3D structural integrity and interactions of single-stranded protein-binding DNA in a functionalized nanopore.
Biomarker-binding nucleotide sequences, like aptamers, have gained recent attention in cancer cell isolation and detection works. Self-assembly and 3D conformation of aptamers enable them to selectively capture and bind diseased cells and related biomarkers. One mode of utilizing such an extraordinary selective property of the aptamers is by grafting these in nanopores. Coating the inside walls of the nanopore with biomarker specific ligands, like DNA, changes the statistics of the dynamic translocation events. When the target protein passes through the nanopore, it interacts with ligand coated inside the nanopore, and the process alters the overall potential energy profile which is essentially specific to the protein detected. The fundamental goal in this process is to ensure that these detection motifs hold their structure and functionality under applied electric field and experimental conditions. We report here all-atom molecular dynamics simulations of the effects of external electric field on the 3D conformation of such DNA structures. The simulations demonstrate how the grafted moieties affect the translocation time, velocity, and detection frequency of the target molecule. We also investigated a novel case of protein translocation, where DNA is prebound to the protein. As model, a thrombin-specific G-quartet and thrombin pair was used for this study.
Nano-Bio Lab, ‡Department of Electrical Engineering, §Nanotechnology Research Center, Shimadzu Institute for Research Technologies, ∥Department of Mechanical and Aerospace Engineering, ⊥Department of Bioengineering, #Joint Graduate Studies Committee of Bioengineering Program, University of Texas at Arlington and University of Texas Southwestern Medical Center at Dallas, University of Texas at Arlington , Arlington, Texas 76019, United States.
Mohammed Arif I
MA
Mahmood
Waqas
W
Ali
Ashfaq
A
Adnan
Samir M
SM
Iqbal
D052157:Aptamers, Nucleotide / Q000737:chemistry / Q000378:metabolism*; D001483:Base Sequence; D004277:DNA, Single-Stranded / Q000737:chemistry*; D055664:Electrochemical Techniques / Q000295:instrumentation; D004867:Equipment Design; D006801:Humans; D056004:Molecular Dynamics Simulation; D058608:Nanopores / Q000648:ultrastructure*; D009690:Nucleic Acid Conformation; D011487:Protein Conformation; D021381:Protein Transport; D013917:Thrombin / Q000032:analysis / Q000378:metabolism*
D052157:Aptamers, Nucleotide; D004277:DNA, Single-Stranded; D013917:Thrombin