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BMRB: 25723


25723
2N5O
Universal Base oligonucleotide structure
Authors
Spring-Connell, A.M., Evich, M.G., Seela, F., Germann, M.W.
Assembly
Universal Base oligonucleotide with UB at point 5
Entity
1. DNA (5'-D(*AP*TP*GP*GP*(UB)P*GP*CP*TP*C)-3') (polymer, Thiol state: not present), 9 monomers, 2818.795 Da Detail

ATGGXGCTC


2. DNA (5'-D(*GP*AP*GP*CP*TP*CP*CP*AP*T)-3') (polymer, Thiol state: not present), 9 monomers, 2778.771 Da Detail

GAGCTCCAT


Total weight
5597.566 Da
Max. entity weight
2818.795 Da
Exptl. method
solution NMR
Data set
assigned_chemical_shifts
Chem. Shift Complete
Sequence coverage: 94.4 %, Completeness: 74.5 %, Completeness (bb): 79.4 % Detail
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Polymer type: polydeoxyribonucleotide

Total1H31P
All74.5 % (137 of 184)73.1 % (122 of 167)88.2 % (15 of 17)
Suger, PO479.4 % (108 of 136)78.2 % (93 of 119)88.2 % (15 of 17)
Nucleobase60.4 % (29 of 48)60.4 % (29 of 48)
Aromatic73.5 % (25 of 34)73.5 % (25 of 34)
Methyl100.0 % (4 of 4)100.0 % (4 of 4)

1. DNA (5'-D(*AP*TP*GP*GP*(UB)P*GP*CP*TP*C)-3')

ATGGXGCTC

2. DNA (5'-D(*GP*AP*GP*CP*TP*CP*CP*AP*T)-3')

GAGCTCCAT

Show sample condition
Sample #1

Solvent system 100% D2O, Pressure 1 atm, Temperature 294 K, Details 100% D2O sample, pH* 6.36


#NameIsotope labelingTypeConcentration
1DNA (5'-D(*AP*TP*GP*GP*(UB)P*GP*CP*TP*C)-3')natural abundance1 mM
2DNA (5'-D(*GP*AP*GP*CP*TP*CP*CP*AP*T)-3')natural abundance1 mM
3D2O100% deuterium100 %
4sodium chloridenatural abundance100 mM
5sodium phosphatenatural abundance10 mM
Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 294 K, Details 90% H2O / 10% D2O, pH 6.79


#NameIsotope labelingTypeConcentration
6DNA (5'-D(*AP*TP*GP*GP*(UB)P*GP*CP*TP*C)-3')natural abundance1 mM
7DNA (5'-D(*GP*AP*GP*CP*TP*CP*CP*AP*T)-3')natural abundance1 mM
8sodium chloridenatural abundance100 mM
9sodium phosphatenatural abundance10 mM
10D2O100% deuterium10 %
11H2Onatural abundance90 %

Release date
2016-09-05
Citation
Using NMR and molecular dynamics to link structure and dynamics effects of the universal base 8-aza, 7-deaza, N8 linked adenosine analog
Spring-Connell, A.M., Evich, M.G., Debelak, H., Seela, F., Germann, M.W.
Nucleic Acids Res. (2016), 44, 8576-8587, PubMed 27566150 , DOI 10.1093/nar/gkw736 ,
Experiments performed 12 experiments Detail
nullKeywords DNA, Nucleic Acid, Synthetic Base, Universal Base