dNaM is an artificial

nucleobase Nucleobases, also known as ''nitrogenous bases'' or often simply ''bases'', are nitrogen-containing biological compounds that form nucleosides, which, in turn, are components of nucleotides, with all of these monomers constituting the basic b ...

containing a 3-methoxy-2-naphthyl group instead of a natural base. When it was originally successfully introduced into DNA for replication in an

E. coli ''Escherichia coli'' (),Wells, J. C. (2000) Longman Pronunciation Dictionary. Harlow ngland Pearson Education Ltd. also known as ''E. coli'' (), is a Gram-negative, facultative anaerobic, rod-shaped, coliform bacterium of the genus ''Escher ...

semi-synthetic organism, it was paired up with

d5SICS d5SICS is an artificial nucleoside containing 6-methylisoquinoline-1-thione-2-yl group instead of a base. It pairs up with dNaM in a hydrophobic interaction. It was not able to be removed by the error-correcting machinery of the '' E. coli'' into ...

. For short it is called ''X'' whilst the

being called Y.

was replaced by dTPT3 in revised versions due to its improved ability to replicate in a wider range of sequence contexts. X pairs with Y using hydrophobic and packing interactions instead of hydrogen bonding, which occurs in natural base pairs. Inside the semi-synthetic organism, methyl directed mispatch repair pathway ( MMR) actually fixes unnatural-natural mispairs, whereas

recombinational repair Homologous recombination is a type of genetic recombination in which genetic information is exchanged between two similar or identical molecules of double-stranded or single-stranded nucleic acids (usually DNA as in cellular organisms but may be ...

actually cuts out the unnatural. The E. coli semi-synthetic organism managed to hold onto the new base for an extended time both while on a plasmid as well as when stored in the chromosome. In free DNA,

rings Ring may refer to: * Ring (jewellery), a round band, usually made of metal, worn as ornamental jewelry * To make a sound with a bell, and the sound made by a bell :(hence) to initiate a telephone connection Arts, entertainment and media Film and ...

of d5SICS and dNaM are placed in parallel planes instead of the same plane, but when inside of a DNA polymerase, they pair using an edge-to-edge conformation. dNaM and dTPT3 can also template transcription of mRNAs and tRNAs by T7 RNA polymerase that have the ability to produce decode at the E. coli ribosome to produce proteins with unnatural amino acids, expanding the

genetic code The genetic code is the set of rules used by living cells to translate information encoded within genetic material ( DNA or RNA sequences of nucleotide triplets, or codons) into proteins. Translation is accomplished by the ribosome, which links ...

References

Nucleosides Synthetic biology {{molecular-biology-stub