7-Deaza-7-propargylamino-ddGTP
[CAS# 114748-61-7]

Identification

• Classification: Biochemical >> Nucleoside drugs >> Deoxynucleotides and their analogues
• Name: 7-Deaza-7-propargylamino-ddGTP
• Synonyms: [[(2S,5R)-5-[2-amino-5-(3-aminoprop-1-ynyl)-4-oxo-3H-pyrrolo[2,3-d]pyrimidin-7-yl]oxolan-2-yl]methoxy-hydroxyphosphoryl] phosphono hydrogen phosphate
• Molecular Formula: C₁₄H₂₀N₅O₁₂P₃
• Molecular Weight: 543.26
• CAS Registry Number: 114748-61-7
• SMILES: C1C[C@@H](O[C@@H]1COP(=O)(O)OP(=O)(O)OP(=O)(O)O)N2C=C(C3=C2N=C(NC3=O)N)C#CCN

Properties

• Density: 2.2±0.1 g/cm³ Calc.^*
• Index of refraction: 1.788 (Calc.)^*

^* Calculated using Advanced Chemistry Development (ACD/Labs) Software.

Discovory and Applicatios

7-Deaza-7-propargylamino-2',3'-dideoxyguanosine 5'-triphosphate (7-deaza-7-propargylamino-ddGTP) is a chemically modified analog of 2',3'-dideoxyguanosine triphosphate (ddGTP), featuring two key structural alterations: the substitution of a nitrogen atom at position 7 of the purine ring with a carbon atom (7-deazaguanine modification), and the addition of a propargylamino group at this same position. These modifications endow the molecule with distinctive properties that expand its application in biochemical, diagnostic, and molecular biology research.

The core structure of 7-deaza-guanine was originally introduced to investigate nucleobase modifications that retain base-pairing capability while altering chemical reactivity and hydrogen-bonding patterns. The absence of the nitrogen atom at the 7-position increases the chemical stability of the base under certain conditions and reduces sensitivity to acid-catalyzed depurination. The propargylamino group at position 7 introduces a terminal alkyne functional group, making the nucleotide a useful tool in bioconjugation strategies utilizing click chemistry. The dideoxy configuration of the sugar moiety (lacking a 3'-OH group) ensures that incorporation into DNA during polymerase reactions results in chain termination.

The synthesis of 7-deaza-7-propargylamino-ddGTP involves selective modification of a 7-deazaguanosine precursor, often through electrophilic substitution or palladium-catalyzed coupling to introduce the propargylamino substituent. This is followed by phosphorylation to yield the active triphosphate form. The final compound is generally purified through anion-exchange chromatography and characterized using spectroscopic methods such as NMR and mass spectrometry to confirm structural integrity and purity.

Functionally, 7-deaza-7-propargylamino-ddGTP serves as a substrate for DNA polymerases, which incorporate it into DNA strands during primer extension or sequencing reactions. Due to the 3'-dideoxy structure, its incorporation terminates DNA synthesis, similar to traditional ddNTPs. However, the alkyne moiety introduced via the propargylamino group allows for selective post-incorporation conjugation with azide-containing labels using copper(I)-catalyzed azide-alkyne cycloaddition (CuAAC), a widely adopted bioorthogonal labeling method.

Applications of 7-deaza-7-propargylamino-ddGTP are broad, particularly in DNA labeling and detection. It is utilized in the preparation of fluorescently labeled DNA for use in electrophoretic sequencing, hybridization assays, and fluorescence microscopy. The terminal alkyne group facilitates the covalent attachment of fluorescent dyes, biotin, or affinity tags via click chemistry, enabling the labeled DNA to be detected with high sensitivity. This property is also useful in creating DNA microarrays, molecular barcodes, and labeled probes for real-time PCR.

In addition to its role in labeling, the 7-deaza modification can reduce the susceptibility of the DNA to oxidative damage or enzymatic cleavage at the modified base, potentially improving the stability of synthetic DNA constructs. Furthermore, this nucleotide analog is applied in research involving the study of polymerase selectivity, as its incorporation efficiency varies among different DNA polymerases. Understanding these interactions informs enzyme engineering and the design of improved systems for nucleic acid synthesis and manipulation.

Because the propargylamino modification is introduced at a position that does not disrupt Watson-Crick base pairing, 7-deaza-7-propargylamino-ddGTP maintains compatibility with native DNA structures. Its use does not significantly impair duplex formation, making it a practical choice for introducing functional groups into DNA without altering its hybridization characteristics. This is especially valuable in applications that require labeled DNA to participate in hybridization, such as nucleic acid-based diagnostics or sensor development.

Overall, 7-deaza-7-propargylamino-ddGTP exemplifies the power of rational nucleotide modification to merge biological functionality with chemical versatility. Its dual role as a chain-terminating nucleotide and a chemical handle for conjugation makes it an important reagent in modern biochemical and molecular biology techniques.