From polymerase engineering to semi-synthetic life: artificial expansion of the central dogma

Abstract

Nucleic acids have been extensively modified in different moieties to expand the scope of genetic materials in past decades. While the development of unnatural base pairs (UBPs) has expanded the...

How proton transfer impacts hachimoji DNA

“…Understanding the intrinsic stability of hachimoji DNA and the relative populations of their zwitterionic and tautomeric forms could impact medicinal chemistry and the development of antisense therapeutics and articial oligo chemistries. [70][71][72][73][74][75] Lastly, we highlight some limitations of the present study and the need for future work to determine the minimum free energy pathway of the proton transfer schemes explored in this paper. Several QM/MM studies on proton transfer in DNA highlight that complex interactions with the solvent, the rest of the DNA structure, and the DNA replisome could signicantly alter the DNA shape.…”

“…Understanding the intrinsic stability of hachimoji DNA and the relative populations of their zwitterionic and tautomeric forms could impact medicinal chemistry and the development of antisense therapeutics and artificial oligo chemistries. 70–75…”

Thermophilic Nucleic Acid Polymerases and Their Application in Xenobiology

“…The engineering of polymerases can be carried out via directed evolution, rational design, or semi-rational design [ 5 , 17 , 19 , 94 ]. Directed evolution mimics Darwinian evolution in nature, and yet with significantly shortened evolution time for desired phenotypic traits [ 95 ].…”

“…For example, enzymatic synthesis and amplification of XNAs are essential for efficiently producing and evolving functional XNA molecules [ 16 ]. However, due to their exotic structures, the unnatural nucleoside triphosphates of many XNAs are poor substrates for natural nucleic acid polymerases, and thus employing protein engineering approaches to make efficient XNA polymerases (XNAPs) is one of the most urgent tasks in xenobiology, which has drawn broad research interest in recent years [ 17 , 18 , 19 , 20 ]. Many of the thermophilic nucleic acid polymerases have been used as the starting scaffolds for generating XNAPs, and their great thermostability is a useful feature for high-temperature synthesis and thermocycling amplification of XNAs [ 21 ].…”

Synthesis, Reverse Transcription, Replication, and Inter-Transcription of 2′-Modified Nucleic Acids with Evolved Thermophilic Polymerases: Efforts toward Multidimensional Expansion of the Central Dogma

“…1,2 Some of these nucleic acids have been produced by replacing the deoxyribose or ribose with totally unnatural sugars, exemplified by arabino nucleic acid (ANA), 2′-fluoro-arabino nucleic acid (FANA), α-L-threofuranosyl nucleic acid (TNA), hexitol nucleic acid (HNA), and cyclohexenyl nucleic acid (CeNA), while some have been produced by simply substituting atoms or groups in the sugar, exemplified by those with modification at the 2′-position of the ribose or the deoxyribose, including 2′-azido (2′-Az), 2′-amino (2′-Am), 2′fluoro (2′-F), and 2′-methoxy (2′-OMe). 1,3,4 Among all 2′modifications of nucleic acids, 2′-F and 2′-OMe (Figure 1) are studied and applied the most extensively, due to the fact that these two modifications lead to significantly increased duplex melting temperature, faster hybridization kinetics, and enhanced nuclease resistance of the nucleic acids. 4,5 2′-F and 2′-OMe-modified DNA and RNA molecules have been broadly used to produce aptamers, ribozymes, antisense oligonucleotides, and guide RNAs of the clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 system with improved performances.…”