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- PDB-1w86: Solution structure of an dsDNA:LNA triplex -

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Basic information

Entry
Database: PDB / ID: 1w86
TitleSolution structure of an dsDNA:LNA triplex
Components(INTRAMOLECULAR DSDNA-LNA TRIPLEX) x 3
KeywordsDNA / DNA COMPLEX / LNA / TRIPLEX / NMR SPECTROSCOPY
Function / homologyDNA
Function and homology information
MethodSOLUTION NMR / simulated annealing
AuthorsSorensen, J.J. / Nielsen, J.T. / Petersen, M.
CitationJournal: Nucleic Acids Res. / Year: 2004
Title: Solution Structure of a DsDNA:Lna Triplex
Authors: Sorensen, J.J. / Nielsen, J.T. / Petersen, M.
History
DepositionSep 16, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 25, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 15, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_nmr_software / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_mr / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: INTRAMOLECULAR DSDNA-LNA TRIPLEX
B: INTRAMOLECULAR DSDNA-LNA TRIPLEX
C: INTRAMOLECULAR DSDNA-LNA TRIPLEX


Theoretical massNumber of molelcules
Total (without water)7,3223
Polymers7,3223
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2030 Å2
ΔGint-16 kcal/mol
Surface area3840 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20
Representative

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Components

#1: DNA chain INTRAMOLECULAR DSDNA-LNA TRIPLEX


Mass: 2508.694 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: HEXAKIS (ETHYLENE GLYCOL) LINKERS BETWEEN A8 AND T9
#2: DNA chain INTRAMOLECULAR DSDNA-LNA TRIPLEX


Mass: 2343.552 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: HEXAKIS (ETHYLENE GLYCOL) LINKERS BETWEEN T16 AND T17
#3: DNA chain INTRAMOLECULAR DSDNA-LNA TRIPLEX


Mass: 2469.663 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: C18, C20 AND C22 (LNA NUCLEOTIDES) ARE PROTONATED AT N3

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121COSY
131TOCSY
141NOESY- TOCSY
NMR detailsText: NONE

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Sample preparation

DetailsContents: D2O OR 90% H2O/10% D2O
Sample conditionsIonic strength: 100 MM NACL / pH: 5.1 / Pressure: 1.0 atm / Temperature: 308.0 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
AmberPEARLMAN,CASE,CALDWELL,ROSS,CHEATHAM, FERGUSON, SEIBEL,SINGH,WEINER,KOLLMANrefinement
Amberstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE
NMR ensembleConformers calculated total number: 20 / Conformers submitted total number: 20

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