Dataset.

Supplementary materials of the article Conformational Rearrangements Regulating the DNA Repair Protein APE1

Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/331322
Digital.CSIC. Repositorio Institucional del CSIC
  • Komaniecka, Nina
  • Porras, Marta
  • Cairn, Louis
  • Santas, Jon Ander
  • Ferreiro, Nerea
  • Penelo, Juan Carlos
  • Bañuelos, Sonia
9 pages. -- Figure S1: SDS‐PAGE of the various APE1 variants. -- Figure S2: (A) Far‐UV spectra of the different APE1 variants: unlabelled (black), Cy3‐APE1 (magenta), Cy5‐APE1 (cyan) and doubly labelled (purple). The protein concentration was 4 mM in buffer 20 mM potassium phosphate pH 7.0, 50 mM NaCl, 5 mM MgCl2. (B) Thermal denaturation profiles as based on the change in ellipticity at 222 nm in the absence (solid line) and presence (broken line) of an equimolar amount of product DNA. The scan rate was 1ºC / min. -- Figure S3: Binding of labelled APE1 to the oligonucleotides mimicking the abasic product (P) and substrate (S). -- Figure S4: Incision kinetics of 2 mM substrate DNA by the various APE1 variants as followed by 18% polyacrylamide‐urea gel electrophoresis. -- Figure S5: Sequence of the oligonucleotides used as model of the abasic APE1 product (left) and substrate (right), highlighting the two labelled thymines. X stands for tetrahydrofurane. -- Figure S6: Original prediction as obtained with AlphaFold of human APE1 (UniProt entry P27695), represented as a cartoon, and aligned to the DNA part (grey sticks) of crystal structure 5DFF [17]. -- Figure S7: Emission spectra of doubly labelled APE1 (black line) and Cy5‐APE1 (cyan solid line) upon excitation at 547 nm. Spectrum of Cy5‐APE1 with exc 647 nm (cyan broken line). -- Figure S8: Charge distribution in full‐length APE1 bound to DNA., Peer reviewed
 
DOI: http://hdl.handle.net/10261/331322
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/331322

HANDLE: http://hdl.handle.net/10261/331322
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/331322
 
Ver en: http://hdl.handle.net/10261/331322
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/331322

Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/331322
Dataset. 2022

SUPPLEMENTARY MATERIALS OF THE ARTICLE CONFORMATIONAL REARRANGEMENTS REGULATING THE DNA REPAIR PROTEIN APE1

Digital.CSIC. Repositorio Institucional del CSIC
  • Komaniecka, Nina
  • Porras, Marta
  • Cairn, Louis
  • Santas, Jon Ander
  • Ferreiro, Nerea
  • Penelo, Juan Carlos
  • Bañuelos, Sonia
9 pages. -- Figure S1: SDS‐PAGE of the various APE1 variants. -- Figure S2: (A) Far‐UV spectra of the different APE1 variants: unlabelled (black), Cy3‐APE1 (magenta), Cy5‐APE1 (cyan) and doubly labelled (purple). The protein concentration was 4 mM in buffer 20 mM potassium phosphate pH 7.0, 50 mM NaCl, 5 mM MgCl2. (B) Thermal denaturation profiles as based on the change in ellipticity at 222 nm in the absence (solid line) and presence (broken line) of an equimolar amount of product DNA. The scan rate was 1ºC / min. -- Figure S3: Binding of labelled APE1 to the oligonucleotides mimicking the abasic product (P) and substrate (S). -- Figure S4: Incision kinetics of 2 mM substrate DNA by the various APE1 variants as followed by 18% polyacrylamide‐urea gel electrophoresis. -- Figure S5: Sequence of the oligonucleotides used as model of the abasic APE1 product (left) and substrate (right), highlighting the two labelled thymines. X stands for tetrahydrofurane. -- Figure S6: Original prediction as obtained with AlphaFold of human APE1 (UniProt entry P27695), represented as a cartoon, and aligned to the DNA part (grey sticks) of crystal structure 5DFF [17]. -- Figure S7: Emission spectra of doubly labelled APE1 (black line) and Cy5‐APE1 (cyan solid line) upon excitation at 547 nm. Spectrum of Cy5‐APE1 with exc 647 nm (cyan broken line). -- Figure S8: Charge distribution in full‐length APE1 bound to DNA., Peer reviewed




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