ArticleNucleic acids research2007
Enzymatic incorporation of a third nucleobase pair.
Article in Nucleic acids research, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 68 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
68 citing papers in PubMed, 173 citations in OpenAlex.
- Derivatives of dPMTO, dMTMO, and dTPT3 as efficient genetic alphabets for artificial DNA.Journal of molecular modeling · 2026Article
- Structural basis of transcription of the hachimoji eight-letter alphabet by E. coli RNA polymerase.Nature communications · 2026Article
- Engineered polymerase-mediated efficient synthesis of site-specifically functionalized RNA and 2'-modified RNA oligonucleotides via genetic alphabet expansion.Nature communications · 2026Article
- Sequence-Specific Targeting of GC-Rich Gene Loci by Parallel Triplex-Forming Oligonucleotides Containing a Modified Nucleobase.bioRxiv : the preprint server for biology · 2026Article
- Recognition of non-standard base pairs by triplex-forming oligonucleotides containing an expanded genetic alphabet.Nature communications · 2026Article
- High-Affinity Six-Letter DNA XenoAptamer Generation by Genetic Alphabet Expansion.Journal of the American Chemical Society · 2026Article
- Recognition of Non-standard Base Pairs by Triplex-Forming Oligonucleotides Containing an Expanded Genetic Alphabet.Research square · 2026Article
- Omega Nucleic Acids (ΩNA), Ultimate Nucleic Acids for Future Technology.Molecules (Basel, Switzerland) · 2026Review
- Engineering and Assay of Enzymes for Expanded Genetic Alphabet Replication.Biochemistry · 2025Article
- Aptamers as a New Frontier in Molecular Cancer Imaging Technologies.Chemical & biomedical imaging · 2025Review
- Nucleic acid joining enzymes: biological functions and synthetic applications beyond DNA.The Biochemical journal · 2025Review
- Recognition and Sequencing of Mutagenic DNA Adduct at Single-Base Resolution Through Unnatural Base Pair.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- Xenobiology for the Biocontainment of Synthetic Organisms: Opportunities and Challenges.Life (Basel, Switzerland) · 2024Review
- A unified Watson-Crick geometry drives transcription of six-letter expanded DNA alphabets by E. coli RNA polymerase.Nature communications · 2023Article
- Structure and stability of different triplets involving artificial nucleobases: clues for the formation of semisynthetic triple helical DNA.Scientific reports · 2023Article
- Artificial Small Molecules as Cofactors and Biomacromolecular Building Blocks in Synthetic Biology: Design, Synthesis, Applications, and Challenges.Molecules (Basel, Switzerland) · 2023Review
- The Expanded Central Dogma: Genome Resynthesis, Orthogonal Biosystems, Synthetic Genetics.Annual review of biophysics · 2023Review
- Embeddability of centrosymmetric matrices capturing the double-helix structure in natural and synthetic DNA.Journal of mathematical biology · 2023Article
- Strategies for Covalent Labeling of Long RNAs.Chembiochem : a European journal of chemical biology · 2021Review
- Article
8 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 1 institution in 1 country.
Funding
Abstract
DNA polymerases are identified that copy a non-standard nucleotide pair joined by a hydrogen bonding pattern different from the patterns joining the dA:T and dG:dC pairs. 6-Amino-5-nitro-3-(1'-beta-D-2'-deoxyribofuranosyl)-2(1H)-pyridone (dZ) implements the non-standard 'small' donor-donor-acceptor (pyDDA) hydrogen bonding pattern. 2-Amino-8-(1'-beta-D-2'-deoxyribofuranosyl)-imidazo[1,2-a]-1,3,5-triazin-4(8H)-one (dP) implements the 'large' acceptor-acceptor-donor (puAAD) pattern. These nucleobases were designed to present electron density to the minor groove, density hypothesized to help determine specificity for polymerases. Consistent with this hypothesis, both dZTP and dPTP are accepted by many polymerases from both Families A and B. Further, the dZ:dP pair participates in PCR reactions catalyzed by Taq, Vent (exo-) and Deep Vent (exo-) polymerases, with 94.4%, 97.5% and 97.5%, respectively, retention per round. The dZ:dP pair appears to be lost principally via transition to a dC:dG pair. This is consistent with a mechanistic hypothesis that deprotonated dZ (presenting a pyDAA pattern) complements dG (presenting a puADD pattern), while protonated dC (presenting a pyDDA pattern) complements dP (presenting a puAAD pattern). This hypothesis, grounded in the Watson-Crick model for nucleobase pairing, was confirmed by studies of the pH-dependence of mismatching. The dZ:dP pair and these polymerases, should be useful in dynamic architectures for sequencing, molecular-, systems- and synthetic-biology.
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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.