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- PDB-1ho6: CHIMERIC ARABINONUCLEIC ACID (ANA) HAIRPIN WITH ANA/RNA HYBRID STEM -

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Basic information

Entry
Database: PDB / ID: 1ho6
TitleCHIMERIC ARABINONUCLEIC ACID (ANA) HAIRPIN WITH ANA/RNA HYBRID STEM
ComponentsDNA/RNA (5'-R(*GP*GP*AP*C)-D(P*TP*TP*CP*G)-(P*(GAO)P*(UAR)P*(CAR)P*(CAR)-3')
KeywordsDNA / RNA / Arabinonucleic acid / Hairpin
Function / homologyDNA/RNA hybrid / DNA/RNA hybrid (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing
AuthorsDenisov, A.Y. / Gehring, K.
Citation
Journal: Nucleic Acids Res. / Year: 2001
Title: Solution structure of an arabinonucleic acid (ANA)/RNA duplex in a chimeric hairpin: comparison with 2'-fluoro-ANA/RNA and DNA/RNA hybrids.
Authors: Denisov, A.Y. / Noronha, A.M. / Wilds, C.J. / Trempe, J.F. / Pon, R.T. / Gehring, K. / Damha, M.J.
#1: Journal: Nucleosides and Nucleotides / Year: 2001
Title: Properties of Arabinonucleic Acids (ANA & 2'F-ANA): Implications for the Design of Antisense Therapeutics that Invoke RNase H Cleavage of RNA
Authors: Damha, M.J. / Noronha, A.M. / Wilds, C.J. / Trempe, J.F. / Denisov, A.Y. / Pon, R.T. / Gehring, K.
History
DepositionDec 8, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 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 ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
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: DNA/RNA (5'-R(*GP*GP*AP*C)-D(P*TP*TP*CP*G)-(P*(GAO)P*(UAR)P*(CAR)P*(CAR)-3')


Theoretical massNumber of molelcules
Total (without water)3,7681
Polymers3,7681
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 10all calculated structures submitted
RepresentativeModel #1the hairpin stem structure closest to the average

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Components

#1: DNA/RNA hybrid DNA/RNA (5'-R(*GP*GP*AP*C)-D(P*TP*TP*CP*G)-(P*(GAO)P*(UAR)P*(CAR)P*(CAR)-3')


Mass: 3768.350 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Solid phase synthesis, phosphoramidite chemistry

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111DQF-COSY
1212D-NOESY
NMR detailsText: This structure was determined using standard 2D homo- and heteronuclear techniques: NOESY, DQF-COSY, TOCSY, H,C-HMQC and H,P-HetCOSY

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM hairpinD2O
21 mM hairpin9:1 H2O/D2O
Sample conditionspH: 7 / Pressure: 1 atm / Temperature: 288 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 spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.843Brungerrefinement
X-PLORBrukerdata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
Details: Starting A- and B-type stem hairpin structures with randomly organized loops were refined by 14 ps restrained molecular dynamics (300-1000 K) with final enegry minimization
NMR representativeSelection criteria: the hairpin stem structure closest to the average
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 10 / Conformers submitted total number: 10

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