July 2010

CHEMISTRY:

Primitive Frameshift Reading of a Synthetic Polymer

An extensive set of (bio)chemical information is stored within your DNA. Much (not all) of the information a cell needs to grow, carry out its normal functions, and repair itself is encoded within its DNA, comprised in part of sequences of four chemical subunits (adenine, thymine, cytosine, and guanine) called nucleotides.

It's hard to overemphasize how much information is stored within a cell's DNA. One human chromosome (there are twenty-three pairs of chromosomes in human cells) can possess over two hundred million nucleotides, all coming together to largely (not entirely) encode for what the cell needs.

There's no reason why chemical information can't be stored within synthetic polymers. It's unrealistic to expect initial efforts to even come close to that achieved through billions of years of evolution, but the effort has to start somewhere.

Howard Colquhoun (University of Reading, United Kingdom) and coworkers have greatly contributed to this effort. They have read out overlapping sequences in synthetic polymer molecules, a primitive version of frameshft reading (the reading of overlapping genes) observed in living cells.

Primitive frameshift reading.

The scientists wanted to chemically encode information within a synthetic polymer. For initial efforts, only two chemical sequences are necessary (analogous to the zeros and ones in computer science).

Their synthetic polymer is comprised of two repeating subunits. One is an imide (I), and the other a sulfone (S).

Importantly, the scientists' synthetic protocol enabled them to synthesize polymers of a precise sequence, i.e. -ISISISIS-. Note that this polymer possesses overlapping segments, i.e. an SIS sequence and an ISI sequence.

The scientists synthesized two molecules to latch onto the two different sequences in their polymer. By latching onto the polymer, these two molecules are known as molecular tweezers.

One of the molecular tweezers latched onto the SIS sequence, and the other to the ISI sequence, through a chemical interaction known as π-π stacking. This interaction occurs when two molecules of (typically) alternating single and double bonds stick together (incidentally, an analogous chemical interaction greatly contributes to the packing of DNA within living cells).

Furthermore, this π-π stacking was readily observed through nuclear magnetic resonance (NMR) spectroscopy, due to the fact that the chemical linkage to the ISI sequence is roughly 500 times stronger than that to the SIS sequence. It was also visualized through crystallography, providing unambiguous proof as to exactly where the molecular tweezers were latched onto the scientists' synthetic polymer.

Overall evaluation.

No one claims that synthesizing molecules which latch onto overlapping chemical sequences in a synthetic polymer is the equivalent of designing a synthetic genome. Nevertheless, it is somewhat (very primitively) reminiscent of frameshift reading within living cells.

Keep in mind that the scientists haven't reported a way to generate a function upon binding of the molecular tweezers to the synthetic polymer, unless you consider the atomic spin within the polymer a "function." Note that molecules which bind to DNA in a living cell do so to elicit a function (e.g. protein synthesis).

These statements are not meant as a criticism of the scientists' research. They're only meant to overemphasize that the scientists aren't anywhere near designing a "synthetic life form" (their research goals may not even be in such a direction).

Moving beyond the primitively biomimetic applications of this research, a more practical shorter-term application is as a new, revolutionary method of data storage. Currently, data is imprinted on a flat surface, serving as a fundamental limitation to how much information can be stored on it.

The technology reported herein has no such limitation. With a great deal of further development, vastly more chemical information could be stored within a single device, as long as methods are available for reading thickly imprinted chemical information.

ResearchBlogging.org for more information:
Zhu, Z., Cardin, C. J., Gan, Y., & Colquhoun, H. M. (2010). Sequence-selective assembly of tweezer molecules on linear templates enables frameshift-reading of sequence information Nature Chemistry, 2 (8), 653-660 DOI: 10.1038/nchem.699