ddNTPene

ddNTPene is a proposed class of nucleotide analogs derived from dideoxynucleotide triphosphates (ddNTPs) that feature an appended ene moiety. The name reflects the combination of ddNTP with an unsaturated “ene” group intended to enable downstream chemical modification after incorporation while maintaining chain termination.

Chemistry and mechanism: Like ddNTPs, ddNTPene lack a 3' hydroxyl, causing DNA synthesis to terminate when incorporated by a DNA polymerase. The ene modification is designed to be relatively inert during replication but reactive in selective post-termination chemistries (for example, click reactions or crosslinking) to attach labels or anchors to the terminated fragment.

Applications: In principle, ddNTPene would enable selective labeling, immobilization, or crosslinking of terminated DNA fragments, facilitating sequencing workflows, mapping polymerase interactions, or generating labeled standards. Practical use requires polymerases that can incorporate the modified nucleotides or engineered enzymes, as well as optimized reaction conditions.

Synthesis and availability: Synthesis involves multi-step nucleotide chemistry to install the ene moiety while preserving a functional triphosphate. As a niche laboratory reagent, ddNTPene are not widely commercialized and are described in selective research reports or preprints.

History: The concept emerged in discussions of combining chain termination with post-termination chemistry; it remains an area of exploratory research rather than a mainstream technology.

See also: ddNTP, nucleotide analogs, DNA sequencing, click chemistry.