ArticleChemistry (Weinheim an der Bergstrasse, Germany)2010
Solution structure, mechanism of replication, and optimization of an unnatural base pair.
Article in Chemistry (Weinheim an der Bergstrasse, Germany), 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed.
- Derivatives of dPMTO, dMTMO, and dTPT3 as efficient genetic alphabets for artificial DNA.Journal of molecular modeling · 2026Article
- Quantifying replication fidelity of unnatural base pairs using nanopore sequencing.Nature communications · 2026Article
- Synthetic Biology Pathway to Nucleoside Triphosphates for Expanded Genetic Alphabets.ACS synthetic biology · 2023Article
- The Expanded Central Dogma: Genome Resynthesis, Orthogonal Biosystems, Synthetic Genetics.Annual review of biophysics · 2023Review
- Complementary base pair interactions between different rare tautomers of the second-generation artificial genetic alphabets.Journal of molecular modeling · 2023Article
- 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
- Transcriptional processing of an unnatural base pair by eukaryotic RNA polymerase II.Nature chemical biology · 2021Article
- Method for Rapid Analysis of Mutant RNA Polymerase Activity on Templates Containing Unnatural Nucleotides.International journal of molecular sciences · 2021Article
- De Novo Nucleic Acids: A Review of Synthetic Alternatives to DNA and RNA That Could Act as Bio-Information Storage Molecules.Life (Basel, Switzerland) · 2020Review
- Building better polymerases: Engineering the replication of expanded genetic alphabets.The Journal of biological chemistry · 2020Review
- The Structural Basis for Processing of Unnatural Base Pairs by DNA Polymerases.Chemistry (Weinheim an der Bergstrasse, Germany) · 2020Review
- The Role of Orthogonality in Genetic Code Expansion.Life (Basel, Switzerland) · 2019Article
- Expansion of the Genetic Alphabet: A Chemist's Approach to Synthetic Biology.Accounts of chemical research · 2018Article
- Structure and Biophysics for a Six Letter DNA Alphabet that Includes Imidazo[1,2-a]-1,3,5-triazine-2(8H)-4(3H)-dione (X) and 2,4-Diaminopyrimidine (K).ACS synthetic biology · 2017Article
- Synthetic Biology Parts for the Storage of Increased Genetic Information in Cells.ACS synthetic biology · 2017Article
- 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
- Biological phosphorylation of an Unnatural Base Pair (UBP) using a Drosophila melanogaster deoxynucleoside kinase (DmdNK) mutant.PloS one · 2017Article
- The expanded genetic alphabet.Angewandte Chemie (International ed. in English) · 2015Review
- Structural basis for a six nucleotide genetic alphabet.Journal of the American Chemical Society · 2015Article
- The RNA World: molecular cooperation at the origins of life.Nature reviews. Genetics · 2015Review
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Authors and funding
6 authors.
Funding
Abstract
As part of an ongoing effort to expand the genetic alphabet for in vitro and eventual in vivo applications, we have synthesized a wide variety of predominantly hydrophobic unnatural base pairs and evaluated their replication in DNA. Collectively, the results have led us to propose that these base pairs, which lack stabilizing edge-on interactions, are replicated by means of a unique intercalative mechanism. Here, we report the synthesis and characterization of three novel derivatives of the nucleotide analogue dMMO2, which forms an unnatural base pair with the nucleotide analogue d5SICS. Replacing the para-methyl substituent of dMMO2 with an annulated furan ring (yielding dFMO) has a dramatically negative effect on replication, while replacing it with a methoxy (dDMO) or with a thiomethyl group (dTMO) improves replication in both steady-state assays and during PCR amplification. Thus, dTMO-d5SICS, and especially dDMO-d5SICS, represent significant progress toward the expansion of the genetic alphabet. To elucidate the structure-activity relationships governing unnatural base pair replication, we determined the solution structure of duplex DNA containing the parental dMMO2-d5SICS pair, and also used this structure to generate models of the derivative base pairs. The results strongly support the intercalative mechanism of replication, reveal a surprisingly high level of specificity that may be achieved by optimizing packing interactions, and should prove invaluable for the further optimization of the unnatural base pair.
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