---
title: "ConA Bead Binding Success in CUT&RUN | Best Practices"
slug: "cona-bead-binding-success-cut-and-run"
description: "Learn how to confirm successful ConA bead binding in CUT&RUN and optimize cell capture for reliable assay performance and results."
updated: 2026-02-27T15:14:24Z
published: 2026-02-27T15:14:24Z
canonical: "support.epicypher.com/cona-bead-binding-success-cut-and-run"
---

> ## Documentation Index
> Fetch the complete documentation index at: https://support.epicypher.com/llms.txt
> Use this file to discover all available pages before exploring further.

# How do I know ConA bead binding was successful?

> This article also applies to meCUT&RUN and Multiomic CUT&RUN.

To know if ConA bead binding was successful, we recommend performing [Trypan Blue staining](/v1/docs/trypan-blue-staining) following bead binding steps. Save an aliquot of supernatant after ConA bead binding and an aliquot of the cell-bead reaction slurry, and perform [Trypan Blue staining](/v1/docs/trypan-blue-staining) for each sample as described. Successful ConA bead binding is indicated when:

- The supernatant, or unbound fraction, contains few cells/nuclei (**Figure 1A**).
- The cell-bead reaction slurry contains permeabilized, Trypan Blue positive cells surrounded by ConA beads (**Figure 1B**).

Should you not observe this, ensure:

- Count/integrity of cells before binding to ConA beads.
- ConA beads were never frozen.
- Cells/nuclei were not clumped.
- Beads did not become clumped or dried out.
- All buffers were correctly prepared.

![cell integrity C D@2x-8](https://cdn.document360.io/1fc69f91-cf1e-45ab-bc51-4063eb80e37c/Images/Documentation/cell%20integrity%20C%20D@2x-8.png)

**Figure 1.** (**A**) Supernatant from ConA bead prep shows few cells/nuclei, whereas (**B**) cell-bead slurry contains permeabilized (Trypan Blue positive) cells/nuclei surrounded by beads (brown spheres).