Biosensor Design through Molecular Dynamics Simulation

The beginning of 21st century has witnessed new
advancements in the design and use of new materials for biosensing
applications, from nano to macro, protein to tissue. Traditional
analytical methods lack a complete toolset to describe the
complexities introduced by living systems, pathological relations,
discrete hierarchical materials, cross-phase interactions, and
structure-property dependencies. Materiomics – via systematic
molecular dynamics (MD) simulation – can provide structureprocess-
property relations by using a materials science approach
linking mechanisms across scales and enables oriented biosensor
design. With this approach, DNA biosensors can be utilized to detect
disease biomarkers present in individuals’ breath such as acetone for
diabetes. Our wireless sensor array based on single-stranded DNA
(ssDNA)-decorated single-walled carbon nanotubes (SWNT) has
successfully detected trace amount of various chemicals in vapor
differentiated by pattern recognition. Here, we present how MD
simulation can revolutionize the way of design and screening of DNA
aptamers for targeting biomarkers related to oral diseases and oral
health monitoring. It demonstrates great potential to be utilized to
build a library of DNDA sequences for reliable detection of several
biomarkers of one specific disease, and as well provides a new
methodology of creating, designing, and applying of biosensors.

• Wenjun Zhang
• Yunqing Du
• Steven W. Cranford
• Ming L. Wang

• Biosensor
• design
• DNA
• molecular dynamics simulation.

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