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.

Nanopore sequencing of DNA is a single-molecule technique that may achieve long reads, low cost and high speed with minimal sample preparation and instrumentation. Here, we build on recent progress with respect to nanopore resolution and DNA control to interpret the procession of ion current levels observed during the translocation of DNA through the pore MspA. As approximately four nucleotides affect the ion current of each level, we measured the ion current corresponding to all 256 four-nucleotide combinations (quadromers). This quadromer map is highly predictive of ion current levels of previously unmeasured sequences derived from the bacteriophage phi X 174 genome. Furthermore, we show nanopore sequencing reads of phi X 174 up to 4,500 bases in length that can be unambiguously aligned to the phi X 174 reference genome, and demonstrate proof-of-concept utility with respect to hybrid genome assembly and polymorphism detection. This work provides the foundation for nanopore sequencing of long, complex, natural DNA strands.

Precise and efficient mapping of epigenetic markers on DNA may become an important clinical tool for prediction and identification of ailments. Methylated CpG sites are involved in gene expression and are biomarkers for diseases such as cancer. Here, we use the engineered biological protein pore Mycobacterium smegmatis porin A (MspA) to detect and map 5-methylcytosine and 5-hydroxymethylcytosine within single strands of DNA. In this unique single-molecule tool, a phi29 DNA polymerase draws ssDNA through the pore in single-nucleotide steps, and the ion current through the pore is recorded. Comparing current levels generated with DNA containing methylated CpG sites to current levels obtained with unmethylated copies of the DNA reveals the precise location of methylated CpG sites. Hydroxymethylation is distinct from methylation and can also be mapped. With a single read, the detection efficiency in a quasirandom DNA strand is 97.5 ± 0.7% for methylation and 97 ± 0.9% for hydroxymethylation.nanopore DNA sequencing | DNA methylation | DNA hydroxymethylation | nanotechnology | next generation sequencing

Present techniques for measuring the motion of single motor proteins, such as FRET and optical tweezers, are limited to a resolution of ~300 pm. We use ion current modulation through the protein nanopore MspA to observe translocation of helicase Hel308 on DNA with up to ~40 picometer sensitivity. This approach should be applicable to any protein that translocates on DNA or RNA, including helicases, polymerases, recombinases and DNA repair enzymes.