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BMRB: 30940

Hairpin near 3'-Splice Site of Influenza A Segment 7 Bound to 5-nt Oligonucleotide
Authors
Kauffmann, A.D., Kennedy, S.D., Turner, D.H.
Assembly
RNA (5'-R(*AP*UP*CP*CP*AP*GP*AP*AP*AP*CP*GP*GP*AP*UP*GP*GP*AP*UP*A)-3'), RNA (5'-D(*(MU5)P*(MLC)P*(MRC))-R(P*(LG)P*(MU3))-3')
Entity
1. RNA (5'-R(*AP*UP*CP*CP*AP*GP*AP*AP*AP*CP*GP*GP*AP*UP*GP*GP*AP*UP*A)-3'), RNA (5'-D(*(MU5)P*(MLC)P*(MRC))-R(P*(LG)P*(MU3))-3'), entity 1 (polymer, Thiol state: not present), 19 monomers, 6211.732 Da Detail

AUCCAGAAAC GGAUGGAUA


2. RNA (5'-R(*AP*UP*CP*CP*AP*GP*AP*AP*AP*CP*GP*GP*AP*UP*GP*GP*AP*UP*A)-3'), RNA (5'-D(*(MU5)P*(MLC)P*(MRC))-R(P*(LG)P*(MU3))-3'), entity 2 (polymer, Thiol state: not present), 5 monomers, 1666.043 Da
Total weight
7877.775 Da
Max. entity weight
6211.732 Da
Source organism
Influenza A virus , synthetic construct
Exptl. method
solution NMR
Data set
assigned_chemical_shifts
Chem. Shift Complete
Sequence coverage: 79.2 %, Completeness: 72.8 %, Completeness (bb): 63.2 % Detail
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Polymer type: polyribonucleotide polydeoxyribonucleotide

Total1H31P
All72.8 % (131 of 180)75.2 % (121 of 161)52.6 % (10 of 19)
Suger, PO463.2 % (84 of 133)64.9 % (74 of 114)52.6 % (10 of 19)
Nucleobase100.0 % (47 of 47)100.0 % (47 of 47)
Aromatic100.0 % (41 of 41)100.0 % (41 of 41)

1. entity 1

AUCCAGAAAC GGAUGGAUA

Show sample condition
Sample #1

Solvent system 100% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 6.2, Details 0.5 mM RNA (5'-R(*AP*UP*CP*CP*AP*GP*AP*AP*AP*CP*GP*GP*AP*UP*GP*GP*AP*UP*A)-3'), 0.49 mM RNA (5'-D(*(MU5)P*(MLC)P*(MRC))-R(P*(LG)P*(MU3))-3'), 10 mM potassium phosphate, 0.05 mM sodium EDTA, 100% D2O


#NameIsotope labelingTypeConcentration
1RNA (5'-R(*AP*UP*CP*CP*AP*GP*AP*AP*AP*CP*GP*GP*AP*UP*GP*GP*AP*UP*A)-3')natural abundance0.5 (±0.02) mM
2RNA (5'-D(*(MU5)P*(MLC)P*(MRC))-R(P*(LG)P*(MU3))-3')natural abundance0.49 (±0.02) mM
3potassium phosphatenatural abundance10 (±0.5) mM
4sodium EDTAnatural abundance0.05 (±0.01) mM
Sample #2

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 (±1) K, pH 6.2, Details 0.5 mM RNA (5'-R(*AP*UP*CP*CP*AP*GP*AP*AP*AP*CP*GP*GP*AP*UP*GP*GP*AP*UP*A)-3'), 0.49 mM RNA (5'-D(*(MU5)P*(MLC)P*(MRC))-R(P*(LG)P*(MU3))-3'), 10 mM potassium phosphate, 0.05 mM sodium EDTA, 95% H2O/5% D2O


#NameIsotope labelingTypeConcentration
5RNA (5'-R(*AP*UP*CP*CP*AP*GP*AP*AP*AP*CP*GP*GP*AP*UP*GP*GP*AP*UP*A)-3')natural abundance0.5 (±0.02) mM
6RNA (5'-D(*(MU5)P*(MLC)P*(MRC))-R(P*(LG)P*(MU3))-3')natural abundance0.49 (±0.02) mM
7potassium phosphatenatural abundance10 (±0.5) mM
8sodium EDTAnatural abundance0.05 (±0.01) mM

Release date
2021-08-29
Citation
Nuclear magnetic resonance reveals a two hairpin equilibrium near the 3'-splice site of influenza A segment 7 mRNA that can be shifted by oligonucleotides
Kauffmann, A.D., Kennedy, S.D., Moss, W.N., Kierzek, E., Kierzek, R., Turner, D.H.
RNA (2022), 28, 508-522, PubMed 34983822 , DOI 10.1261/rna.078951.121 ,
Experiments performed 6 experiments Detail
Chemical shift validation 4 contents Detail
Keywords Hairpin, RNA, Splice-site, bound modified-oligonucleotide