homopurinehomopyrimidine

Homopurinehomopyrimidine refers to a class of synthetic or expanded nucleobases designed to form a complementary pair in nucleic acids where a homopurine base pairs with a homopyrimidine base. The terms describe elongated or otherwise modified versions of the standard purine and pyrimidine scaffolds, often featuring additional rings or fused-ring systems. The goal of these designs is to preserve the overall geometry of natural base pairs while providing new hydrogen-bond donors and acceptors that enable selective pairing.

In many implementations, homopurine and homopyrimidine bases are engineered so that their pairing resembles the Watson–Crick framework but with altered hydrogen-bonding patterns and steric properties. The modifications aim to maintain compatibility with the DNA duplex, enabling formation of stable, isosteric base pairs that can slot into the helix without major distortions. Because the structural changes can affect duplex stability and polymerase recognition, researchers study these pairs to understand how expanded alphabets influence replication, transcription, and overall genetic information storage.

Applications of homopurinehomopyrimidine concepts appear in the broader field of synthetic biology and chemical biology, particularly in the development of expanded genetic alphabets and XNA systems. Such base pairs are explored for purposes including increasing information density in DNA, creating novel aptamers or nanostructures, and probing the limits of enzymatic processing by polymerases and reverse transcriptases. Their practical use often requires careful optimization of synthesis, duplex stability, and biological compatibility.

Limitations and challenges remain, including synthesis cost, efficiency of enzymatic incorporation, fidelity of replication, and potential cytotoxicity in cellular contexts. Ongoing research seeks to refine designs that balance structural compatibility with robust, selective pairing.

See also: noncanonical base pair, expanded genetic alphabet, xeno-nucleic acid.