duplex DNA
Authors: Somerville, L. / Krynetski, E.Y. / Krynetskaia, N.F. / Beger, R.D. / Zhang, W. / Marhefka, C.A. / Evans, W.E. / Kriwacki, R.W.
History
DepositionOct 16, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5'-D(*GP*CP*TP*AP*AP*GP*GP*AP*AP*AP*GP*CP*C)-3'
B: 5'-D(*GP*GP*CP*TP*TP*TP*CP*CP*TP*TP*AP*GP*C)-3'


Theoretical massNumber of molelcules
Total (without water)7,9432
Polymers7,9432
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200back calculated data agree with experimental NOESY spectrum
Representative

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Components

#1: DNA chain 5'-D(*GP*CP*TP*AP*AP*GP*GP*AP*AP*AP*GP*CP*C)-3'


Mass: 4009.637 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*GP*GP*CP*TP*TP*TP*CP*CP*TP*TP*AP*GP*C)-3'


Mass: 3933.558 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
131DQF-COSY

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Sample preparation

DetailsContents: Single-stranded oligodeoxyribonucleotides, d(5-GCTAAGGAAAGCC-3) and the complementary strand d(5-GGCTTTCCTTAGC-3), were synthesized using standard phosphoramidite chemistry. Single-stranded ...Contents: Single-stranded oligodeoxyribonucleotides, d(5-GCTAAGGAAAGCC-3) and the complementary strand d(5-GGCTTTCCTTAGC-3), were synthesized using standard phosphoramidite chemistry. Single-stranded DNA molecules were purified using anion exchange chromatography (MonoQ HR 5/5, Pharmacia Biotech). Purity was confirmed by UV spectroscopy, analytical anion exchange chromatography, and mass spectrometry. The GC and thioGC DNA duplexes were each prepared by annealing either equimolar amounts of complimentary strands or a 1.2 molar excess of the unmodified strand to the modified strand in Buffer A (10 mM sodium phosphate, 50 mM NaCl, pH 7.0) at 70 C for 5 min., followed by slow cooling over 12 hours to room temperature. DNA duplexes were purified using gel filtration chromatography (Superdex Peptide HR 10/30, Pharmacia Biotech) in Buffer A.
Solvent system: Buffer A (10 mM sodium phosphate, 50 mM NaCl, pH 7.0)
Sample conditionsIonic strength: approx. 65 mM / pH: 7.0 / Pressure: ambient / Temperature: 293 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.1Brunger, A.iterative matrix relaxation
X-PLOR3.1Brunger, A.refinement
RefinementMethod: restrained molecular dynamics, relaxation matrix analysis
Software ordinal: 1
Details: Restrained molecular dynamics (rMD) structure refinement of B-DNA starting structures was performed using an XPLOR 3.1 (26) simulated annealing protocol employing the Cheatham, et al. (19), ...Details: Restrained molecular dynamics (rMD) structure refinement of B-DNA starting structures was performed using an XPLOR 3.1 (26) simulated annealing protocol employing the Cheatham, et al. (19), force field. This force field was modified to include parameterization of thioG, as described above. Starting structures were energy minimized by 160 steps of Powells conjugate gradient minimization followed by rMD while heating to 600 K at 50 K sec-1, cooling to 300 K at 25 K sec-1, and equilibrating at 293 K over 250 ps.
NMR ensembleConformer selection criteria: back calculated data agree with experimental NOESY spectrum
Conformers calculated total number: 200 / Conformers submitted total number: 20

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