Adv Biochem Eng Biotechnol (2020) 174: 1–16
DOI: 10.1007/10_2019_103
© Springer Nature Switzerland AG 2019
Published online: 3 August 2019
Biophysical Characterization
of Aptamer-Target Interactions
Maximilian Plach and Thomas Schubert
Contents
1 Basic Binding Parameters in Aptamer Development . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
2 Biophysical Techniques to Study Basic Binding Parameters of Aptamers and Their Target
Molecules . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
2.1 Biophysical Principles and Readouts of Selected Techniques . . . . . . . . . . . . . . . . . . . . . . . . 4
2.2 Sample Material Requirements of the Selected Biophysical Methods . . . . . . . . . . . . . . . . 8
2.3 Application Range of the Selected Biophysical Techniques . . . . . . . . . . . . . . . . . . . . . . . . . . 10
3 The Characterization Strategy: Aspects to Consider . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
4 Affinity Constant: Estimated by Biophysical Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
5 Summary and Outlook . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
Abstract Aptamers are single-stranded nucleic acid molecules forming welldefined 3D structures. Aptamers typically bind to their ligands with high affinity
and specificity. They are capable of interacting with various kinds of ligands: ions,
small molecules, peptides, proteins, viruses, bacteria, and even cells. Therefore,
aptamers are in widespread use as sensor molecules or as targeting agents in
diagnostics and pharmaceutics. As a prerequisite for their use in these economic
high-value areas, aptamers must be studied in detail with respect to different
biophysical characteristics. Of central importance are basic binding parameters of
the aptamer-target interaction, such as binding affinity and kinetics. Numerous
biophysical methods with different features, characteristics, and capabilities are
used in the field today for this purpose.
This chapter provides an overview of the current state-of-the-art technologies for
studying interactions between aptamers and targets and discusses their advantages
as well as drawbacks. Furthermore, essential aspects influencing any aptamer
M. Plach and T. Schubert (*)
2bind GmbH, Regensburg, Germany
e-mail: schubert@2bind.com
DOI: 10.1007/10_2019_103
© Springer Nature Switzerland AG 2019
Published online: 3 August 2019
Biophysical Characterization
of Aptamer-Target Interactions
Maximilian Plach and Thomas Schubert
Contents
1 Basic Binding Parameters in Aptamer Development . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
2 Biophysical Techniques to Study Basic Binding Parameters of Aptamers and Their Target
Molecules . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
2.1 Biophysical Principles and Readouts of Selected Techniques . . . . . . . . . . . . . . . . . . . . . . . . 4
2.2 Sample Material Requirements of the Selected Biophysical Methods . . . . . . . . . . . . . . . . 8
2.3 Application Range of the Selected Biophysical Techniques . . . . . . . . . . . . . . . . . . . . . . . . . . 10
3 The Characterization Strategy: Aspects to Consider . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
4 Affinity Constant: Estimated by Biophysical Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
5 Summary and Outlook . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
Abstract Aptamers are single-stranded nucleic acid molecules forming welldefined 3D structures. Aptamers typically bind to their ligands with high affinity
and specificity. They are capable of interacting with various kinds of ligands: ions,
small molecules, peptides, proteins, viruses, bacteria, and even cells. Therefore,
aptamers are in widespread use as sensor molecules or as targeting agents in
diagnostics and pharmaceutics. As a prerequisite for their use in these economic
high-value areas, aptamers must be studied in detail with respect to different
biophysical characteristics. Of central importance are basic binding parameters of
the aptamer-target interaction, such as binding affinity and kinetics. Numerous
biophysical methods with different features, characteristics, and capabilities are
used in the field today for this purpose.
This chapter provides an overview of the current state-of-the-art technologies for
studying interactions between aptamers and targets and discusses their advantages
as well as drawbacks. Furthermore, essential aspects influencing any aptamer
M. Plach and T. Schubert (*)
2bind GmbH, Regensburg, Germany
e-mail: schubert@2bind.com