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XNA and semi-synthetic DNA

Life on Earth developed thanks to ability of DNA and RNA to replicate and transfer information about all living processes in the cell to the next generation. This unique and highly efficient natural strategy is billions years old but scientists still struggle to mimic this event in laboratory conditions. Although it sounds like a science fiction, technological improvements in the past decade allowed different scientific teams to successfully create synthetic nucleotides, XNA as well as synthetic and poly-synthetic organisms, which opened a whole new window of opportunities in the field of nanotechnology, medicine and biotechnology.

DNA molecule has specific double helix structure that consists of four complementary connected nucleotides. These four nucleotides create numerous genetic combinations. Their expression result in proteins responsible for all metabolic processes in living creatures. Different species have different sized genomes, but DNA in all species in the world is organized in the same way. No matter if you are yeast or a bird - you will still have DNA made of four nucleotides. Although they form enough genetic combinations, scientists wanted to explore why nature favored these four nucleotides to build entire life on the Earth and to examine ability of artificial nucleic acids to act like DNA and RNA.

More than a decade, scientists are experimenting with synthetic nucleotides. XNA is synthetic DNA molecule created out of artificial nucleotides. It is able to carry the same information as DNA and to replicate when needed. Basic difference between natural and XNA nucleotides lays in sugar component: pentose is replaced with synthetic analogs. New nucleotides named: ANA, FANA, TNA, LNA, CeNA, HNA contain between 4 and 7 carbon atoms (natural nucleotides have 5) and FANA even contains fluorine. Chemical alterations allow artificial nucleotides to resemble classic DNA molecule both structurally and functionally. Polymerase is an enzyme essential for DNA replication. Compartmentalized self-tagging technique is applied to build a polymerase that could recognize and successfully synthesize XNA from a DNA template. Another enzyme that works as “reverse transcriptase” is able to convert XNA back to DNA. With high accuracy in replication (over 95%), this system allows scientists to replicate and propagate genetic information efficiently. XNAs proved to be able to store and copy data just like natural DNA, but their ability to change and adapt to the environmental conditions was questionable. To test this issue, XNAs were subjected to the natural selection artificially, through different mutations. HNA successfully coped with selective pressure and evolved in different forms, proving that artificial XNA is able to evolve just like DNA and RNA during classical Darwinian evolution. Unlike DNA, XNA is resistant to natural enzymes. This characteristic is very important because application of DNA and RNA in biotechnology and medicine is restricted due to high biodegradability in living organisms. Since XNAs couldn’t be degraded, they could easily replace DNA and RNA in the field of diagnostics and therapeutics.

Another experiment using synthetic nucleotides focused on specific letters that form genetic code. Idea of expanding genetic code with additional nucleotides is not new, but lot of potential molecules failed in the past due to inability to connect with other nucleotides or to replicate. One synthetic pair, however, blends with four other nucleotides and replicate in the tube easily. These nucleotides are better known as NaM and 5SICS. They are complementary, but unlike other four nucleotides, they don’t form hydrogen bonds. Strong hydrophobic forces hold these nucleotides in DNA molecule. They change DNA shape from double helix to overlapped and intercalated DNA structure. Main concern with this altered DNA helix was ability of enzyme polymerase to approach DNA and complete replication successfully. Double helix structure is essential for the enzyme and despite low expectations, newly incorporated nucleotides showed ability to align perfectly (edge to edge) when gripped by the enzyme. One explanation of this unusual phenomenon is associated with chemical bonds; it is quite possible that NaM and 5SICS would not be able to form desirable structure during replication if they are connected through rigid covalent bonds. Discovery of new bases that could easily blend with natural nucleotides opened some new possibilities. Additional nucleotides could “spell” more words in genetic language, and if they become able to self-replicate efficiently - first semi-synthetic organism could develop soon. Scientists believe that expanded genetic code will be highly appreciated in precise molecular probing and in nanotechnology.