2',3'-Dideoxycytidine 5'-triphosphate
[CAS# 66004-77-1]

Identification

• Classification: Biochemical >> Nucleoside drugs >> Deoxynucleotides and their analogues
• Name: 2',3'-Dideoxycytidine 5'-triphosphate
• Synonyms: ddCTP; [[(2S,5R)-5-(4-amino-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl] phosphono hydrogen phosphate
• Protein Sequence: N
• Molecular Formula: C₉H₁₆N₃O₁₂P₃
• Molecular Weight: 451.16
• CAS Registry Number: 66004-77-1
• SMILES: C1C[C@@H](O[C@@H]1COP(=O)(O)OP(=O)(O)OP(=O)(O)O)N2C=CC(=NC2=O)N

Discovory and Applicatios

2',3'-Dideoxycytidine 5'-triphosphate (commonly abbreviated as ddCTP) is a synthetic analog of the natural nucleotide cytidine triphosphate (CTP), distinguished by the absence of hydroxyl groups at the 2' and 3' positions of its sugar moiety. This structural modification results in the loss of the 3'-hydroxyl group essential for forming phosphodiester bonds during DNA chain elongation. Consequently, when incorporated into a growing DNA strand by DNA polymerase, ddCTP acts as a chain terminator, preventing further nucleotide addition.

The compound is a triphosphorylated form of 2',3'-dideoxycytidine (ddC), also known as zalcitabine, which was one of the first nucleoside analog reverse transcriptase inhibitors (NRTIs) developed for the treatment of HIV infection. The antiviral activity of ddC and its phosphorylated derivatives stems from their ability to inhibit the reverse transcriptase enzyme by terminating viral DNA synthesis. Although ddC was approved for clinical use as an antiretroviral drug, its triphosphate form ddCTP is primarily used in biochemical and molecular biology research rather than directly as a therapeutic agent.

In molecular biology, ddCTP is extensively utilized in DNA sequencing techniques, particularly in the Sanger dideoxy chain termination method. During DNA synthesis reactions, DNA polymerase incorporates nucleotides complementary to the template strand. When ddCTP is incorporated, its lack of a 3'-hydroxyl group prevents the addition of subsequent nucleotides, resulting in termination of the DNA chain at cytidine positions. By including fluorescent or radiolabeled primers and conducting electrophoretic separation, the DNA sequence can be deduced. This technique revolutionized genomics and remains a fundamental tool in DNA sequencing and analysis.

The synthesis of ddCTP involves chemical or enzymatic phosphorylation of ddC, typically via multi-step reactions that require precise control to ensure the stability of the triphosphate group. Commercially available ddCTP is widely used in sequencing laboratories and enzymatic assays.

Beyond sequencing, ddCTP serves as an important substrate analog for studying DNA polymerase mechanisms and fidelity. Its incorporation kinetics and inhibition profiles provide insights into enzyme function and help in the design of polymerase inhibitors. Additionally, ddCTP is used in assays evaluating nucleic acid synthesis and repair processes.

While ddCTP itself is not administered as a drug, its parent nucleoside ddC was employed in antiretroviral therapy to suppress HIV replication. The mechanism of chain termination at the viral reverse transcriptase level helped establish the therapeutic principle of nucleoside analogs. This class of compounds, including ddC and other dideoxynucleosides, laid the groundwork for the development of numerous effective NRTIs in current HIV treatment regimens.

In summary, 2',3'-dideoxycytidine 5'-triphosphate is a key nucleotide analog used primarily as a chain terminator in DNA sequencing and polymerase studies. Its structure prevents further DNA elongation upon incorporation, making it invaluable for elucidating DNA sequences and enzyme mechanisms. Although it is not a direct therapeutic agent, its parent compound's clinical use highlights the significance of this molecule in both research and medicine.

References

1983. Inhibition of Vesicular Stomatitis Virus RNA Synthesis by 2',3'-Dideoxycytidine 5'-Triphosphate. The Journal of general virology, 64(3).
DOI: 10.1099/0022-1317-64-3-743

1987. Inhibition of HIV reverse transcriptase by 2',3'-dideoxynucleoside triphosphates. Biochemical Pharmacology, 36(24).
DOI: 10.1016/0006-2952(87)90685-x

2012. Structural Factors That Determine Selectivity of a High Fidelity DNA Polymerase for Deoxy-, Dideoxy-, and Ribonucleotides. The Journal of biological chemistry, 287(34).
DOI: 10.1074/jbc.m112.366609