ArticleNucleic acids research2011
Recognition of an expanded genetic alphabet by type-II restriction endonucleases and their application to analyze polymerase fidelity.
Article in Nucleic acids research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Hydroxyl radical-induced C1'-H abstraction reaction of different artificial nucleotides.Journal of molecular modeling · 2024Article
- Structure and stability of different triplets involving artificial nucleobases: clues for the formation of semisynthetic triple helical DNA.Scientific reports · 2023Article
- Building better polymerases: Engineering the replication of expanded genetic alphabets.The Journal of biological chemistry · 2020Review
- Nanopore Sequencing of an Expanded Genetic Alphabet Reveals High-Fidelity Replication of a Predominantly Hydrophobic Unnatural Base Pair.Journal of the American Chemical Society · 2020Article
- Proton Transfer and Nitro Rotation Tuned Photoisomerization of Artificial Base Pair-ZP.Frontiers in chemistry · 2020Article
- Advances and Challenges in Cell-Free Incorporation of Unnatural Amino Acids Into Proteins.Frontiers in pharmacology · 2019Review
- Review
- Auxotrophy to Xeno-DNA: an exploration of combinatorial mechanisms for a high-fidelity biosafety system for synthetic biology applications.Journal of biological engineering · 2018Review
- Consecutive non-natural PZ nucleobase pairs in DNA impact helical structure as seen in 50 μs molecular dynamics simulations.Nucleic acids research · 2017Article
- Biological phosphorylation of an Unnatural Base Pair (UBP) using a Drosophila melanogaster deoxynucleoside kinase (DmdNK) mutant.PloS one · 2017Article
- Synthetic biology approaches to biological containment: pre-emptively tackling potential risks.Essays in biochemistry · 2016Review
- Alternative Watson-Crick Synthetic Genetic Systems.Cold Spring Harbor perspectives in biology · 2016Review
- In vitro selection with artificial expanded genetic information systems.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- Conversion strategy using an expanded genetic alphabet to assay nucleic acids.Analytical chemistry · 2013Article
- Amplification, mutation, and sequencing of a six-letter synthetic genetic system.Journal of the American Chemical Society · 2011Article
- Beyond DNA origami: the unfolding prospects of nucleic acid nanotechnology.Wiley interdisciplinary reviews. Nanomedicine and nanobiotechnologyReview
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
To explore the possibility of using restriction enzymes in a synthetic biology based on artificially expanded genetic information systems (AEGIS), 24 type-II restriction endonucleases (REases) were challenged to digest DNA duplexes containing recognition sites where individual Cs and Gs were replaced by the AEGIS nucleotides Z and P [respectively, 6-amino-5-nitro-3-(1'-β-D-2'-deoxyribofuranosyl)-2(1H)-pyridone and 2-amino-8-(1'-β-D-2'-deoxyribofuranosyl)-imidazo[1,2-a]-1,3,5-triazin-4(8H)-one]. These AEGIS nucleotides implement complementary hydrogen bond donor-donor-acceptor and acceptor-acceptor-donor patterns. Results allowed us to classify type-II REases into five groups based on their performance, and to infer some specifics of their interactions with functional groups in the major and minor grooves of the target DNA. For three enzymes among these 24 where crystal structures are available (BcnI, EcoO109I and NotI), these interactions were modeled. Further, we applied a type-II REase to quantitate the fidelity polymerases challenged to maintain in a DNA duplex C:G, T:A and Z:P pairs through repetitive PCR cycles. This work thus adds tools that are able to manipulate this expanded genetic alphabet in vitro, provides some structural insights into the working of restriction enzymes, and offers some preliminary data needed to take the next step in synthetic biology to use an artificial genetic system inside of living bacterial cells.
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