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Improved methods for CRISPR homology-directed repair (HDR) using Alt-R HDR Enhancer and ssDNA donors with optimized design

Improving HDR rates in induced pluripotent stem cells

Webinar summary: Learn how to improve HDR rates in CRISPR genome editing, and get guidance on best practices and design recommendations for HDR templates. Optimizing conditions for HDR in induced pluripotent stem cells (iPSCs) can lead to high levels of HDR in these cells. The first half of the webinar is presented by IDT’s own Mollie Schubert, and the second half of the webinar is presented by Justin McDonough of The Jackson Laboratory for Genomic Medicine in Farmington, CT. This webinar was hosted by Front Line Genomics.

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CRISPR-Cas proteins introduce double-stranded breaks (DSBs) at targeted genomic loci. These are repaired by endogenous cellular pathways such as non-homologous end joining (NHEJ) and homology-directed repair (HDR). Researchers often want to introduce a precise mutation, which requires utilizing the HDR pathway. Providing a ssDNA template during repair allows introduction of a precise desired mutation, but the rates of successful HDR are often low compared to NHEJ-mediated repair.

Methods to improve HDR rates

In the first part of this webinar, Mollie Schubert, MS, IDT Research Scientist, describes methods to improve the rate of HDR vs. NHEJ-mediated repair in various cell lines. The topics include tips for:

  1. Selection of the right gRNA and CRISPR enzyme
  2. HDR template design
  3. Use of Alt-R HDR Enhancer, a small molecule compound that increases the rate of HDR by inhibiting NHEJ-mediated repair

Mollie also describes the upcoming release of the Alt-R CRISPR HDR Design Tool, a novel bioinformatics tool for ssDNA HDR template design. The tool will support designs up to 3 kb, single- and dual-guide designs (i.e., for use with Cas9 nickases), and more.

Improving homology-directed repair efficiency in human stem cells

In the second part of this webinar, Justin McDonough, PhD, Scientist at The Jackson Laboratory for Genomic Medicine, describes methods he and his colleagues have used to improve HDR efficiency in human induced pluripotent stem cells (iPSCs). The topics include:

  1. Introducing CRISPR-Cas9 components into iPSCs
  2. Fluorescence and flow cytometry assays for determining the HDR-edited status of iPSCs
  3. Cell culture parameters to increase HDR rates in iPSCs
  4. Strategic design considerations for donor oligos to introduce a desired single nucleotide variant in iPSCs

By combining all these optimized methods, The Jackson Laboratory scientists dramatically increased the ratio of HDR to NHEJ when either Cas9 or Cas12a Ultra was used along with the Alt-R HDR Enhancer in iPSCs.

To learn more, view the webinar on demand:

Webinar: Improved methods for CRISPR homology-directed repair (HDR) using Alt-R HDR Enhancer and ssDNA donors with optimized design, watch now

Author(s)

Netanya Y Spencer, MD, PhD, Scientific Writer, IDT

Published Oct 14, 2019

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Additional resources

Product focus

CRISPR Nucleases

Cas9, Cpf1, and high fidelity nucleases with NLS for increased CRISPR genome editing efficiency.

Available nickases increase specificity in homology directed repair (HDR) experiments.

Alt-R HDR Enhancer

A small molecule compound that has demonstrated an ability to increase the rate of homology-directed repair (HDR).

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