Efforts toward Further Integration of an Unnatural Base Pair into the Biology of a Semisynthetic Organism

Hashimoto, Koji; Fischer, Emil C.; Romesberg, Floyd E.

doi:10.1021/jacs.1c03860

Cited by 15 publications

(12 citation statements)

References 19 publications

(32 reference statements)

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“…Meanwhile, DNA polymerases in organisms are different from commercial DNA polymerases, so replication and transcription experiments in vivo are also necessary. , The effects of these nucleotides on physiology should be taken into account to build a healthier cellular system with unnatural nucleotides . To evaluate replication in vivo, the previously reported D6 containing dNaM flanked on each side by three randomized natural nucleotides was synthesized .…”

Section: Resultsmentioning

confidence: 99%

Access to Photostability-Enhanced Unnatural Base Pairs via Local Structural Modifications

Wang

et al. 2021

ACS Synth. Biol.

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Completing the storage and retrieval of increased genetic information in vivo and producing therapeutic proteins have been achieved by the unnatural base pair dNaM-dTPT3. Up to now, some biological and chemical approaches are implemented to improve the semi-synthetic organism (SSO). However, the photosensitivity of this pair, suggested as a potential threat to the healthy growth of cells, is still a problem to solve. Hence, we designed and synthesized a panel of TPT3 analogues with the basic structural skeletons of TPT3 but modified thiophene rings at variant sites to improve the photostability of unnatural base pairs. A comprehensive screening strategy, including photosensitivity tests, kinetic experiments, and replication in vitro by PCR and in vivo by amplification, was implemented. A new pair, dNaM-dTAT1, which had almost equally high efficiency and fidelity with the dNaM-dTPT3 pair itself both in vivo and in vitro, was proven to be more photostable and thermostable and less toxic to E. coli cells. The discovery of dNaM-dTAT1 represents our first progress for the optimization of this type of bases toward more photostable properties; our data also suggest that less photosensitive unnatural base pairs will be beneficial to build a healthier cellular replication system.

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Section: Resultsmentioning

confidence: 99%

Access to Photostability-Enhanced Unnatural Base Pairs via Local Structural Modifications

Wang

et al. 2021

ACS Synth. Biol.

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“…30,151 Recent in vivo experiments suggested that E. coli RNAP could also transcribe DNA containing some of these UBPs. 152 Recently, reverse transcription of RNA containing TPT3 or NaM has been investigated with several reverse transcriptases or DNAP mutants, including avian myeloblastosis virus (AMV) reverse transcriptase, Moloney murine leukemia virus (MMLV) reverse transcriptase, SuperScript II reverse transcriptase, SuperScript III reverse transcriptase, Super-Script IV reverse transcriptase, and an engineered Taq DNAP with reverse transcription activity, Volcano2G (V2G). 153,154 It was found that the UBP reverse transcription efficiencies of different reverse transcriptases were sharply different.…”

Section: Polymerases For the Synthesis Reverse Transcription And Repl...mentioning

confidence: 99%

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

Sun

Zhang

et al. 2022

RSC Chem. Biol.

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“…acids (Zhang et al, 2017a;Zhang et al, 2017b;Fischer et al, 2020;Hashimoto et al, 2021;Manandhar et al, 2021), so we can confidently expect the broad application of unnatural components in future construction of nucleic acid scaffolds for building nanostructures and multi-enzyme machineries, both in vitro and in vivo.…”

Section: Author Contributionsmentioning

confidence: 99%

Application of Nucleic Acid Frameworks in the Construction of Nanostructures and Cascade Biocatalysts: Recent Progress and Perspective

Zhu

Song

et al. 2022

Front. Bioeng. Biotechnol.

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Nucleic acids underlie the storage and retrieval of genetic information literally in all living organisms, and also provide us excellent materials for making artificial nanostructures and scaffolds for constructing multi-enzyme systems with outstanding performance in catalyzing various cascade reactions, due to their highly diverse and yet controllable structures, which are well determined by their sequences. The introduction of unnatural moieties into nucleic acids dramatically increased the diversity of sequences, structures, and properties of the nucleic acids, which undoubtedly expanded the toolbox for making nanomaterials and scaffolds of multi-enzyme systems. In this article, we first introduce the molecular structures and properties of nucleic acids and their unnatural derivatives. Then we summarized representative artificial nanomaterials made of nucleic acids, as well as their properties, functions, and application. We next review recent progress on constructing multi-enzyme systems with nucleic acid structures as scaffolds for cascade biocatalyst. Finally, we discuss the future direction of applying nucleic acid frameworks in the construction of nanomaterials and multi-enzyme molecular machines, with the potential contribution that unnatural nucleic acids may make to this field highlighted.

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Efforts toward Further Integration of an Unnatural Base Pair into the Biology of a Semisynthetic Organism

Cited by 15 publications

References 19 publications

Access to Photostability-Enhanced Unnatural Base Pairs via Local Structural Modifications

Access to Photostability-Enhanced Unnatural Base Pairs via Local Structural Modifications

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

Application of Nucleic Acid Frameworks in the Construction of Nanostructures and Cascade Biocatalysts: Recent Progress and Perspective

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