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- PDB-8pwr: TINA-conjugated antiparallel DNA triplex -

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Basic information

Entry
Database: PDB / ID: 8pwr
TitleTINA-conjugated antiparallel DNA triplex
Components
  • DNA (5'-D(*AP*GP*GP*AP*GP*GP*A)-3')
  • DNA (5'-D(*TP*CP*CP*TP*CP*CP*T)-3')
  • DNA (5'-D(*TP*GP*GP*TP*GP*(J32)P*GP*T)-3')
KeywordsDNA / Triplex / TINA / Antiparallel / Conjugate
Function / homologyDNA
Function and homology information
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
AuthorsGaravis, M. / Edwards, P.J.B. / Serrano-Chacon, I. / Doluca, O. / Filichev, V.V. / Gonzalez, C.
Funding support Spain, 2items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBFU2017-89707-P Spain
Spanish Ministry of Science, Innovation, and UniversitiesPID2020-116620GB-I00 Spain
CitationJournal: Nucleic Acids Res. / Year: 2024
Title: Understanding intercalative modulation of G-rich sequence folding: solution structure of a TINA-conjugated antiparallel DNA triplex.
Authors: Garavis, M. / Edwards, P.J.B. / Serrano-Chacon, I. / Doluca, O. / Filichev, V.V. / Gonzalez, C.
History
DepositionJul 21, 2023Deposition site: PDBE / Processing site: PDBE
SupersessionJan 17, 2024ID: 6QHI
Revision 1.0Jan 17, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Mar 27, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(*TP*CP*CP*TP*CP*CP*T)-3')
B: DNA (5'-D(*AP*GP*GP*AP*GP*GP*A)-3')
C: DNA (5'-D(*TP*GP*GP*TP*GP*(J32)P*GP*T)-3')


Theoretical massNumber of molelcules
Total (without water)6,8733
Polymers6,8733
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints, First strand is connected to second strand through a linker of six ethylenglycol units. The same linker is used to connect second with third strand.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 15structures with the lowest energy
RepresentativeModel #2lowest energy

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Components

#1: DNA chain DNA (5'-D(*TP*CP*CP*TP*CP*CP*T)-3')


Mass: 2024.348 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: DNA chain DNA (5'-D(*AP*GP*GP*AP*GP*GP*A)-3')


Mass: 2211.486 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(*TP*GP*GP*TP*GP*(J32)P*GP*T)-3')


Mass: 2636.882 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
112isotropic12D 1H-1H NOESY
122isotropic12D 1H-1H TOCSY
131isotropic12D 1H-1H NOESY
242isotropic22D DQF-COSY
252isotropic12D 1H-1H NOESY
262isotropic12D 1H-1H TOCSY
271isotropic12D 1H-1H NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.5 mM Triplex-TINA, 90% H2O/10% D2O1H_sample90% H2O/10% D2O
solution20.5 mM Triplex-TINA, 90% H2O/10% D2O1D_sample90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMTriplex-TINAnatural abundance1
0.5 mMTriplex-TINAnatural abundance2
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
1125 mMTriplex-TINA_571 atm279.6 K
2125 mMTriplex-TINA_2571 atm300.4 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Bruker AVANCEBrukerAVANCE8002

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Processing

NMR software
NameDeveloperClassification
NMRFAM-SPARKYLee W, Tonelli M, Markley JLpeak picking
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanstructure calculation
NMRFAM-SPARKYLee W, Tonelli M, Markley JLchemical shift assignment
TopSpinBruker Biospincollection
RefinementMethod: molecular dynamics / Software ordinal: 2
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 15 / Conformers submitted total number: 10

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