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BMRB: 18835


18835
2M11
Structure of perimidinone-derived synthetic nucleoside paired with guanine in DNA duplex
Authors
Kowal, E.A., Lad, R., Pallan, P.S., Muffly, E., Wawrzak, Z., Egli, M., Sturla, S.J., Stone, M.P.
Assembly
dodecamer duplex
Entity
1. dodecamer duplex (polymer, Thiol state: not present), 12 monomers, 3799.456 × 2 Da Detail

CGCGAATTXG CG


Total weight
7598.912 Da
Max. entity weight
3799.456 Da
Exptl. method
solution NMR
Data set
assigned_chemical_shifts, homonucl_NOEs
Chem. Shift Complete
Sequence coverage: 91.7 %, Completeness: 86.9 %, Completeness (bb): 97.4 % Detail
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Polymer type: polydeoxyribonucleotide

Total1H
All86.9 % (93 of 107)86.9 % (93 of 107)
Suger, PO497.4 % (75 of 77)97.4 % (75 of 77)
Nucleobase60.0 % (18 of 30)60.0 % (18 of 30)
Aromatic72.7 % (16 of 22)72.7 % (16 of 22)
Methyl100.0 % (2 of 2)100.0 % (2 of 2)

1. 5'-D(*CP*GP*CP*GP*AP*AP*TP*TP)[D3N]P-D(*GP*CP*GP)-3'

CGCGAATTXG CG

Show sample condition
Sample #1

Solvent system 100% D2O, Pressure 1 atm, Temperature 283 K, pH 7, Details 10 mM NaH2PO4 100 mM NaCl 50 uM Na2EDTA


#NameIsotope labelingTypeConcentration
15'-D(*CP*GP*CP*GP*AP*AP*TP*TP)[D3N]P-D(*GP*CP*GP)-3'natural abundance0.53 mM
2D2O[U-100% 2H]100 %
3sodium chloridenatural abundance100 mM
4EDTAnatural abundance50 uM
5sodium phosphatenatural abundance10 mM
Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 283 K, pH 7, Details 10 mM NaH2PO4 100 mM NaCl 50 uM Na2EDTA


#NameIsotope labelingTypeConcentration
65'-D(*CP*GP*CP*GP*AP*AP*TP*TP)[D3N]P-D(*GP*CP*GP)-3'natural abundance0.53 mM
7D2O[U-100% 2H]90 %
8H2Onatural abundance10 %
9sodium phosphatenatural abundance10 mM
10EDTAnatural abundance50 uM
11sodium chloridenatural abundance100 mM

Release date
2013-06-09
Citation
Recognition of O6-benzyl-2'-deoxyguanosine by a perimidinone-derived synthetic nucleoside: a DNA interstrand stacking interaction
Kowal, E.A., Lad, R.R., Pallan, P.S., Dhummakupt, E., Wawrzak, Z., Egli, M., Sturla, S.J., Stone, M.P.
Nucleic Acids Res. (2013), 41, 7566-7576, PubMed 23748954 , DOI 10.1093/nar/gkt488 ,
Experiments performed 3 experiments Detail
NMR combined restraints 4 contents Detail
Keywords B-form DNA, Dickerson-Drew Dodecamer, dPer, NMR solution structure, Perimidinone-Derived Nucleoside