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Series GSE133365 Query DataSets for GSE133365
Status Public on Mar 27, 2020
Title Custom DNA microarrays reveal diverse binding preferences of proteins and small molecules to thousands of G-quadruplexes [design 1]
Organism synthetic construct
Experiment type Other
Summary Single-stranded DNA (ssDNA) containing guanine repeats can form G-quadruplex (G4) structures. While cellular proteins and small molecules can bind G4s, it has been difficult to broadly assess their sequence specificity. Here, we use custom DNA microarrays to examine the binding specificities of proteins, small molecules, and antibodies across ~15,000 G4 structures. Molecules used include fluorescently labeled pyridostatin (Cy5-PDS, a small molecule), BG4 (Cy5-BG4, a G4-specific antibody), and eight proteins (GST-tagged nucleolin, IGF2, CNBP, FANCJ, PIF1, BLM, DHX36, and WRN). Cy5-PDS and Cy5-BG4 selectively bind sequences known to form G4s, confirming their formation on the microarrays. Cy5-PDS binding decreased when G4 formation was inhibited using lithium or when ssDNA features on the microarray were made double-stranded. Similar conditions inhibited the binding of all other molecules except for CNBP and PIF1. We report that proteins have different G4 binding preferences suggesting unique cellular functions. Finally, competition experiments are used to assess the binding of an unlabeled small molecule, revealing the structural features in the G4 required to achieve selectivity. These data demonstrate that the microarray platform can be used to assess the binding preferences of molecules to G4s on a broad scale, helping to understand the properties that govern molecular recognition.
 
Overall design Binding microarray experiments were performed for G-quadruplex (G4) DNA interacting proteins and helicases (nucleolin, IGF2, CNBP,BLM,FANCJ), the anti-G4 antibody BG4, and the small molecule pyridostatin (PDS). Briefly, the binding experiments involved incubating GST-tagged proteins or Cy5-conjugated molecules (BG4, PDS) to 180K feature Agilent microarrays pre-incubated with 100mM potassium chloride (KCl) in order to determine their binding preferences to G4-forming sequences.
 
Contributor(s) Tillo D
Citation(s) 32216326
Submission date Jun 26, 2019
Last update date Apr 08, 2020
Contact name Desiree Tillo
E-mail(s) desiree.tillo@nih.gov
Phone +1-240-760-7289
Organization name NIH/NCI
Street address 41 Center Dr, Room D310
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
 
Platforms (1)
GPL26848 Agilent-085206 Gquad G4125A
Samples (32)
GSM3906278 G4_d1_Cy5-PDS_0.03uM
GSM3906279 G4_d1_Cy5-PDS_0.1uM
GSM3906280 G4_d1_Cy5-PDS_0.3uM_rep1
This SubSeries is part of SuperSeries:
GSE133368 Custom DNA microarrays reveal diverse binding preferences of proteins and small molecules to thousands of G-quadruplexes
Relations
BioProject PRJNA551273

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE133365_RAW.tar 100.6 Mb (http)(custom) TAR (of TXT)
Processed data included within Sample table

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