International team expands the genetic alphabet to create new DNA-like structures

The hereditary material of humans and other organisms is stored as a code in DNA, deoxyribonucleic acid. The canonical structure of DNA, called B-DNA, is a right-handed double helix with a major and minor groove. In addition to B-DNA, there are other non-canonical structures that DNA can take on. Some of the more well-known, non-canonical structures are Z-DNA (a left handed form of DNA without a difference in major and minor grooves), hairpins, and triplexes.

 Now synthetic biologists are examining expansion of the familiar DNA code could result in new geometries that could be engineered into new forms with new properties and potential uses.

In a preprint posted online on Research Square Sept. 23, 2022,an international team of researchers has proposed specific ways to alter the formation of DNA structure by adding nucleotide pairs to the alphabet.

The lead author of the article, Steven Benner, and several co-authors are affiliated with the Foundation for Applied Molecular Evolution in Florida.

In the double helix model of DNA, the four chemical bases that compose DNA are arranged in sequences in long spiraling strands. The bases are adenine (A), guanine (G), cytosine (C), and thymine (T). These bases pair up, A with T, and C with G. The particular order of the base pairs conveys the information needed to maintain the organism's homeostasis.

Each base pair is attached to a sugar molecule and a phosphate molecule, which are together called a nucleotide. These nucleotides form the two strands of the double helix.

Changing the geometry

The authors of the preprint show that it's possible to form 12 different nucleotides and six new nucleotide pairs. These are called non-canonical nucleotides, and the authors give them letter names, thus adding to the genetic "alphabet" of the Watson-Crick canonical pairs.

The new nucleotides make possible new ways of folding the DNA, such as into pentaflex structures, instead of those limited to the four-letter combinations of the standard DNA pairs.

The researchers used different analytical methods to image these new structures.

First they used fluorescent thioflavin T and looked at the changes it produced in fluorescence emission spectra of synthesized DNA molecules. They examined what happened to this fluorescence as a function of pH, the measure of how acidic or basic a substance is.

Another probe used was UV-visible absorption spectroscopy, looking at wavelengths absorbed by the natural DNA and the synthesized DNA.

The researchers also used NMR, nuclear magnetic resonance, to look at the spectra of differently folded DNA structures. They also tested the change in fluorescence in the presence of different metal ion species.

Potential uses

These synthetic biologists hope that by exploring the design space of DNA-like molecules, they can understand how these new structures might support "alien" genetic systems in the cosmos.

Researchers are also looking at how such new structures might support "alien" genetic systems in the cosmos. 

After reviewing some of the new DNA topologies that may be possible, the authors concluded, “...These studies show that such motifs do form with alien genetic systems. Thus it opens the door not only to addressing the theoretical and stability issues addressed in the paragraph above, but also the use of these in nanostructures that have practical value as nanomachines, signaling architectures and medical devices.”

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Steven Benner et al. "A New Folding Motif Formed with an Expanded Genetic Alphabet."Research Square,Sept. 23, 2022.

DOI: https://doi.org/10.21203/rs.3.rs-1754248/v1