DNA, genes and nanotechnologies – what they are and what they are not

One of the areas of research that exemplifies the interface between biology and nanotechnology and the raises new questions about what technology is and can be is the field of DNA nanotechnology. To address these questions, it is important to first understand what DNA is. In this post, we will move slowly through the world of DNA to analyze its function in biology, before finally arriving in the DNA nanotechnology.

Of all existing molecular structures, the double helix of DNA is probably one of the most well known. Schematic representations of DNA, showing a twisted, ladder-like structure are commonplace in advertising and popular culture. DNA plays an important role in the formation of societies on a multitude of levels, both living and non-living. The foundation to the importance of DNA lies in its ability to act as a carrier of information. In biological cells, DNA forms genes, which essentially are packages of information that can be translated into discrete objects that perform specific functions within the cell. DNA is transcribed into the bridging molecule RNA, which is, in turn, translated into a string of amino acids. Finally, the string of amino acids folds into a functional protein. DNA-RNA-protein – this is the central dogma of molecular cell biology. After being identified as the carrier of genetic information in 1944, and after the discovery of its double helical structure by James D. Watson in 1953 (Watson and Crick, 1953), DNA has been placed at the core of biology and, in a wider sense, bio-societies. By bio-societies I mean societies of living and non-living objects that are, in any way, transverse by biology. This includes societies of bio-molecules, cellular societies, and animal and human societies. (see previous post on Whitehead’s conception of societies)

In the context of bio-societies, genes have a very central position and interact in numerous ways. I would like to divide the function of genes in this context into two principal (albeit closely related) cases:

  1. The first case states that expression of a gene corresponds to a biological function and genetic differences can be associated to functional differences. Here, focus is the properties of the products from specific genes or groups of genes when expressed in an organism.
  2. The second case deals with genes as carriers of evolutionary information. The primary concern here is the evolutionary process and how it links organisms and properties together over space and time.

I want to do the division into two cases as they function in slightly different ways and need to be addressed somewhat differently. Here, we will mostly deal with the first case, how genes function. How genes act, and are acted upon, is in many was a matter of debate. One perspective places individual genes in the center of all biosocial interactions. This is perhaps most clearly expressed in Richard Dawkins’ The extended phenotype. Here, Dawkins states that

“Evolution is the external and visible manifestations of the differential survival of alternative replicators. Genes are replicators; organisms and groups of organisms …are vehicles in which replicators travel about” (Dawkins, 1982: 82).

In this gene-centric view, genes become very determining and dominating in the formation of bio-societies. The consequence of this is a world where genes become monolithic objects, free of all interrelations.

Donna Haraway labels this reductive position as gene fetishism. Gene fetishism mistakes genes as things-in-themselves and not as complex abstract assemblages.

“The gene as a fetish is a phantom object, lake and unlike the commodity. Gene fetishism involves “forgetting” that bodies are nodes in web of integrations, forgetting the tropic quality of all knowledge claims” (Haraway, 1997: 142).

Further,

“A gene is not a thing, much less a “master molecule” or a self-contained code. Instead, the term gene signifies a node of durable action where many actors, human and nonhuman, meet” (Haraway, 1997: 142).

Following a gene-centric perspective, there is a probability that genes become synonymous with DNA. When genes appear as discrete objects, it is tempting to only see the DNA sequence and not all the complex set of other factors acting upon DNA and influencing how the information coded in the DNA sequence is expressed. This way, we crate a misunderstanding of not only what genes are, but also what DNA is.

In order to describe DNA in a way that does not hide the society of object that form the assembled gene and where DNA does not automatically mean gene, we need to strip DNA of all its relations and focus on the molecule itself.

DNA is an abbreviation of deoxyribonucleic acid and is a polymer consisting of repeating nucleotide units. The backbone of the DNA polymer is built of the phosphate and sugar moieties of the nucleotides. In addition to this, the nucleotides also comprise a base moiety, which can be adenine (A), thymine (T), guanine (G) or cytosine (C). The bases form two separate pairs, A and T, and G and C. In the polymer, the nucleotide units form a sequence of bases that enables the assembly of the double helix together with another unpaired strand with a matching sequence of bases. It is this sequence of bases that is the code intrinsic to DNA and which gives DNA its information potential. However, DNA does not do anything on its own. What the information carried within the DNA sequence means is entirely dependent on the interrelation of DNA with other objects. In the gene fetishistic perspective this dependence on association is obscured.

Because the information stored in DNA depends of complex assemblies of a wide variety of objects, there is a potential to let DNA form other things than genes. This leads us to DNA nanotechnology. DNA nanotechnology is the non-biological utilization of the programmability of DNA to create nanometer scale DNA-based objects in a controlled way. In the 1980’s Nadrian Seaman pioneered the field of DNA nanotechnology creating molecular lattices made from DNA. (Seeman, 1982) The potential of DNA as a building block for technology is described by Seeman in an article in Nature in 2003:

“The nucleic acids seem to be unique …, providing a tractable, diverse and programmable system with remarkable control over intermolecular interactions, coupled with known structures for their complexes” (Seeman, 2003).

Instead of using the DNA code to construct genes, the base sequence of multiple strands is designed so that when they interact, a well-defined object is formed. Thus, the information contained within the DNA does no longer represent genes, but instead function as a manual for how the DNA molecules themselves should self-assemble into a specified shape.

A division can be made between two different types of DNA nanotechnology. Structural DNA nanotechnology deals with the creation of geometrical shapes and nano-scale machines. Here, the physical properties of the assembled structure are in focus. One of the most remarkable innovations in structural DNA-nanotechnology in recent years is DNA origami, which was invented in 2006 by Paul Rothemund. (Rothemund, 2006). DNA origami utilizes the genome from a virus together with a large number of shorter DNA strands to enable the creation of numerous DNA-based structures (Figure 1). The shorter DNA strands forces the long viral DNA to fold into a pattern that is defined by the interaction between the long and the short DNA strands.

DNA origami

Figure 1. Structures made from DNA using the DNA-origami method (Rothemund, 2006).

The second type instead uses the programmability of DNA to create devices that are capable of computing. Here, the structure of the assembled DNA is not of primary interest. Instead, control of the DNA sequence is used in the creation of computational algorithms, like e.g. artificial neural networks. (Qian et al., 2011)

In DNA nanotechnology, DNA is no longer treated as a distinctly biological object. Instead, DNA becomes a technological object with a potential to form new kinds of devices. This makes DNA a hybrid object, both biology and technology, both nature and culture. This way, DNA nanotechnology disrupts the unification of DNA and genes.

References

Dawkins, R. (1982). The Extended Phenotype: The Gene as a Unit of Selection. (London: Oxford University Press).

Haraway, D.J. (1997). Modest_Witness@Second_Millennium.Femaleman©_Meets_OncoMouse™ (New York: Routledge).

Qian, L.L., Winfree, E., and Bruck, J. (2011). Neural Network Computation with DNA Strand Displacement Cascades. Nature 475, 368-372.

Rothemund, P.W.K. (2006). Folding DNA to Create Nanoscale Shapes and Patterns. Nature 440, 297-302.

Seeman, N.C. (1982). Nucleic-Acid Junctions and Lattices. Journal of Theoretical Biology 99, 237-247.

Seeman, N.C. (2003). DNA in a Material World. Nature 421, 427-431.

Watson, J.D., and Crick, F.H.C. (1953). Molecular Structure of Nucleic Acids – a Structure for Deoxyribose Nucleic Acid. Nature 171, 737-738.

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One thought on “DNA, genes and nanotechnologies – what they are and what they are not

  1. […] describes the construction of nanometer-scale DNA-assemblies along the lines described in the “DNA, genes and nanotechnologies” post.  What is striking about DNA nanotechnology is how it combines programmability, offered […]

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