PCR Modification Kit

Product Information

High‑Density Fluorescent Labeling of PCR Products using Click Chemistry

The ClickTech PCR Modification Kit is a versatile, next‑generation solution for generating highly fluorescent, alkyne‑modified DNA products directly during PCR. Built on the same proven click chemistry platform as baseclick’s FISH labeling technology, this kit offers a powerful way to prepare intensely labeled DNA fragments for a broad range of downstream applications — from probe generation and hybridization workflows to general molecular detection tasks.

By incorporating EdUTP, an alkyne‑modified nucleotide, during amplification with baseclick´s optimized Ethynyl Polymerase, the resulting PCR products contain precisely placed alkyne handles. These can then be coupled to a clickable fluorescent dye of your choice via a highly selective copper‑catalyzed azide‑alkyne cycloaddition (CuAAC) reaction.

The result: bright, stable, cleanly labeled DNA products compatible with a wide range of hybridization and visualization techniques.

Key Features

1. Efficient Two‑Step Labeling Workflow

PCR incorporation of EdUTP using Ethynyl Polymerase: The Ethynyl Polymerase amplifies the target sequence while incorporating EdUTP, an alkyne‑modified nucleotide into the DNA strand. These alkyne groups function as reactive click handles for later fluorescent labeling.

Click labeling with included azide‑functional fluorescent dye: Azide‑functionalized dyes (488, 555, 594, 647) react efficiently with the alkyne groups via CuAAC click chemistry. This yields densely labeled DNA FISH probes decorated with numerous covalently attached fluorophores, providing strong, clean, and highly stable fluorescence signals for hybridization assays.

2. Complete Kit – Everything Included

• • dNTP Mix (10 mM)
  • EdUTP (5 mM)
  • baseclick Ethynyl Polymerase (2 U/µL)
  • PCR Buffer (5×)
  • 10× Activator²
  • Click reagent + dye (488, 555, 594, or 647)

3. Supports 20 PCR Reactions and 40 Labeling Reactions per Kit with

Four Dye Choices for Multiplexing

• • 488 (green) – Ex 496 / Em 516 nm
  • 555 (yellow) – Ex 546 / Em 579 nm
  • 594 (orange) – Ex 584 / Em 603 nm
  • 647 (red) – Ex 643 / Em 662 nm

4. High Labeling Density & Low Background

Click chemistry ensures selective, efficient labeling with minimal nonspecific fluorescence.

Applications

The ClickTech PCR Modification Kit is positioned for broader DNA labeling needs, including:

• Generation of fluorescent probes for hybridization assays: ideal for FISH‑like workflows or any DNA‑targeting application requiring strong signal contrast.
• Labeling of PCR products for visualization or tracking: useful in molecular genetics, DNA mapping, or tracer experiments.
• Multi‑color detection studies: using four dye options for simultaneous analysis of multiple targets.
• Detection and quantification in microarray or blotting systems.
• Preparation of custom fluorescent DNA probes: for labs that prefer producing their own probes rather than purchasing pre‑labeled oligos.

How It Works

1. PCR Amplification with EdUTP

During amplification, the Ethynyl Polymerase incorporates EdUTP alongside natural dNTPs, creating alkyne-modified DNA.

2. Click‑Labeling Reaction

The alkyne groups on the DNA react selectively with the kit’s azide‑linked fluorescent dye under mild copper‑catalyzed conditions, producing a stable covalent bond.

This method ensures highly efficient conversion of PCR product into bright fluorescent DNA.

LITERATURE

Orthogonal End Labelling of Oligonucleotides through Dual Incorporation of Click-Reactive NTP Analogues. E. Schönegger et al., 2024, ChemBioChem., Vol. 25(1), e202300701.

https://doi.org/10.1002/cbic.202300701

Divergent Synthesis of Ultrabright and Dendritic Xanthenes for Enhanced Click-Chemistry-Based Bioimaging. L. Montiel et al., 2023, Eur. J., Vol. 29(5), e202202633.

https://doi.org/10.1002/chem.202202633

Click Chemistry Enables Rapid Amplification of Full-Length Reverse Transcripts for Long-Read Third Generation Sequencing. E. Schönegger et al., 2022, Bioconjugate Chem., 33(10), p. 1789–1795.

https://doi.org/10.1021/acs.bioconjchem.2c00353

ClampFISH detects individual nucleic acid molecules using click chemistry–based amplification. S. H. Rouhanifard et al., 2019, Biotechnol., Vol 37, p. 84–89.

https://doi.org/10.1038/nbt.4286