Quantitative Characterization of RCA‐Based DNA Hydrogels – Towards Rational Materials Design

• Published in: Chemistry : a European journal Vol. 30; no. 53; pp. e202401788 - n/a
• Main Authors: Moench, Svenja A., Lemke, Phillip, Weisser, Julia, Stoev, Iliya D., Rabe, Kersten S., Domínguez, Carmen M., Niemeyer, Christof M.
• Format: Journal Article
• Language: English
• Published: Weinheim Wiley Subscription Services, Inc 19-09-2024
• Subjects: Biomedical materials; Chemical synthesis; Deoxyribonucleic acid; Design standards; DNA; DNA hydrogels; DNA structure; Efficiency; Experimental methods; Gels; Gene sequencing; Hydrogels; Material properties; Mechanical properties; Nucleotide sequence; Nucleotides; Reagents; Rolling circle amplification; Viscosity
• DOI: 10.1002/chem.202401788
• EISSN: 1521-3765
• ISSN: 0947-6539; 1521-3765

DNA hydrogels hold significant promise for biomedical applications and can be synthesized through enzymatic Rolling Circle Amplification (RCA). Due to the exploratory nature of this emerging field, standardized RCA protocols specifying the impact of reaction parameters are currently lacking. This study varied template sequences and reagent concentrations, evaluating RCA synthesis efficiency and hydrogel mechanical properties through quantitative PCR (qPCR) and indentation measurements, respectively. Primer concentration and stabilizing additives showed minimal impact on RCA efficiency, while changes in polymerase and nucleotide concentrations had a stronger effect. Concentration of the circular template exerted the greatest influence on RCA productivity. An exponential correlation between hydrogel viscosity and DNA amplicon concentration was observed, with nucleobase sequence significantly affecting both amplification efficiency and material properties, particularly through secondary structures. This study suggests that combining high‐throughput experimental methods with structural folding prediction offers a viable approach for systematically establishing structure‐property relationships, aiding the rational design of DNA hydrogel material systems.
The impact of template sequences and reaction conditions on the synthesis of DNA hydrogels via Rolling Circle Amplification (RCA) was systematically investigated. The employed methodology is high‐throughput capable and facilitates the development of sequence‐property relationships by correlating reaction process parameters with synthesis efficiency and mechanical material properties.