ArticleNucleic acids research2012
Highly specific unnatural base pair systems as a third base pair for PCR amplification.
Article in Nucleic acids research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 68 papers.
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Who cites it
68 citing papers in PubMed.
- Toward Expanded Genetic Alphabets: Insights into Functionalized Ds-Px Unnatural Base Pairs.ACS physical chemistry Au · 2026Article
- Quantifying replication fidelity of unnatural base pairs using nanopore sequencing.Nature communications · 2026Article
- High-Affinity Six-Letter DNA XenoAptamer Generation by Genetic Alphabet Expansion.Journal of the American Chemical Society · 2026Article
- Mini-Hairpin DNA: Extraordinarily Stable Structure and Its Applications.Chemistry (Weinheim an der Bergstrasse, Germany) · 2026Review
- Advances and challenges in non-canonical nucleic acids data storage.Nature communications · 2026Review
- π-π Stacking Determines the Selectivity of Unnatural DNA Base Pairs Even without Polymerase.ACS physical chemistry Au · 2026Article
- Recognition of unnatural base pairs by a eukaryotic DNA polymerase enables universal sequencing of an expanded genetic alphabet.Nucleic acids research · 2026Article
- Aptamer Engineering: Strategies for Discovering Functional Nucleic Acids for Next-Generation Diagnostics and Biosensing.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
- Expanded genetic alphabet increases structural and chemical diversity of six-letter DNA for high-affinity protein-targeting aptamers.Nature communications · 2025Article
- Structure-informed models for ionic current prediction in nanopore sequencing of expanded dna alphabets.Nucleic acids research · 2025Article
- Direct high-throughput deconvolution of non-canonical bases via nanopore sequencing and bootstrapped learning.Nature communications · 2025Article
- Nucleic acid joining enzymes: biological functions and synthetic applications beyond DNA.The Biochemical journal · 2025Review
- Reverse transcription as key step in RNARSC chemical biology · 2024Article
- Investigation of the stability of D5SIC-DNAM-incorporated DNA duplex inPhysical chemistry chemical physics : PCCP · 2024Article
- Investigation of dynamical flexibility of D5SIC-DNAM inside DNA duplex in aqueous solution: a systematic classical MD approach.Physical chemistry chemical physics : PCCP · 2024Article
- Strict Interactions of Fifth Letters, Hydrophobic Unnatural Bases, in XenoAptamers with Target Proteins.Journal of the American Chemical Society · 2023Article
- The Expanded Central Dogma: Genome Resynthesis, Orthogonal Biosystems, Synthetic Genetics.Annual review of biophysics · 2023Review
- Success probability of high-affinity DNA aptamer generation by genetic alphabet expansion.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2023Article
- Synthesis of 6-Alkynylated Purine-Containing DNA via On-Column Sonogashira Coupling and Investigation of Their Base-Pairing Properties.Molecules (Basel, Switzerland) · 2023Article
- From polymerase engineering to semi-synthetic life: artificial expansion of the central dogma.RSC chemical biology · 2022Review
8 more citing papers are in PubMed but not listed here.
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Toward the expansion of the genetic alphabet of DNA, we present highly efficient unnatural base pair systems as an artificial third base pair for PCR. Hydrophobic unnatural base pair systems between 7-(2-thienyl)imidazo[4,5-b]pyridine (Ds) and 2-nitro-4-propynylpyrrole (Px) were fine-tuned for efficient PCR, by assessing the amplification efficiency and fidelity using different polymerases and template sequence contexts and modified Px bases. Then, we found that some modifications of the Px base reduced the misincorporation rate of the unnatural base substrates opposite the natural bases in templates without reducing the Ds-Px pairing selectivity. Under optimized conditions using Deep Vent DNA polymerase, the misincorporation rate was extremely low (0.005%/bp/replication), which is close to that of the natural base mispairings by the polymerase. DNA fragments with different sequence contexts were amplified ∼10(10)-fold by 40 cycles of PCR, and the selectivity of the Ds-Px pairing was >99.9%/replication, except for 99.77%/replication for unfavorable purine-Ds-purine motifs. Furthermore, >97% of the Ds-Px pair in DNA survived in the 10(28)-fold amplified products after 100-cycle PCR (10 cycles repeated 10 times). This highly specific Ds-Px pair system provides a framework for new biotechnology.
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