Calibrating Catalytic DNA Nanostructures for Site‐Selective Protein Modification

• Published in: Chemistry : a European journal Vol. 28; no. 51; pp. e202200895 - n/a
• Main Authors: Keijzer, Jordi F., Zuilhof, Han, Albada, Bauke
• Format: Journal Article
• Language: English
• Published: WEINHEIM Wiley 12.09.2022; Wiley Subscription Services, Inc
• Subjects: acylation catalyst; bioconjugation chemistry; Catalysts; Chemistry; Chemistry, Multidisciplinary; Computer applications; Deoxyribonucleic acid; DNA; hGQ DNAzyme; Intermediates; Physical Sciences; protein-DNA conjugate; Proteins; Science & Technology; Selectivity; site-selective modification; CONJUGATION; hGQ DNAzyme; COMPLEX; ACYLATION; bioconjugation chemistry; acylation catalyst; site-selective modification; protein-DNA conjugate; NUCLEIC-ACIDS
• ISSN: 0947-6539; 1521-3765
• DOI: 10.1002/chem.202200895

Many biomedical fields rely on proteins that are selectively modified. These can be attached using reactive or catalytic moieties, but the position where these moieties are attached is often poorly controlled. We assessed how catalyst position affects the efficiency and selectivity of protein modification. For this, we anchored a template DNA strand to three different proteins, which were subsequently hybridized to DNA strands that contained catalysts at different positions. We found a strong correlation between the catalyst‐to‐protein distance and the efficiency of protein modification for acyl transfer catalysts, which operate via a covalently bound reactant intermediate. Additionally, we found that the catalyst's distance and orientation with respect to the protein surface, also influences its site‐selectivity. A catalyst operating with unbound reactant intermediates showed only enhanced efficiency. Our results are rationalized using computational simulations, showing that one‐point anchoring of the DNA construct leads to notable differences in the site of modification. Three protein‐DNA conjugates were designed to calibrate the protein modification abilities of catalyst‐functionalized DNA. For two catalysts, a clear correlation between distance and efficiency was found and both linker between DNA and protein as well as position and type of catalyst influenced the site of modification. Computational simulations were used to corroborate the findings.