Macromolecular Interactions: Aptamers

Christopher L Warren, VistaMotif LLC, Madison, Wisconsin, USA
Appesh Mohandas, University of Wisconsin–Madison, Madison, Wisconsin, USA
Ishan Chaturvedi, Indian Institute of Technology, Kharagpur, India
Aseem Z Ansari, University of Wisconsin–Madison, Madison, Wisconsin, USA

Published online: September 2009

DOI: 10.1002/9780470015902.a0003146

Aptamers are composed of nucleic acids or peptides and target many types of different molecules, including proteins and ligands, such as hormones and antibiotics. Nucleic acid aptamers can adopt diverse structures, including G-quadruplexes, bubbles, bulges, multiway junctions and pseudoknots. Aptamers have been developed against a multitude of proteins and small molecules. The versatility of aptamers to recognize nearly any biomolecule in a very specific manner makes them effective as diagnostic tools and attractive as potential therapeutics. Currently, the systematic evolution of ligands by exponential enrichment (SELEX) technique is the standard method to isolate an aptamer to a specific molecule. However, recent advances in microarrays offer much potential for isolating aptamers in a more efficient and effective method than SELEX.

Key Concepts

  • Aptamers are nucleic acids or peptides designed to target a wide variety of molecules such as proteins and small molecules such as hormones and antibiotics, with exquisite precision.
  • Nucleic acid aptamers can adopt diverse structures, including G-quadruplexes, bubbles, bulges, multiway junctions and pseudoknots.
  • Aptamers have been developed against a multitude of proteins and small molecules; an abridged table is included in this article.
  • The versatility of aptamers to recognize nearly any biomolecule in a very specific manner makes them effective as diagnostic tools and attractive as potential therapeutics.
  • Systematic evolution of ligands by exponential enrichment (SELEX) technique is the standard method to isolate an aptamer to a specific molecule.
  • Recent advances in microarrays present a new method for isolating aptamers in a potentially more efficient and effective manner than SELEX.

Keywords: aptamers; SELEX; diagnostics; therapeutics; microarray

Figure 1. Examples of nucleic acid aptamers. Left: DNA stem-loop aptamer targeted against angiogenin (Kim and Jeong, 2003; Nobile et al., 1998; Wiegand et al., 1996). Middle: RNA G-quadruplex aptamer targeted against immunoglobulin E (Kim and Jeong, 2003; Nobile et al., 1998; Wiegand et al., 1996). Right: RNA pseudoknot targeted against nucleocapsid protein of HIV-1 (Kim and Jeong, 2003; Nobile et al., 1998; Wiegand et al., 1996).
Figure 2. Schematic of a SELEX experiment. The general SELEX process starts at Step 1 with a large library of nucleic acids (approximately 1015 different sequences). During Steps 2–4, a target molecule is bound to the nucleic acid pool, and the bound nucleic acids are separated from the population. In Step 5, the bound nucleic acids are removed from the target molecule. The selection rounds of Steps 2–5 are repeated until a final set of aptamers are chosen with the desired affinity and specificity for the target molecule, and finishing with Step 6 in which the final pool of aptamers are cloned and sequenced. For counter-selection, the nucleic acids that do not bind the counter-selecting molecule are kept (rather than bound) and these are taken directly to Step 5.
Figure 3. Schematic of a microarray-based aptamer discovery system. A fluorescently labelled target molecule (e.g. cy3 labelled) is incubated with a microarray bearing millions of different aptamers (left panel). Each feature (square) on the microarray represents a unique aptamer that is repeated millions of times within that feature. The target molecule will preferentially bind certain aptamers (features) resulting in various intensities (middle panel). The percentage of aptamer bound at each feature is directly related to the affinity of the aptamer for the target molecule (right panel).
Figure 4. Rational search of aptamer structure and sequence space. The starting pool of nucleic acids for a SELEX experiment has approximately 1015 different sequences, whereas a standard microarray only has approximately 106. However, neither sequence set is able to exhaustively cover all possible 30–40 nucleotide sequences. Through the iterative microarray design earlier, the entire sequence space can be effectively searched rationally rather than randomly as by SELEX. In this case, a microarray that contains rough coverage of a multitude of different aptamer shapes is used initally (top panel). General shapes recognized by the target molecule are expanded upon in the second microarray design (middle panel). In the final design, the sequence of certain regions within the structural part of the best-binding aptamer are permuted (each colour represents a different sequence) (bottom panel).
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 Further Reading
    book Klussman S (2006) The Aptamer Handbook – Functional Oligonucleotides and their Applications. Weinheim: Wiley-VCH.
    book Toulme J, Dausse E, Santamaria F and Rayner B (2002) "Aptamers for controlling gene expression". In: Mahato RI and Kim SW (eds) Pharmaceutical Perspectives of Nucleic Acid-Based Therapeutics, pp. 89–120. London: CRC Press.
    book Win MN and Smolke CD (2007) "RNA as a versatile and powerful platform for engineering genetic regulatory tools". In: Harding SE and Harding S (eds) Biotechnology and Genetic Engineering Reviews, vol. 24, pp. 311–346. Nottingham, UK: Nottingham University Press.

Related Sub-Topics:

Protein Structure | Nucleic Acid Structure | Biochemical and Biophysical Techniques | Biomolecular Interactions | Proteins: Structure, Function, Metabolism | Nucleic Acids: Structure, Function, Metabolism
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Article Title: Macromolecular Interactions: Aptamers
 
How to Cite close
Warren, Christopher L, Mohandas, Appesh, Chaturvedi, Ishan, and Ansari, Aseem Z(Sep 2009) Macromolecular Interactions: Aptamers. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0003146]