Small molecule microarrays

Small molecule microarrays (SMM)

A microarray is a miniaturised assay with many hundreds or thousands of samples arranged in a 2-dimensional grid on a glass slide. Each microarray can be interrogated with a sample of interest for high-throughput and simultaneous analysis. Established in the 1990’s, microarrays are an ideal and economical front-end discovery tool.  Recently, they have been used for screening expansive small molecule libraries.

Small molecule microarrays (SMM) with up to 100,000 compounds can now be printed on single microscope slides with Arrayjet technology in batches up to 1000 slides. Each array can then be interrogated with a different target to identify novel binding interactions (Figure 1).  Key pharmaceutical applications include identifying hits with novel protein biomarker candidates or druggable RNA or DNA targets (Yang et al).

Get in touch for a free, no obligation consultation about your requirements.



Figure 1: Example small molecule microarray.
Compounds printed on the slide are assessed for binding interaction with a protein of interest. Hits are detected using a fluorescent-labelled antibody and read using a fluorescence scanner.


At Arrayjet, we are expertly equipped to meet your small molecule microarray requirements.  Our experienced team has established processes for developing and manufacturing SMM’s and our contactless, inkjet microarray printers are specifically adapted for SMM manufacture:

  • Print on any SMM compatible slides - including epoxy and isocyanate
  • Use our established SMM protocols to identify hits with protein, peptide, DNA and RNA targets
  • Print small molecule libraries directly in 100% DMSO or dilutions thereof
  • Our SMM platform is scalable to any library size
  • Up to 100,000 compounds can be printed on a single slide
  • Iris™ Optical QC evaluates printing quality in real-time for guaranteed yields - never miss a hit
  • Arrayjet Ltd, including Arrayjet Advance lab service and our instrument manufacturing, are accredited to ISO13485

How can I work with Arrayjet for SMM?

You can either choose one of our fully supported instrument options to print small molecule microarrays, or you can outsource your SMM needs to our laboratory services division called Arrayjet Advance.

If you choose to outsource to us then you will be assigned a lead scientist who will guide you through the process. Our SMM services cover assay development, SMM printing, sample interrogation, data analysis and hit identification.

Our team has been servicing microarray clients worldwide for over 20 years.

Get in touch for a free, no obligation consultation about your requirements.


“Arrayjet's efficiency allows for fast array spotting that is also very reproducible. The high-capacity platform is helpful in producing multiple array slides per printing run. The software is user-friendly, and the tech support has been nothing short of outstanding with any situations we have encountered." 

Dr Robert Ullrich, USAMRIID

Application note

Read how Arrayjet optimised a DMSO buffer for printing high density small molecules microarrays here.


Selected publications

Targeting a noncanonical, hairpin-containing G-quadruplex structure from the MYCN gene
M. Yang, S. Carter, S. Parmar, D. D Bume, D. R. Calabrese, X. Liang, K. Yazdani, M. Xu, Z. Liu, C. J. Thiele, and J. S. Schneekloth, Jr
Nucleic Acids Research

High-resolution crystal structures of the D1 and D2 domains of protein tyrosine phosphatase epsilon for structure-based drug design
G. T. Lountos, S. Raran-Kurussi, B. M. Zhao, B. K. Dyas, T. R. Burke Jr, R. G. Ulrich and D. S. Waugh
Structural Biology

Mercury for Small Molecule Screening

Mercury for Small Molecule Screening

A ready-to-use hit-detection platform.

100,000 compounds can be immobilized on one microarray slide, for screening against your target.

Example applications include:

  • Investigating the druggable genome
  • Modulating protein