AAT Bioquest


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Physical properties
Molecular weight575.26
Storage, safety and handling
H-phraseH303, H313, H333
Hazard symbolXN
Intended useResearch Use Only (RUO)
R-phraseR20, R21, R22
StorageFreeze (< -15 °C); Minimize light exposure


Molecular weight
5-Aminopropargyl 3’-azidomethyl dCTP is a key building block for preparing fluorescent conjugates that are used in the next generation sequencing (NGS). NGS uses a similar chain termination method to the earlier Sanger sequencing, but NGS is carried out by fluorescence-labeled nucleotide analogs acting as reversible terminators of the amplification reaction. NGS relies on the blockade of DNA polymerization that is reversible while the Sanger sequencing uses the irreversible blockade of DNA polymerization by ddNTPs. Another different feature of NGS is that the clonal amplification in vitro to multiply the number of molecules to be sequenced is conducted by means of bridge PCR. In this platform, the fragments are joined to primers immobilized on a solid surface, performing an amplification in situ, generating clusters of DNA with identical molecules. In each cycle, the four nucleotides of reversible termination are simultaneously added and incorporated by the polymerase they complement. These nucleotides are chemically blocked—by substituting the 3′-OH group for a 3′-o-azidomethyl group—to prevent the polymerase from incorporating more than one nucleotide in each cycle. Upon incorporation of a nucleotide, a fluorescence signal is measured in different channels for different bases. Concerning the next cycle, the nucleotides that have not been incorporated are washed and the chemical blockade of the 3′ end is removed with TCEP. Once the fluorescence signal is collected, a new cycle begins, repeating this dynamic until the sequencing of each fragment is finished. In summary, the NGS sequencing reaction is carried out in three steps: addition of nucleotides, imaging, and regeneration of 3′-OH by fluorophore cleavage.


Common stock solution preparation

Table 1. Volume of Water needed to reconstitute specific mass of 5-Propargylamino-3'-azidomethyl-dCTP to given concentration. Note that volume is only for preparing stock solution. Refer to sample experimental protocol for appropriate experimental/physiological buffers.

0.1 mg0.5 mg1 mg5 mg10 mg
1 mM173.834 µL869.172 µL1.738 mL8.692 mL17.383 mL
5 mM34.767 µL173.834 µL347.669 µL1.738 mL3.477 mL
10 mM17.383 µL86.917 µL173.834 µL869.172 µL1.738 mL

Molarity calculator

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View all 5 references: Citation Explorer
Genome-wide analysis of the specificity and mechanisms of replication infidelity driven by imbalanced dNTP pools.
Authors: Watt, Danielle L and Buckland, Robert J and Lujan, Scott A and Kunkel, Thomas A and Chabes, Andrei
Journal: Nucleic acids research (2016): 1669-80
Hi-C in Budding Yeast.
Authors: Belton, Jon-Matthew and Dekker, Job
Journal: Cold Spring Harbor protocols (2015): 649-61
Fluorescence polarization-based method with bisulfite conversion-specific one-label extension for quantification of single CpG dinucleotide methylation.
Authors: Li, Shufen and Wang, Zhongju and Zhou, Lin and Luo, Fu and Zhao, Cunyou
Journal: Genome (2015): 357-63
Transcriptome analysis of Capsicum annuum varieties Mandarin and Blackcluster: assembly, annotation and molecular marker discovery.
Authors: Ahn, Yul-Kyun and Tripathi, Swati and Kim, Jeong-Ho and Cho, Young-Il and Lee, Hye-Eun and Kim, Do-Sun and Woo, Jong-Gyu and Cho, Myeong-Cheoul
Journal: Gene (2014): 494-9
Structures of an apo and a binary complex of an evolved archeal B family DNA polymerase capable of synthesising highly cy-dye labelled DNA.
Authors: Wynne, Samantha A and Pinheiro, Vitor B and Holliger, Philipp and Leslie, Andrew G W
Journal: PloS one (2013): e70892