C8-Alkyne-dUTP

Product Information

A Click-Functionalized Nucleotide for DNA Labeling and Post-Synthetic Modification

C8-Alkyne-dUTP is a modified deoxyuridine triphosphate (dUTP) featuring a C8 alkyne group at the C5 position of the uracil base. It enables site-specific DNA labeling via Cu(I)-catalyzed azide-alkyne cycloaddition (CuAAC), supporting a wide range of downstream applications in molecular biology, diagnostics, and nanobiotechnology.

The Molecular Engine for DNA Functionalization and Bioorthogonal Chemistry

C8-Alkyne-dUTP introduces a chemically orthogonal alkyne moiety into DNA during enzymatic synthesis. This modification allows for precise post-synthetic conjugation with azide-bearing molecules, including fluorophores, biotin, peptides, and other functional groups. It is designed to overcome limitations in traditional nucleotide labeling strategies and expand the toolkit for DNA-based technologies.

Challenges in DNA Labeling and Modification

Prior to the development of click-functionalized nucleotides, researchers faced several limitations:

• Polymerase Compatibility
  Many modified nucleotides were poorly tolerated by DNA polymerases, resulting in inefficient incorporation.
• Limited Functional Labeling Options
  Conventional dUTPs lacked reactive groups for selective post-synthetic modification.
• Non-Specific Conjugation Chemistry
  Labeling often relied on NHS esters or maleimides, which lacked positional control and reproducibility.

C8-Alkyne-dUTP as a Bioorthogonal Solution

• Click-Ready Functionality
  The terminal alkyne group enables selective and efficient CuAAC reactions with azide-functionalized probes under mild conditions.
• High Incorporation Efficiency
  The C8 modification is positioned on the nucleobase, away from the polymerase active site, allowing incorporation by Taq, KOD, Vent, Pwo, and Deep Vent exo- polymerases.
• Versatile Post-Synthesis Labeling
  Once incorporated, the alkyne-modified base can be conjugated to a wide range of azide-bearing molecules without disrupting DNA structure or function.

Applications in Research and Biotechnology

• DNA Labeling
  Enables site-specific modifications for imaging, purification, and molecular tracking.
• Biotinylation and Affinity Tagging
  Facilitates streptavidin-based capture and purification of labeled DNA strands.
• PCR and Primer Extension
  Compatible with enzymatic incorporation for advanced genetic studies.
• DNA Nanotechnology
  Supports spatially controlled modification of DNA origami and nanostructures.
• Oligonucleotide–Drug Conjugates
  Enables site-specific attachment of small molecules or peptides for therapeutic and diagnostic use.
• Gene Silencing
  Enhances triplex-forming oligonucleotides (TFOs) with improved stability and gene-targeting efficiency.
• DNA Hydrogel Functionalization
  Allows post-synthetic modification of DNA hydrogels via CuAAC without compromising mechanical properties.
• Aptamer Discovery
  Used in Click-Particle Display for screening base-modified aptamers with enhanced binding properties.
• dNTP Quantification
  Provides a safer alternative to radioisotope-based assays using fluorophore conjugation.

LITERATURE

Synthesis of Highly Modified DNA by a Combination of PCR with Alkyne-Bearing Triphosphates and Click Chemistry, J. Gierlich et al., 2007, Chem. – A Eur. J., Vol. 13, p. 9486–9494.

https://doi.org/10.1002/chem.200700502

Directed DNA Metallization, G. A. Burley et al., 2006, J. Am. Chem. Soc., Vol. 128, p. 1398–1399.

https://doi.org/10.1021/ja055517v

Fluorescent labelling of in situ hybridisation probes through the copper-catalysed azide-alkyne cycloaddition reaction, S. Hesse et al., 2016, Chromosome Research, Vol. 24(3), p. 299–307.

https://doi.org/10.1007/s10577-016-9522-z

Enzymatic Synthesis of Chemical Nuclease Triplex-Forming Oligonucleotides with Gene-Silencing Applications, B. McGorman et al., 2022, Nucleic Acids Research, Vol. 50(10), p. 5467–5481.

https://doi.org/10.1093/nar/gkac438

Revolutionizing DNA: advanced modification techniques for next-gen nanotechnology, P. Panda et al., 2024, Nucleosides, Nucleotides & Nucleic Acids, 1–32.

https://doi.org/10.1080/15257770.2024.2432992

Modified Nucleosides, Nucleotides and Nucleic Acids via Click Azide-Alkyne Cycloaddition for Pharmacological Applications, D. Perrone et al., 2021, Molecules, Vol. 26(11), 3100.

https://doi.org/10.3390/molecules26113100