BMRB: 25724

Universal base control oligonucleotide structure

Authors

Spring-Connell, A.M., Evich, M.G., Seela, F., Germann, M.W.

Assembly

Control DNA oligonucleotide for the universal base

Entity

1. DNA (5'-D(*AP*TP*GP*GP*AP*GP*CP*TP*C)-3') (polymer, Thiol state: not present), 9 monomers, 2818.795 Da Detail

ATGGAGCTC

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: 100.0 %, Completeness: 72.7 %, Completeness (bb): 76.4 % Detail

Download

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Polymer type: polydeoxyribonucleotide

	Total	1H	31P
All	72.7 % (141 of 194)	71.0 % (125 of 176)	88.9 % (16 of 18)
Suger, PO4	76.4 % (110 of 144)	74.6 % (94 of 126)	88.9 % (16 of 18)
Nucleobase	62.0 % (31 of 50)	62.0 % (31 of 50)
Aromatic	75.0 % (27 of 36)	75.0 % (27 of 36)
Methyl	100.0 % (4 of 4)	100.0 % (4 of 4)

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

ATGGAGCTC

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

#	Name	Isotope labeling	Type	Concentration
1	DNA (5'-D(*AP*TP*GP*GP*AP*GP*CP*TP*C)-3')	natural abundance		1 mM
2	DNA (5'-D(*GP*AP*GP*CP*TP*CP*CP*AP*T)-3')	natural abundance		1 mM
3	D2O	natural abundance		100 %
4	sodium chloride	natural abundance		100 mM
5	sodium phosphate	natural abundance		10 mM

Sample #2

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

#	Name	Isotope labeling	Type	Concentration
6	DNA (5'-D(*AP*TP*GP*GP*AP*GP*CP*TP*C)-3')	natural abundance		1 mM
7	DNA (5'-D(*GP*AP*GP*CP*TP*CP*CP*AP*T)-3')	natural abundance		1 mM
8	sodium chloride	natural abundance		100 mM
9	sodium phosphate	natural abundance		10 mM
10	H2O	natural abundance		90 %
11	D2O	natural abundance		10 %

Hide sample codition

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 , Abstract

Entries sharing articles BMRB: 1 entries Detail

Experiments performed 11 experiments Detail