BMRB Entry 36411

Title:
Aptamer enhancing peroxidase activity of myoglobin
Deposition date:
2021-02-19
Original release date:
2021-08-26
Authors:
Tsukakoshi, K.; Matsugami, A.; Khunathai, K.; Kanazashi, M.; Yamagishi, Y.; Nakama, K.; Oshikawa, D.; Hayashi, F.; Kuno, H.; Ikebukuro, K.
Citation:

Citation: Tsukakoshi, Kaori; Yamagishi, Yasuko; Kanazashi, Mana; Nakama, Kenta; Oshikawa, Daiki; Savory, Nasa; Matsugami, Akimasa; Hayashi, Fumiaki; Lee, Jinhee; Saito, Taiki; Sode, Koji; Khunathai, Kanjana; Kuno, Hitoshi; Ikebukuro, Kazunori. "G-quadruplex-forming aptamer enhances the peroxidase activity of myoglobin against luminol."  Nucleic Acids Res. 49, 6069-6081 (2021).
PubMed: 34095949

Assembly members:

Assembly members:
DNA (5'-D(*GP*GP*GP*TP*GP*GP*GP*TP*TP*GP*GP*GP*AP*GP*GP*G)-3'), polymer, 16 residues, 5131.298 Da.

Natural source:

Natural source:   Common Name: not available   Taxonomy ID: 32630   Superkingdom: not available   Kingdom: not available   Genus/species: not available not available

Experimental source:

Experimental source:   Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
DNA (5'-D(*GP*GP*GP*TP*GP*GP*GP*TP*TP*GP*GP*GP*AP*GP*GP*G)-3'): GGGTGGGTTGGGAGGG

Data sets:
Data typeCount
13C chemical shifts67
1H chemical shifts153

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1unit_11

Entities:

Entity 1, unit_1 16 residues - 5131.298 Da.

1   DGDGDGDTDGDGDGDTDTDG
2   DGDGDADGDGDG

Samples:

sample_1: DNA (5'-D(*(GUA)P*GP*GP*TP*GP*GP*GP*TP*TP*GP*GP*GP*AP*GP*GP*G)-3') 1 mM; DSS 100 uM; Potassium phosphate buffer pH 6.5 10 mM; D2O, [U-2H], 100%

sample_2: DNA (5'-D(*(GUA)P*GP*GP*TP*GP*GP*GP*TP*TP*GP*GP*GP*AP*GP*GP*G)-3') 1 mM; DSS 100 uM; Potassium phosphate buffer pH 6.5 10 mM; H2O 95%; D2O, [U-2H], 5%

sample_conditions_1: ionic strength: 10 mM; pH: 6.5; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-1H NOESY 500mssample_1isotropicsample_conditions_1
2D 1H-1H NOESY 50mssample_1isotropicsample_conditions_1
2D 1H-1H TOCSY 120mssample_1isotropicsample_conditions_1
2D DQF-COSYsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_1isotropicsample_conditions_1
2D 1H-1H NOESY 50mssample_2isotropicsample_conditions_1
2D 1H-1H NOESY 250mssample_2isotropicsample_conditions_1
2D JR-HMBCsample_2isotropicsample_conditions_1
2D 1H-15N HSQCsample_2isotropicsample_conditions_1

Software:

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

Sparky v3.114, Goddard - peak picking

TopSpin v3.5, Bruker Biospin - processing

X-PLOR NIH v2.48, Schwieters, Kuszewski, Tjandra and Clore - structure calculation

NMR spectrometers:

  • Bruker AVANCE III 700 MHz
  • Bruker AVANCE III 800 MHz