The importance of small molecule analysis through BLI

“Small molecules” have a molecular mass below 900 Daltons in molecular biology and pharmacology.1 However, this distinction is far from arbitrary: The smaller a molecule is, the more easily it can permeate living systems.

Small molecules can diffuse across cell membranes more easily, enabling them to reach intracellular action sites more efficiently, enabling them to reach intracellular action sites, and giving them higher bioavailability than larger “macromolecules” such as proteins or RNA.2 

The vast majority of pharmaceutical drugs are thus small molecules. A few notable exceptions exist, such as insulin, a protein.

In molecular biology and pharmacology, small molecule analysis is a central research focus. In this context, it refers to identifying and quantifying the molecules themselves and investigating their interactions with other molecules of interest, such as receptors.

Generating information on molecular attributes such as kinetics, binding affinities, and concentration makes small molecule analysis a fundamental element of biomolecular research and drug discovery.

What is biolayer interferometry and how does it work?

Biolayer interferometry (BLI) is a novel analytical technique first developed in the 21st century. The application of BLI to small molecule analysis is fairly recent.3-5

BLI is based on the principle of optical interference to monitor binding activity between ligands and analytes.6 The ligand is immobilized on the surface of a fiber optic tip which has been coated with a biocompatible matrix. This matrix enables selective binding. The tip is dipped into a solution containing the other molecule in the pair (the analyte).

The optical thickness of the biological layer (consisting of ligand and analyte) on the surface of the sensing tip increases as the analyte interacts with the ligand on the sensor tip.

Small molecule analysis is facilitated by monitoring the precise thickness interacting molecules using white light interferometry, which compares the spectral shift to that of a reference surface.

How can biolayer interferometry be used for small molecule analysis?

BLI provides real-time label-free monitoring of molecular interactions on the sensor surface by constantly measuring the layer thickness formed by ligand-analyte interactions. This is why BLI is such a powerful tool for small molecule analysis.

In addition to surface plasmon resonance, BFI is one of the few biosensing techniques commercially available that does not require labeling. However, BFI does also come with a few advantages for small molecule analysis.

Only molecules binding to or dissociating from the sensor can shift the produced interference pattern and generate a response profile. This implies that alterations in flow rate, unbound molecules, or changes in the refractive index of the surrounding medium do not affect measurements.

BLI is also fluidics-free and can be used for small molecule analysis for either purified or crude samples.

Thanks to its simple operation and reusable fiber-optic tips, BLI is well-suited to parallelized high-throughput applications as it is sensitive enough for peptide and small molecule analysis.

BLI small molecule analysis from Gator Bio

Gator Bio is a world-leading producer of BLI platforms for small molecule analysis applications, which was originally founded by the inventors of biolayer interferometry.7

Combining a 1 mm glass rod with patented optical layers and specialized biosensor surface chemistry, Gator® BLI systems allow for high-capacity immobilization of biotinylated proteins for a wide range of molecular weights.

After immobilization, Gator® systems allow for rapid and accurate small molecule analysis to determine critical interaction parameters such as Kon, Koff, and KD for molecules down to 150 Da.

References and further reading

  1. Dougherty, T. J. & Pucci, M. J. Antibiotic Discovery and Development. (Springer Science & Business Media, 2011).
  2. Veber, D. F. et al. Molecular Properties That Influence the Oral Bioavailability of Drug Candidates. J. Med. Chem. 45, 2615–2623 (2002).
  3. Label-free detection of biomolecular interactions using BioLayer interferometry for kinetic characterization – PubMed.
  4. Biosensor-based small molecule fragment screening with biolayer interferometry – PubMed.
  5. Biolayer Interferometry | Gator Bio.
  6. Apiyo, D. O. Chapter 10:Biolayer Interferometry (Octet) for Label-free Biomolecular Interaction Sensing. in Handbook of Surface Plasmon Resonance 356–397 (2017). doi:10.1039/9781788010283-00356.
  7. About | Gator Bio.

About Gator Bio, Inc.

Gator Bio is a world-leading biosensor company headquartered in Palo Alto, CA. At Gator Bio, we provide researchers the tools and instrumentation to advance their research. From antibody engineering to small molecule drug discovery to basic research, Gator Bio can be used to bring meaning to the unknown. From the original inventors of label-free biolayer interferometry (BLI), Gator Bio provides the next generation of BLI technology.

Sponsored Content Policy: publishes articles and related content that may be derived from sources where we have existing commercial relationships, provided such content adds value to the core editorial ethos of News-Medical.Net which is to educate and inform site visitors interested in medical research, science, medical devices and treatments.

Last updated: Apr 3, 2023 at 6:06 AM


Please use one of the following formats to cite this article in your essay, paper or report:

  • APA

    Gator Bio, Inc.. (2023, April 03). The importance of small molecule analysis through BLI. News-Medical. Retrieved on June 05, 2023 from

  • MLA

    Gator Bio, Inc.. "The importance of small molecule analysis through BLI". News-Medical. 05 June 2023. <>.

  • Chicago

    Gator Bio, Inc.. "The importance of small molecule analysis through BLI". News-Medical. (accessed June 05, 2023).

  • Harvard

    Gator Bio, Inc.. 2023. The importance of small molecule analysis through BLI. News-Medical, viewed 05 June 2023,

Other White Papers by this Supplier