Nanopore technologies are being developed for fast and direct sequencing of single DNA molecules through detection of ionic current modulations as DNA passes through a pore's constriction 1,2 . Here we demonstrate the ability to resolve changes in current that correspond to a known DNA sequence by combining the high sensitivity of a mutated form of the protein pore Mycobacterium smegmatis porin A (MspA) 3 with phi29 DNA polymerase (DNAP) 4 , which controls the rate of DNA translocation through the pore. As phi29 DNAP synthesizes DNA and functions like a motor to pull a single-stranded template through MspA, we observe well-resolved and reproducible ionic current levels with median durations of ~28 ms and ionic current differences of up to 40 pA. Using six different DNA sequences with readable regions 42-53 nucleotides long, we record current traces that map to the known DNA sequences. With singlenucleotide resolution and DNA translocation control, this system integrates solutions to two longstanding hurdles to nanopore sequencing 2 .In nanopore DNA sequencing, a pore inserted into a membrane permits the flow of ionic current when a voltage is applied across the membrane. As a strand of DNA passes through the pore, it causes changes in current that can be related to the sequence of the DNA. Such a strategy offers the promise of rapidly sequencing long single molecules of DNA 2 , amplification-free sample preparation 1 and direct detection of epigenetic modifications such as base methylation 3,5 . Recent progress toward nanopore sequencing has included determining the resolution and characterizing the recognition sites of biological nanopores MspA 3,6 and α-hemolysin 7-9 as well as developing a method to slow DNA translocation though a nanopore 4,6,10 . However, to our knowledge no system has yet been reported that can read nucleotide-specific current levels as an unmodified strand of DNA passes through a nanopore. In this work, we read DNA by detecting current levels associated with singlenucleotide movement of the strand through MspA. Base-calling algorithms will need to be developed to translate these ionic current reads into a DNA sequence.

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 Ϸ20 higher interaction rates, required only half as much voltage to observe interaction, and allowed ssDNA to reside in the vestibule Ϸ100 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.DNA sequencing ͉ protein engineering ͉ bio-nanotechnology

Nanopore sequencing has the potential to become a direct, fast, and inexpensive DNA sequencing technology. The simplest form of nanopore DNA sequencing utilizes the hypothesis that individual nucleotides of single-stranded DNA passing through a nanopore will uniquely modulate an ionic current flowing through the pore, allowing the record of the current to yield the DNA sequence. We demonstrate that the ionic current through the engineered Mycobacterium smegmatis porin A, MspA, has the ability to distinguish all four DNA nucleotides and resolve single-nucleotides in single-stranded DNA when double-stranded DNA temporarily holds the nucleotides in the pore constriction. Passing DNA with a series of double-stranded sections through MspA provides proof of principle of a simple DNA sequencing method using a nanopore. These findings highlight the importance of MspA in the future of nanopore sequencing.bionanotechnology | next generation sequencing | single-molecule | stochastic sensing | protein pore T he information encoded in DNA is of paramount importance to medicine and to the life sciences. The mapping of the human genome is revolutionizing the understanding of genetic disorders and the prediction of disease and will aid in developing therapies as in refs. 1-3. The ability to sequence DNA quickly and inexpensively is essential to individualized medicine and to scientific research and has prompted the development of new sequencing techniques beyond the original Sanger sequencing (4-7). Nanopore DNA sequencing represents one of the approaches being developed to rapidly sequence a human genome for under $1,000 (www.genome.gov/12513210).In the most elementary form of nanopore DNA sequencing, a nanometer-scale pore provides the sole pathway for an ionic current. Single-stranded DNA (ssDNA) is electrophoretically driven through the pore, and as the ssDNA passes through, it reduces the ionic current through the pore. If each passing nucleotide yields a characteristic residual ionic current then the record of the current will correspond to the DNA sequence. This simple and reagent-free sequencing technique holds the promise to inexpensively read long lengths of DNA molecules at intrinsically fast rates (8). Due to its inherently small size, this system is amenable to parallelization (9).Lately, nanopore sequencing techniques have progressed substantially. This progress and the remaining challenges in nanopore DNA sequencing are summarized in a review article by Branton et al. (8). While nanotechnology usually involves materials such as Si and SiN, nanopore DNA sequencing first evolved using the well-studied protein porin α-hemolysin (10). In contrast to pores made from inorganic materials (11, 12), protein pores can be easily modified and produced with repeatable subnanometer accuracy. Stoddart (13) and Purnell (14) demonstrated that several locations within the beta barrel of α-hemolysin exhibit nucleotide-specific sensitivity with immobilized ssDNA (13). However, α-hemolysin's 5 nm-long cylindrical beta barrel presents...

The cell walls of mycobacteria form an exceptional permeability barrier, and they are essential for virulence. They contain extractable lipids and long-chain mycolic acids that are covalently linked to peptidoglycan via an arabinogalactan network. The lipids were thought to form an asymmetrical bilayer of considerable thickness, but this could never be proven directly by microscopy or other means. Cryo-electron tomography of unperturbed or detergenttreated cells of Mycobacterium smegmatis embedded in vitreous ice now reveals the native organization of the cell envelope and its delineation into several distinct layers. The 3D data and the investigation of ultrathin frozen-hydrated cryosections of M. smegmatis, Myobacterium bovis bacillus Calmette-Gué rin, and Corynebacterium glutamicum identified the outermost layer as a morphologically symmetrical lipid bilayer. The structure of the mycobacterial outer membrane necessitates considerable revision of the current view of its architecture. Conceivable models are proposed and discussed. These results are crucial for the investigation and understanding of transport processes across the mycobacterial cell wall, and they are of particular medical relevance in the case of pathogenic mycobacteria.bacterial cell wall ͉ Corynebacterium glutamicum ͉ Mycobacterium bovis ͉ Mycobacterium smegmatis ͉ mycolic acid layer M ycobacteria have evolved a complex cell wall, comprising a peptidoglycan-arabinogalactan polymer with covalently bound mycolic acids of considerable size (up to 90 carbon atoms), a variety of extractable lipids, and pore-forming proteins (1-3). The cell wall provides an extraordinarily efficient permeability barrier to noxious compounds and contributes to the high intrinsic resistance of mycobacteria to many drugs (4). Because of the paramount medical importance of Mycobacterium tuberculosis, the ultrastructure of mycobacterial cell envelopes has been intensively studied during recent decades. The current view of the cell wall architecture is essentially based on a model suggested by Minnikin (5). He proposed that the covalently bound mycolic acids form the inner leaflet of an asymmetrical bilayer. Other lipids extractable by organic solvents were thought to form the outer leaflet, either intercalating with the mycolates (5, 6) or forming a more clearly defined interlayer plane (7). Elegant x-ray diffraction studies proved that the mycolic acids are oriented parallel to each other and perpendicular to the plane of the cell envelope (8). Furthermore, freeze-fracture studies showed a second fracture plane in electron micrographs (9), indicating the existence of a hydrophobic bilayer structure external to that of the cytoplasmic membrane. Mutants or treatments affecting mycolic acid biosynthesis and the production of extractable lipids resulted in an increase of cell wall permeability in various mycobacteria and related microorganisms (10-12) and a drastic decrease of virulence, underlining the importance of the integrity of the cell wall for intracellular survival...

Mycobacteria have low-permeability outer membranes that render them resistant to most antibiotics. Hydrophilic nutrients can enter by way of transmembrane-channel proteins called porins. An x-ray analysis of the main porin from Mycobacterium smegmatis, MspA, revealed a homooctameric goblet-like conformation with a single central channel. This is the first structure of a mycobacterial outer-membrane protein. No structure-related protein was found in the Protein Data Bank. MspA contains two consecutive beta barrels with nonpolar outer surfaces that form a ribbon around the porin, which is too narrow to fit the thickness of the mycobacterial outer membrane in contemporary models.