title: Ranking of Molecular Biomarker Interaction with Targeted DNA Nucleobases via Full Atomistic Molecular Dynamics.
abstract: DNA-based sensors can detect disease biomarkers, including acetone and ethanol for diabetes and H2S for cardiovascular diseases. Before experimenting on thousands of potential DNA segments, we conduct full atomistic steered molecular dynamics (SMD) simulations to screen the interactions between different DNA sequences with targeted molecules to rank the nucleobase sensing performance. We study and rank the strength of interaction between four single DNA nucleotides (Adenine (A), Guanine (G), Cytosine (C), and Thymine (T)) on single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) with acetone, ethanol, H2S and HCl. By sampling forward and reverse interaction paths, we compute the free-energy profiles of eight systems for the four targeted molecules. We find that dsDNA react differently than ssDNA to the targeted molecules, requiring more energy to move the molecule close to DNA as indicated by the potential of mean force (PMF). Comparing the PMF values of different systems, we obtain a relative ranking of DNA base for the detection of each molecule. Via the same procedure, we could generate a library of DNA sequences for the detection of a wide range of chemicals. A DNA sensor array built with selected sequences differentiating many disease biomarkers can be used in disease diagnosis and monitoring.
authors.affiliation: Laboratory for Nanotechnology In Civil Engineering (NICE), Boston, MA 02115 United States.|Interdisciplinary Engineering Program, College of Engineering, Northeastern University, Boston, MA 02115 United States.
authors.forename: Wenjun
authors.initials: W
authors.lastname: Zhang
authors.affiliation: Department of Civil &Environmental Engineering, Northeastern University, Boston, MA 02115 United States.
authors.forename: Ming L
authors.initials: ML
authors.lastname: Wang
authors.affiliation: Laboratory for Nanotechnology In Civil Engineering (NICE), Boston, MA 02115 United States.|Department of Civil &Environmental Engineering, Northeastern University, Boston, MA 02115 United States.
authors.forename: Steven W
authors.initials: SW
authors.lastname: Cranford
mesh_terms: D000096:Acetone / Q000032:analysis / Q000737:chemistry; D000225:Adenine / Q000737:chemistry*; D015415:Biomarkers / Q000032:analysis / Q000737:chemistry; D015374:Biosensing Techniques / Q000295:instrumentation / Q000379:methods*; D002318:Cardiovascular Diseases / Q000175:diagnosis / Q000378:metabolism / Q000503:physiopathology; D003596:Cytosine / Q000737:chemistry*; D004277:DNA, Single-Stranded / Q000737:chemistry*; D003920:Diabetes Mellitus / Q000175:diagnosis / Q000378:metabolism / Q000503:physiopathology; D055664:Electrochemical Techniques; D000431:Ethanol / Q000032:analysis / Q000737:chemistry; D045853:Exhalation; D006147:Guanine / Q000737:chemistry*; D006801:Humans; D006851:Hydrochloric Acid / Q000032:analysis / Q000737:chemistry; D006862:Hydrogen Sulfide / Q000032:analysis / Q000737:chemistry; D056004:Molecular Dynamics Simulation; D050500:Pancreatitis, Chronic / Q000175:diagnosis / Q000378:metabolism / Q000503:physiopathology; D013816:Thermodynamics; D013941:Thymine / Q000737:chemistry*
chemical_list: D015415:Biomarkers; D004277:DNA, Single-Stranded; D000096:Acetone; D000431:Ethanol; D006147:Guanine; D003596:Cytosine; D000225:Adenine; D013941:Thymine; D006851:Hydrochloric Acid; D006862:Hydrogen Sulfide