Toward Safe Genetically Modified Organisms through the Chemical Diversification of Nucleic Acids

@article{Herdewijn2009TowardSG,
  title={Toward Safe Genetically Modified Organisms through the Chemical Diversification of Nucleic Acids},
  author={Piet Herdewijn and Philippe Marli{\`e}re},
  journal={Chemistry \& Biodiversity},
  year={2009},
  volume={6}
}
It is argued that genetic proliferation should be rationally extended so as to enable the propagation in vivo of additional types of nucleic acids (XNA for 'xeno-nucleic acids'), whose chemical backbone motifs would differ from deoxyribose and ribose, and whose polymerization would not interfere with DNA and RNA biosynthesis. Because XNA building blocks do not occur in nature, they would have to be synthesized and supplied to cells which would be equipped with an appropriate enzymatic machinery… 
Binary genetic cassettes for selecting XNA-templated DNA synthesis in vivo.
TLDR
It could thus be demonstrated that cyclohexenyl nucleic acid (CeNA) can serve in vivo as template, mobilizing a limited effort of chemical synthesis.
Beyond DNA and RNA: The Expanding Toolbox of Synthetic Genetics.
TLDR
This review outline XNA polymerase and reverse transcriptase engineering as a key enabling technology and summarize the application of "synthetic genetics" to the development of aptamers, enzymes, and nanostructures.
In Vivo Expression of Genetic Information from Phosphoramidate–DNA
TLDR
The development of an alternative genetic system carrying phosphoramidate linkages that successfully propagates genetic information in bacteria and at the same time is labile to acidic conditions is outlined.
Directed evolution of artificial enzymes (XNAzymes) from diverse repertoires of synthetic genetic polymers
TLDR
This protocol describes the directed evolution of artificial endonuclease and ligase enzymes composed of synthetic genetic polymers (XNAzymes), using 'cross-chemistry selective enrichment by exponential amplification' (X-SELEX), which enables the development of fully substituted catalysts.
An efficient and faithful in vitro replication system for threose nucleic acid.
TLDR
The development of a transcription and reverse-transcription system that can replicate unnatural genetic polymers composed of threose nucleic acids and shows that TNA polymers are stable to enzymes that degrade DNA and RNA is reported.
Functional Comparison of Laboratory-Evolved XNA Polymerases for Synthetic Biology.
TLDR
Comparisons of substrate specificity, thermal stability, reverse transcriptase activity, and fidelity of laboratory-evolved polymerases that were established to synthesize XNA polymers find that the mutations acquired to facilitate XNA synthesis increase the tolerance of the enzymes for sugar-modified substrates with some sacrifice to protein-folding stability.
On the road towards chemically modified organisms endowed with a genetic firewall.
TLDR
This is the first successful attempt to cross the canonical/noncanonical chemical barrier by artificially evolving bacteria with a chlorinated DNA genome by showing that T could be "transliterated" to its noncanonical analogue 5-chorouracil (c) in the genome of Escherichia coli.
The XNA world: progress towards replication and evolution of synthetic genetic polymers.
Noncanonical DNA polymerization by aminoadenine-based siphoviruses
TLDR
Congruent phylogenetic clustering of the polymerases and biosynthesis enzymes suggests that aminoadenine has propagated in DNA alongside adenine since archaic stages of evolution.
Invading Escherichia coli Genetics with a Xenobiotic Nucleic Acid Carrying an Acyclic Phosphonate Backbone (ZNA).
TLDR
An investigation into the in vivo propagation of ( S)-ZNA culminated with the demonstration of the first synthetic nucleic acid with an acyclic backbone that can be transliterated to DNA by the E. coli cellular machinery.
...
...

References

SHOWING 1-10 OF 65 REFERENCES
Expanding the substrate repertoire of a DNA polymerase by directed evolution.
Nucleic acid polymerases are the most important reagents in biotechnology. Unfortunately, their high substrate specificity severely limits their applications. Polymerases with tailored substrate
Efforts toward expansion of the genetic alphabet: structure and replication of unnatural base pairs.
TLDR
It is shown that the rate of synthesis and extension of the self-pair formed between two d3FB analogues is sufficient for in vitro DNA replication, and the results help explain the replication properties of many previously examined unnatural base pairs and should help design natural base pairs that are better replicated.
Man-made cell-like compartments for molecular evolution
TLDR
It is demonstrated the linkage of genotype to phenotype in man-made compartments using a model system and a selection for target-specific DNA methylation was based on the resistance of the product (methylated DNA) to restriction digestion.
Understanding nucleic acids using synthetic chemistry.
  • S. Benner
  • Biology
    Accounts of chemical research
  • 2004
This Account describes work done in these laboratories that has used synthetic, physical organic, and biological chemistry to understand the roles played by the nucleobases, sugars, and phosphates of
Evolution of a T7 RNA polymerase variant that transcribes 2′-O-methyl RNA
TLDR
This work has modified the original procedure to identify polymerases that can efficiently incorporate multiple modified nucleotides at the 2′ position of the ribose and allows the selection of polymerase that have good processivities and can be combined to simultaneously incorporate several different modifieducleotides in a transcript.
Discovery, characterization, and optimization of an unnatural base pair for expansion of the genetic alphabet.
TLDR
An optimized base pair is designed, d5SICS:dMMO2, which is efficiently and selectively synthesized by Kf within the context of natural DNA.
Complete Chemical Synthesis, Assembly, and Cloning of a Mycoplasma genitalium Genome
TLDR
The methods described here will be generally useful for constructing large DNA molecules from chemically synthesized pieces and also from combinations of natural and synthetic DNA segments.
...
...