Research Summary

Boranophosphate Backbone: a Mimic of Phosphodiesters, Phosphorothioates, and Methyl Phosphonates

A new class of boron modified nucleotides designed for use as potential therapeutic and diagnostic agents were first reported in 1990 by this laboratory. These nucleoside boranophosphates, or borane phosphonates, are distinctive in that one of the nonbridging oxygens in the phosphate diester is replaced by a borane moiety (BH₃). The BH₃ group maintains the negative charge of a phosphate, but it does not form classical H-bonds and it coordinates metals poorly. This modification imparts unique characteristics to boranophosphate nucleotides and nucleic acids.

The boranophosphate can be considered as a "hybrid" of three well-studied types modified phosphates, i.e., normal phosphate, phosphorothioate, and non-ionic methylphosphonate. The BH₃ group in the boranophosphates is isoelectronic with oxygen (O) in the normal phosphates, and isolobal (pseudo-isoelectronic) with sulfur (S) in phosphorothioates. The BH₃ group is isosteric with the CH₃ group in the methylphosphonates. Boranophosphates would be expected to share a number of chemical and biochemical properties with phosphorothioate and methylphosphonate analogs. The changes in polarity, lipophilicity, nuclease resistance, and activation of RNase H cleavage of RNA in RNA:boranophosphate hybrids of the boranophosphates make them attractive for use in enzymology and molecular biology, and as potential antisense agents.

Base-Boronated Nucleic Acids

We performed a series of chemical and biochemical, and genetic experiments to characterize a new class of nucleic acids that contain boronated bases. Boron induces subtle changes in the chemical properties of the nucleic acids, giving them unique biological properties.

Base-boronated nucleosides are more stable than other nucleosides that are modified at endocyclic nitrogens. In our compounds boron forms coordinate bonds with nitrogen in the pyrimidine and purine bases, where the boron substituent serves as an alkylating agent. Some of our compounds, particularly those in which the boron is coordinated with the more basic nitrogens, form stable analogues. The N7-cyanoborane derivative of 2'-deoxyguanosine is far more stable than the corresponding methyl, ethyl, etc. alkylated derivatives (decomposing much slower in water). Particularly interesting is that at acidic pH 7^bdG is even more stable to depurination than is normal dG.

Base-boronated nucleosides have unusual base-pairing properties. The 7^bdG boron analogue has Watson-Crick base pairing similar to that of the normal base, guanine; yet it is blocked at the N7-position, which interferes with Hoogsteen type bonding. This property should reduce aggregation associated with tetraplex and polymer formation normally found with polymers of high guanine content. Polymers with high dG content often aggregate because they can hydrogen bond on two faces, i.e, the Watson-Crick and the Hoogsteen faces. A blocked N-7 may reduce the number of pairing possibilities and make the polymers useful as aptamers or antisense agents or as competitors of both. The 1^bdA analog is blocked at the Watson-Crick face, but permits hydrogen bonding via Hoogsteen bonding.

Base-boronated oligonucleotides can be synthesized in solution and by solid phase phosphoramidite chemistries if appropriate boronating agents and Fmoc protecting groups are used.

Base-boronated oligonucleotides can be synthesized by DNA polymerase, RNA polymerase, and polynucleotide phosphorylase. We found that modified deoxynucleotide triphosphate, 7^bdGTP, can be incorporated into DNA by DNA polymerase and by thermostable polymerases. The efficiency of incorporation with DNA polymerase is even greater than that of normal dGTP. The ribose analog, 7^bGTP, can be incorporated into RNA by T7 RNA polymerases (unpublished). We also found that the boronated diphosphates, 1^bADP and 7^bADP, are good substrates for synthesis of RNA adenylate polymers by polynucleotide phosphorylase (unpublished). We thus demonstrated the ability to synthesize our first base-boronated RNA polymers.

Base-boronated oligonucleotides form good duplexes with DNA and RNA.