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Review
. 2020 Apr 3;21(7):2485.
doi: 10.3390/ijms21072485.

Antibodies, Nanobodies, or Aptamers-Which Is Best for Deciphering the Proteomes of Non-Model Species?

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Free PMC article
Review

Antibodies, Nanobodies, or Aptamers-Which Is Best for Deciphering the Proteomes of Non-Model Species?

Poshmaal Dhar et al. Int J Mol Sci. .
Free PMC article

Abstract

This planet is home to countless species, some more well-known than the others. While we have developed many techniques to be able to interrogate some of the "omics", proteomics is becoming recognized as a very important part of the puzzle, given how important the protein is as a functional part of the cell. Within human health, the proteome is fairly well-established, with numerous reagents being available to decipher cellular pathways. Recent research advancements have assisted in characterizing the proteomes of some model (non-human) species, however, in many other species, we are only just touching the surface. This review considers three main reagent classes-antibodies, aptamers, and nanobodies-as a means of continuing to investigate the proteomes of non-model species without the complications of understanding the full protein signature of a species. Considerations of ease of production, potential applications, and the necessity for producing a new reagent depending on homology are presented.

Keywords: antibodies; aptamers; nanobodies; proteins; proteome; reagents.

Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Current representation of the Tree of Life from Open Tree of Life (opentreeoflife.org). Of the more than two million known species on this planet, only ≈70,000 are vertebrates. Only a limited number of these have genomes sequenced and fewer have information regarding their proteomes. A high resolution image of this figure can be found at http://www.onezoom.org/life.html/@biota=93302#x1033,y1463,w1.9286.
Figure 2
Figure 2
Binding of antibody, nanobody, and aptamer to a protein, highlighting the size differences between the three potential binding reagents. In proteins where the homologous region (highlighted in red) between species is small, only part of the antibody may fit, leading to poor species cross-reactivity. The nanobody and aptamer are 10 and 20 times smaller, respectively, and are more likely to cross-react between species.
Figure 3
Figure 3
Diagrammatic representation of the process involved in the generation of specific binding reagents. Combinatorial phage libraries of antibodies or nanobodies, or combinatorial randomized sequences of aptamers are incubated with a target, followed by removal of unbound species via washing. The bound sequences are propagated in Escherichia coli or via PCR. Re-incubation of these enriched species is continued for 3–7 iterative rounds.

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