Affimers painting cellular structures with DNA, creating a super-resolution image.

Affimers: The Future of Targeted Imaging?

Nico Varela in Science & Nature September 2025 • 4 min read.

"New research combines affimers and DNA-PAINT for high-resolution cellular imaging, offering a potential alternative to traditional antibodies."

Super-resolution microscopy is changing how we see the microscopic world, allowing us to view structures far beyond the limits of traditional light microscopy. These advanced techniques can even visualize individual molecules, but applying this to complex cellular components has been challenging.

The problem lies in the tools we use to label these molecules. Traditional antibodies, while widely used, are large and can sometimes limit access to densely packed areas within cells. Other alternatives like nanobodies and aptamers exist, but they come with their own set of limitations, such as complex development processes or genetic modifications.

Now, a new approach is emerging that combines the best of both worlds: small, highly specific molecules called affimers with a DNA-based imaging technique known as DNA-PAINT. This innovative strategy promises to overcome the limitations of current methods, paving the way for more detailed and multiplexed super-resolution imaging.

What are Affimers and Why Do They Matter?

Affimers painting cellular structures with DNA, creating a super-resolution image.

Affimers are small proteins (around 10-12 kDa) that can be engineered to bind to specific target molecules with high affinity and specificity. They are derived from a large library of diverse protein variants, allowing researchers to quickly identify affimers that recognize a wide range of targets. This makes them a compelling alternative to traditional antibodies, which are larger and more time-consuming to produce.

One of the key advantages of affimers is their small size, which allows them to penetrate dense tissues and access targets that are difficult for antibodies to reach. They can also be easily modified with DNA strands, enabling the use of DNA-PAINT for super-resolution imaging.

Smaller Size: Affimers are significantly smaller than antibodies, improving penetration into dense tissues.
High Specificity: They can be engineered to bind to specific targets with high precision.
Versatile Modification: Affimers can be easily modified with DNA for advanced imaging techniques.
Rapid Development: They can be quickly isolated from large libraries, speeding up the research process.

In this study, researchers used an actin-binding affimer conjugated to a DNA strand. This allowed them to visualize actin filaments in cells with high resolution using DNA-PAINT. The affimer was specifically modified at a defined site with a DNA strand, ensuring precise and controlled labeling.

The Future of Affimer-Based Imaging

This research demonstrates the potential of affimers as versatile tools for super-resolution microscopy. Their small size, high specificity, and ease of modification make them ideal for a wide range of applications, from basic research to drug discovery and diagnostics. By combining affimers with DNA-PAINT and other advanced imaging techniques, scientists can now visualize cellular structures and processes with unprecedented detail.

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This article is based on research published under:

DOI-LINK: 10.1002/ange.201804020, Alternate LINK

Title: Ortsspezifische Funktionalisierung Von Affimeren Für Die Dna-Paint-Mikroskopie

Subject: General Medicine

Journal: Angewandte Chemie

Publisher: Wiley

Authors: Thomas Schlichthaerle, Alexandra S. Eklund, Florian Schueder, Maximilian T. Strauss, Christian Tiede, Alistair Curd, Jonas Ries, Michelle Peckham, Darren C. Tomlinson, Ralf Jungmann

Published: 2018-07-15

Everything You Need To Know

What are Affimers, and how do they compare to traditional antibodies?

Affimers are small proteins, approximately 10-12 kDa in size, engineered to bind to specific target molecules. They offer a compelling alternative to traditional antibodies, which are larger and can have limitations in accessing densely packed cellular areas. Affimers are derived from a diverse library of protein variants, enabling rapid identification of those that recognize a wide range of targets. Key advantages include their smaller size, improving tissue penetration, high specificity, versatile modification capabilities with DNA strands for techniques like DNA-PAINT, and rapid development compared to antibodies.

How does DNA-PAINT work with Affimers to achieve high-resolution cellular imaging?

DNA-PAINT, when used with Affimers, enhances super-resolution microscopy. Researchers modify Affimers with DNA strands. These DNA-labeled Affimers bind to specific targets within the cell. The DNA strands then interact with complementary strands labeled with fluorescent dyes. By controlling the on-off binding of the dye-labeled DNA, scientists can precisely locate the targets, creating high-resolution images of cellular structures. This approach overcomes limitations of traditional methods, improving the detail of visualization.

What are the main benefits of using Affimers in super-resolution microscopy?

The main benefits of using Affimers in super-resolution microscopy include their smaller size compared to antibodies, which improves penetration into dense tissues. Affimers demonstrate high specificity, binding to targets with great precision. Their versatility allows easy modification with DNA strands, facilitating the use of advanced imaging techniques like DNA-PAINT. Furthermore, Affimers offer rapid development and isolation from large libraries. These advantages enable scientists to visualize cellular structures and processes with unprecedented detail.

Can Affimers replace antibodies entirely in biological research and diagnostics?

Affimers present a promising alternative to antibodies in biological research and diagnostics. However, it is unlikely they will entirely replace antibodies. Affimers offer advantages in size, specificity, and ease of modification. Their smaller size allows for better penetration into dense tissues, and their ability to be easily modified with DNA strands makes them suitable for advanced imaging techniques. While Affimers show great potential, antibodies have a long history and are established in many applications. The choice between them often depends on specific experimental requirements and the nature of the target.

What are the potential applications of Affimer-based technology beyond basic research?

Beyond basic research, Affimer-based technology has several potential applications. In drug discovery, Affimers can aid in identifying and targeting specific molecules for therapeutic intervention. In diagnostics, they can be used to develop more sensitive and accurate tests for disease detection. Their use in super-resolution microscopy allows researchers to visualize cellular structures with high precision, aiding in understanding disease mechanisms. As Affimer technology continues to advance, it is anticipated that it will find use in various fields, including personalized medicine and targeted therapies, offering new avenues for biological research and its applications.