Binary Genetic Cassettes for Selecting XNA‐Templated DNA Synthesis In Vivo

Pezo, Valérie; Liu, Feng Wu; Abramov, Mikhail; Froeyen, Mathy; Herdewijn, Piet; Marlière, Philippe

doi:10.1002/anie.201303288

Cited by 47 publications

(38 citation statements)

References 27 publications

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“…[2] Another motivation for exploring chemical variants of nucleic acids has been the elaboration of possible scenarios for the origin of life. [3] More recently the chemical diversification of nucleic acids has been attempted in vivo to propagate additional types of nucleic acids (XNA) as templates for DNA synthesis in E. coli [4,5] and for transcription into RNAi n mammalian cells. [6] In addition, DNAw ith at riazole linker instead of aphosphodiester bound have been accepted by E. coli [7a,b] and human [7c] cells.I th as also been reported that as emisynthetic organism is able to replicate with as ingle unnatural base pair in vivo.…”

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confidence: 99%

Chemical Morphing of DNA Containing Four Noncanonical Bases

et al. 2016

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The ability of alternative nucleic acids, in which all four nucleobases are substituted, to replicate in vitro and to serve as genetic templates in vivo was evaluated. A nucleotide triphosphate set of 5-chloro-2'-deoxyuridine, 7-deaza-2'-deoxyadenosine, 5-fluoro-2'-deoxycytidine, and 7-deaza-2'deoxyguanosine successfully underwent polymerase chain reaction (PCR) amplification using templates of different lengths (57 or 525mer) and Taq or Vent (exo-) DNA polymerases as catalysts. Furthermore, a fully morphed gene encoding a dihydrofolate reductase was generated by PCR using these fully substituted nucleotides and was shown to transform and confer trimethoprim resistance to E. coli. These results demonstrated that fully modified templates were accurately read by the bacterial replication machinery and provide the first example of a long fully modified DNA molecule being functional in vivo.

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Chemical Morphing of DNA Containing Four Noncanonical Bases

et al. 2016

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“…In principle, such an “expanded chimeric‐repeat unit” strategy consisting of two isomeric cyclic‐sugars with differing chirality ( l ‐ribulose and d ‐ribose) and an acyclic (glycerol) unit, demonstrates a simple, yet viable potential of generating nucleic acid systems with diversified properties . For example, a functioning system based on a two‐letter code using only adenine and thymine can, in principle, potentially be developed, since it may be possible to mimic a four letter code (“GC” and “AU”). By using the stronger ribulo‐pyrimidine‐ribo‐purine ( r t ‐rA) combination, the “GC” unit can be impersonated, while the weaker ribulo‐purine‐ribo‐pyrimidine r a ‐rT combinations would simulate the “AU” unit.…”

Section: Discussionmentioning

confidence: 99%

Chimeric XNA: An Unconventional Design for Orthogonal Informational Systems

Efthymiou

Gavette

Stoop

et al. 2018

Chemistry A European J

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The paradigm of homogenous-sugar-backbone of RNA and DNA has reliably guided the construction of many functional and useful xeno nucleic acid (XNA) systems to date. Deviations from this monotonous and canonical design, in many cases, results in oligonucleotide systems that lack base pairing with themselves, or with RNA or DNA. Here we show that nucleotides of two such compromised XNA systems can be combined with RNA and DNA in specific patterns to produce chimeric-backbone oligonucleotides, which in certain cases demonstrate base pairing properties comparable to-or stronger than-canonical systems, while also altering the conventional Watson-Crick pairing behavior. The unorthodox pairing properties generated from these chimeric sugar-backbone oligonucleotides suggest a counterintuitive approach of creating modules consisting of non-base pairing XNAs with RNA/DNA in a set pattern. This strategy has the potential to increase the diversity of unconventional nucleic acids leading to orthogonal backbone-sequence-controlled informational systems.

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“…Chem . 2013 ) . A mix of equimolar (25 ng each) purified NheI and NsiI cut pAK1 and purified EcoRI cut and dephosphorylated pAK2 were resuspended in 10 m m Tris‐HCl pH 7.5 with 100 m m NaCl in 20 μL final volume.…”

Section: Methodsmentioning

confidence: 99%

“…In vivo transliteration and mutational analysis directedby modified oligonucleotides ligated to plasmid DNA Oligonucleotides were dissolved in milliQ water to 1mm and diluted ten fold before assay.O ligonucleotides were tested inside a gapped heteroduplex generated through the enzymatic modification of two different plasmids pAK1 and pAK2. The form of the heteroduplex is described elsewhere in details (S. Pochet, C. R. Biol. 2003 andPezo, Angew.C hem.…”

Section: Primer Extension Experiments By Dna Polymerasesmentioning

confidence: 99%

Methylated Nucleobases: Synthesis and Evaluation for Base Pairing In Vitro and In Vivo

Jabgunde

Jaziri

Bande

et al. 2018

Chemistry A European J

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The synthesis, base pairing properties and in vitro (polymerase) and in vivo (E. coli) recognition of 2'-deoxynucleotides with a 2-amino-6-methyl-8-oxo-7,8-dihydro-purine (X), a 2-methyl-6-thiopurine (Y) and a 6-methyl-4-pyrimidone (Z) base moiety are described. As demonstrated by T measurements, the X and Y bases fail to form a self-complementary base pair. Despite this failure, enzymatic incorporation experiments show that selected DNA polymerases recognize the X nucleotide and incorporate this modified nucleotide versus X in the template. In vivo, X is mainly recognized as a A/G or C base; Y is recognized as a G or C base and Z is mostly recognized as T or C. Replacing functional groups in nucleobases normally involved in W-C recognition (6-carbonyl and 2-amino group of purine; 6-carbonyl of pyrimidine) readily leads to orthogonality (absence of base pairing with natural bases).

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Binary Genetic Cassettes for Selecting XNA‐Templated DNA Synthesis In Vivo

Cited by 47 publications

References 27 publications

Chemical Morphing of DNA Containing Four Noncanonical Bases

Chemical Morphing of DNA Containing Four Noncanonical Bases

Chimeric XNA: An Unconventional Design for Orthogonal Informational Systems

Methylated Nucleobases: Synthesis and Evaluation for Base Pairing In Vitro and In Vivo

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