DNA aptamers against the DUX4 protein reveal novel therapeutic implications for FSHD

Christian Klingler, Jon Ashley, Ke Shi, Adeline Stiefvater, Michael Kyba, Michael Sinnreich, Hideki Aihara, Jochen Kinter

Research output: Contribution to journalArticlepeer-review

4 Scopus citations

Abstract

Aberrant expression of the transcription factor double homeobox protein 4 (DUX4) can lead to a number of diseases including facio-scapulo-humeral muscular dystrophy (FSHD), acute lymphoblastic leukemia, and sarcomas. Inhibition of DUX4 may represent a therapeutic strategy for these diseases. By applying Systematic Evolution of Ligands by EXponential Enrichment (SELEX), we identified aptamers against DUX4 with specific secondary structural elements conveying high affinity to DUX4 as assessed by fluorescence resonance energy transfer and fluorescence polarization techniques. Sequences analysis of these aptamers revealed the presence of two consensus DUX4 motifs in a reverse complementary fashion forming hairpins interspersed with bulge loops at distinct positions that enlarged the binding surface with the DUX4 protein, as determined by crystal structure analysis. We demonstrate that insertion of specific structural elements into transcription factor binding oligonucleotides can enhance specificity and affinity.

Original languageEnglish (US)
Pages (from-to)4573-4590
Number of pages18
JournalFASEB Journal
Volume34
Issue number3
DOIs
StatePublished - Mar 1 2020

Bibliographical note

Funding Information:
We thank Tracy Dinh, Nicholas Moeller, and Kayo Orellana for help with protein purification and crystallization, and the staff of the NE-CAT beamline for assistance with x-ray data collection. This research used resources of the Advanced Photon Source (APS), a US Department of Energy (DOE) Office of Science User Facility operated for the DOE Office of Science under Contract No. DE-AC02-06CH11357. The Northeastern Collaborative Access Team (NE-CAT) beamlines are funded by the National Institutes of Health (NIH) (P30 GM124165). The Eiger 16M detector on 24-ID-E beam line is funded by a NIH grant (S10OD021527). This work was supported by NIH grant GM118047 (to H. A.). We thank CSL Behring AG for an unrestricted research grant.

Funding Information:
We thank Tracy Dinh, Nicholas Moeller, and Kayo Orellana for help with protein purification and crystallization, and the staff of the NE‐CAT beamline for assistance with x‐ray data collection. This research used resources of the Advanced Photon Source (APS), a US Department of Energy (DOE) Office of Science User Facility operated for the DOE Office of Science under Contract No. DE‐AC02‐06CH11357. The Northeastern Collaborative Access Team (NE‐CAT) beamlines are funded by the National Institutes of Health (NIH) (P30 GM124165). The Eiger 16M detector on 24‐ID‐E beam line is funded by a NIH grant (S10OD021527). This work was supported by NIH grant GM118047 (to H. A.). We thank CSL Behring AG for an unrestricted research grant.

Publisher Copyright:
© 2020 The Authors. The FASEB Journal published by Wiley Periodicals, Inc. on behalf of Federation of American Societies for Experimental Biology

Keywords

  • PAX7
  • PROP1
  • bulge loop
  • decoy
  • transcription factor

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