Single-molecule DNA detection with an engineered MspA protein nanopore.
Nanopores hold great promise as single-molecule analytical devices and biophysical model systems because the ionic current blockades they produce contain information about the identity, concentration, structure, and dynamics of target molecules. The porin MspA of Mycobacterium smegmatis has remarkable stability against environmental stresses and can be rationally modified based on its crystal structure. Further, MspA has a short and narrow channel constriction that is promising for DNA sequencing because it may enable improved characterization of short segments of a ssDNA molecule that is threaded through the pore. By eliminating the negative charge in the channel constriction, we designed and constructed an MspA mutant capable of electronically detecting and characterizing single molecules of ssDNA as they are electrophoretically driven through the pore. A second mutant with additional exchanges of negatively-charged residues for positively-charged residues in the vestibule region exhibited a factor of approximately 20 higher interaction rates, required only half as much voltage to observe interaction, and allowed ssDNA to reside in the vestibule approximately 100 times longer than the first mutant. Our results introduce MspA as a nanopore for nucleic acid analysis and highlight its potential as an engineerable platform for single-molecule detection and characterization applications.
Butler
Tom Z
TZ
Department of Physics, University of Washington, Box 351560, 3910 15th Avenue NE, Seattle, WA 98195, USA.
Pavlenok
Mikhail
M
Derrington
Ian M
IM
Niederweis
Michael
M
Gundlach
Jens H
JH
D019943:Amino Acid Substitution; D001426:Bacterial Proteins / Q000737:chemistry* / Q000235:genetics; D015374:Biosensing Techniques; D018360:Crystallography, X-Ray; D004277:DNA, Single-Stranded / Q000032:analysis* / Q000737:chemistry; D055664:Electrochemical Techniques; D020125:Mutation, Missense; D020102:Mycobacterium smegmatis / Q000737:chemistry* / Q000235:genetics; D018272:Porins / Q000737:chemistry* / Q000235:genetics; D020836:Protein Structure, Quaternary / Q000235:genetics
D001426:Bacterial Proteins; D004277:DNA, Single-Stranded; D018272:Porins; C121838:mspA protein, Mycobacterium smegmatis