Charge, Diffusion, and Current Fluctuations of Single-Stranded DNA Trapped in an MspA Nanopore

Stephen J Fleming; Bo Lu; Jene A Golovchenko

doi:10.1016/j.bpj.2016.12.007

Charge, Diffusion, and Current Fluctuations of Single-Stranded DNA Trapped in an MspA Nanopore

Biophys J. 2017 Jan 24;112(2):368-375. doi: 10.1016/j.bpj.2016.12.007.

Authors

Stephen J Fleming¹, Bo Lu¹, Jene A Golovchenko²

Affiliations

¹ Department of Physics, Harvard University, Cambridge, Massachusetts.
² Department of Physics, Harvard University, Cambridge, Massachusetts; School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts. Electronic address: golovchenko@physics.harvard.edu.

Abstract

We report effective charges and diffusion constants of several different single-stranded DNA oligonucleotides trapped in an MspA nanopore. Nucleotide identity is found to have a substantial influence on effective charges and diffusion constants. These quantities are determined from escape time experiments for a DNA molecule attached to a NeutrAvidin molecule that, unlike the DNA, does not pass through the pore. Correlations are reported between oligonucleotide effective charges and current blockages, and between their diffusion constants and DNA-induced current blockage fluctuations. We also report an unanticipated source of current fluctuations that reflects a discrete blockage current level structure. We posit that this is associated with interactions between the NeutrAvidin molecule and the MspA nanopore.

MeSH terms

DNA, Single-Stranded / chemistry*
DNA, Single-Stranded / metabolism*
Diffusion
Electric Conductivity*
Nanopores*
Porins / chemistry*

Substances

DNA, Single-Stranded
Porins
mspA protein, Mycobacterium smegmatis

Grants and funding

R01 HG003703/HG/NHGRI NIH HHS/United States