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- PDB-6gmy: Tc-DNA/RNA duplex -

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Basic information

Entry
Database: PDB / ID: 6gmy
TitleTc-DNA/RNA duplex
Components
  • RNA (5'-R(*GP*UP*AP*AP*GP*CP*CP*GP*AP*G)-3')
  • Tc-DNA (5'-(*(TCJ)P*(TTK)P*(TCJ)P*(TCS)P*(TCS)P*(TCJ)P*(TTK)P*(TTK)P*(TCY)P*(TCJ))-3')
KeywordsDNA-RNA HYBRID / tricyclo-DNA / Modified nucleic acids / Modified oligonucleotide / Tc-DNA
Function / homologyDNA / RNA
Function and homology information
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsIstrate, A. / Johannsen, S. / Istrate, A. / Sigel, R.K.O. / Leumann, C.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: NMR solution structure of tricyclo-DNA containing duplexes: insight into enhanced thermal stability and nuclease resistance.
Authors: Istrate, A. / Johannsen, S. / Istrate, A. / Sigel, R.K.O. / Leumann, C.J.
History
DepositionMay 28, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 13, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
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.name
Revision 1.2May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 2.0May 15, 2019Group: Data collection / Polymer sequence / Category: entity_poly / pdbx_seq_map_depositor_info
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_seq_map_depositor_info.one_letter_code
Revision 2.1May 22, 2019Group: Data collection / Database references
Category: citation / database_PDB_rev ...citation / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.2May 15, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tc-DNA (5'-(*(TCJ)P*(TTK)P*(TCJ)P*(TCS)P*(TCS)P*(TCJ)P*(TTK)P*(TTK)P*(TCY)P*(TCJ))-3')
B: RNA (5'-R(*GP*UP*AP*AP*GP*CP*CP*GP*AP*G)-3')


Theoretical massNumber of molelcules
Total (without water)6,5932
Polymers6,5932
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: DNA chain Tc-DNA (5'-(*(TCJ)P*(TTK)P*(TCJ)P*(TCS)P*(TCS)P*(TCJ)P*(TTK)P*(TTK)P*(TCY)P*(TCJ))-3')


Mass: 3352.575 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: RNA chain RNA (5'-R(*GP*UP*AP*AP*GP*CP*CP*GP*AP*G)-3')


Mass: 3240.012 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H NOESY
222isotropic12D 1H-1H NOESY
131isotropic12D 1H-1H TOCSY
141isotropic12D DQF-COSY
151isotropic12D 1H-13C HSQC

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.5 mM tc-DNA/RNA, 50 mM NaCl, 10 mM NaH2PO4, 100% D2OD2O100% D2O
solution20.5 mM tc-DNA/RNA, 50 mM NaCl, 10 mM NaH2PO4, 90% H2O/10% D2OH2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMtc-DNA/RNAnatural abundance1
50 mMNaClnatural abundance1
10 mMNaH2PO4natural abundance1
0.5 mMtc-DNA/RNAnatural abundance2
50 mMNaClnatural abundance2
10 mMNaH2PO4natural abundance2
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
1NaCl 50 mM, NaH2PO4 10 mM Not definedD2O 298K7.05 1 atm298 K
2NaCl 50 mM, NaH2PO4 10 mM Not definedH2O 283K7.05 1 atm283 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE II / Manufacturer: Bruker / Model: AVANCE II / Field strength: 700 MHz

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Processing

NMR software
NameDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
GROMOSvan Gunsteren and Berendsenrefinement
SparkyGoddardchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
Refinement
MethodSoftware ordinal
simulated annealing1
simulated annealing2
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 10

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