ArticleChemistry (Weinheim an der Bergstrasse, Germany)2012
Major groove substituents and polymerase recognition of a class of predominantly hydrophobic unnatural base pairs.
Article in Chemistry (Weinheim an der Bergstrasse, Germany), 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 48 citations in OpenAlex.
- Single-residue engineering of Klenow fragment enables broad acceptance of chemically modified nucleotides.Nucleic acids research · 2026Article
- Heck-type C-glycosylations in the synthesis of artificial nucleotides and functional nucleic acids.RSC chemical biology · 2026Review
- Investigation of dynamical flexibility of D5SIC-DNAM inside DNA duplex in aqueous solution: a systematic classical MD approach.Physical chemistry chemical physics : PCCP · 2024Article
- Investigation of the stability of D5SIC-DNAM-incorporated DNA duplex inPhysical chemistry chemical physics : PCCP · 2024Article
- Discovery, implications and initial use of semi-synthetic organisms with an expanded genetic alphabet/code.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2023Review
- The Structural Basis for Processing of Unnatural Base Pairs by DNA Polymerases.Chemistry (Weinheim an der Bergstrasse, Germany) · 2020Review
- Expansion of the Genetic Alphabet: A Chemist's Approach to Synthetic Biology.Accounts of chemical research · 2018Article
- In Vivo Structure-Activity Relationships and Optimization of an Unnatural Base Pair for Replication in a Semi-Synthetic Organism.Journal of the American Chemical Society · 2017Article
- Chemical Stabilization of Unnatural Nucleotide Triphosphates for the in Vivo Expansion of the Genetic Alphabet.Journal of the American Chemical Society · 2017Article
- A semisynthetic organism engineered for the stable expansion of the genetic alphabet.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- FRET Characterization of Complex Conformational Changes in a Large 16S Ribosomal RNA Fragment Site-Specifically Labeled Using Unnatural Base Pairs.ACS chemical biology · 2016Article
- Identification of DNA lesions using a third base pair for amplification and nanopore sequencing.Nature communications · 2015Article
- The expanded genetic alphabet.Angewandte Chemie (International ed. in English) · 2015Review
- Article
- Natural-like replication of an unnatural base pair for the expansion of the genetic alphabet and biotechnology applications.Journal of the American Chemical Society · 2014Article
- Systematic exploration of a class of hydrophobic unnatural base pairs yields multiple new candidates for the expansion of the genetic alphabet.Nucleic acids research · 2014Article
- Structural insights into DNA replication without hydrogen bonds.Journal of the American Chemical Society · 2013Article
- Site-specifically arraying small molecules or proteins on DNA using an expanded genetic alphabet.Chemistry (Weinheim an der Bergstrasse, Germany) · 2013Article
- Expanding the scope of replicable unnatural DNA: stepwise optimization of a predominantly hydrophobic base pair.Journal of the American Chemical Society · 2013Article
- Preparing synthetic biology for the world.Frontiers in microbiology · 2013Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
Expansion of the genetic alphabet with an unnatural base pair is a long-standing goal of synthetic biology. We have developed a class of unnatural base pairs, formed between d5SICS and analogues of dMMO2 that are efficiently and selectively replicated by the Klenow fragment (Kf) DNA polymerase. In an effort to further characterize and optimize replication, we report the synthesis of five new dMMO2 analogues bearing different substituents designed to be oriented into the developing major groove and an analysis of their insertion opposite d5SICS by Kf and Thermus aquaticus DNA polymerase I (Taq). We also expand the analysis of the previously optimized pair, dNaM-d5SICS, to include replication by Taq. Finally, the efficiency and fidelity of PCR amplification of the base pairs by Taq or Deep Vent polymerases was examined. The resulting structure-activity relationship data suggest that the major determinants of efficient replication are the minimization of desolvation effects and the introduction of favorable hydrophobic packing, and that Taq is more sensitive than Kf to structural changes. In addition, we identify an analogue (dNMO1) that is a better partner for d5SICS than any of the previously identified dMMO2 analogues with the exception of dNaM. We also found that dNaM-d5SICS is replicated by both Kf and Taq with rates approaching those of a natural base pair.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.