posted on 2023-12-28, 22:16authored byYe-Peng Qiao, Chun-Lai Ren
Thermodynamically, perfect DNA hybridization
can be formed between
probes and their corresponding targets due to the favorable energy.
However, this is not the case dynamically. Here, we use molecular
dynamics (MD) simulations based on the oxDNA model to investigate
the process of DNA microarray hybridization. In general, correlated
hybrid DNA structures are formed, including one probe associated with
several targets as well as one target hybrid with multiple probes
leading to the target-mediated hybridization. The formation of these
two types of correlated structures largely depends on the surface
coverage of the DNA microarray. Moreover, DNA sequence, DNA length,
and spacer length have an impact on the structural formation. Our
findings shed light on the dynamics of DNA hybridization, which is
important for the application of DNA microarray.