New strategies in Bioconjugation : chemical modification of nucleic acids and peptides

One of the open challenges in chemical biology is to identify reactions that proceed with large rate constants in water at neutral pH values. Once assembled, these conjugates may be used for a broad variety of applications (e.g., therapeutics, imaging probes or as a catalytic system). Herein we describe a novel approach for the chemical modification of nucleic acids using guided organometallic-catalysts. Customized dirhodium complexes were prepared using modular ligands bearing various functional groups and connected to peptide nucleic acids through stable oxime linkages. The final constructs have been optimized for aqueous catalysis and were tested in preliminary alkylation studies of single-stranded DNA via dirhodium-carbenoids generated from alpha-diazocarbonyl compounds. During the course of optimizing the rather slow kinetics of oxime formation, we have developed two highly efficient methods for rapid oxime-based bioconjugations. (1) Dialdehydes were found to react with O-alkylhydroxylamines at rates of 500 M-1 s-1 in neutral aqueous buffer in the absence of a catalyst. The key to these conjugations is an unusually stable cyclic intermediate, which ultimately undergoes dehydration to yield an oxime. The scope and limitations of this method are outlined, as well as its application in bioconjugation with a DNA 41-mer and a mechanistic interpretation that will facilitate further developments of reactions with O-alkylhydroxylamines at low substrate concentrations. (2) Oximes proximal to boronic acids form in neutral aqueous buffer with rate constants of more than 104 M−1 s−1, the largest to date for any oxime condensation. The reaction tolerates a variety of biological interfering additives and is suitable for the rapid modification of short peptide sequences. Once formed, the oxime products are stable for days and undergo slow interconversion through a hydrolysis-based mechanism. Boron's dynamic coordination chemistry confers an adaptability that seems to aid a number of elementary steps in the oxime condensation.
In conclusion both methods represent important improvements for oxime-based bioconjugations in water (pH 7) at low equimolar concentrations. The high reaction kinetics are achieved without the need for additional reagents, catalysts or variations of the reaction conditions. In addition, the possibility of using reacting pairs that are commercially available will greatly enhance the applicability of these methods for efficient conjugations of precious biomolecules in the future.