Comparative Analysis of Golden Gate and Classical Cloning Techniques in E. coli: A Study in Molecular Cloning Efficiency

Abstract

Molecular cloning remains a cornerstone technique in genetic engineering and synthetic biology. In this study, we conducted a systematic comparative analysis between the classical cloning method and the Golden Gate assembly technique, utilizing Escherichia coli as the model organism. Through polymerase chain reaction (PCR) amplification, restriction enzyme digestion, ligation, transformation, and Sanger sequencing, we assessed the operational efficiency and cloning fidelity of both strategies. Our results demonstrated that Golden Gate assembly, leveraging type IIS restriction enzymes and simultaneous ligation, significantly enhanced cloning efficiency and precision, particularly for seamless multi-fragment assembly. In contrast, the classical cloning approach maintained certain advantages in simplicity and robustness for specific experimental conditions. Challenges encountered during transformation and sequencing highlighted the critical impact of technical accuracy on experimental outcomes. This study underscores the importance of selecting appropriate cloning methodologies tailored to experimental objectives and laboratory capabilities, providing a foundation for optimized molecular cloning workflows in future synthetic biology and biotechnology applications.