Meller Group : Single Molecule Biophysics & Nano-biotechnologyTechnion Logo

DNA 'bar-coding' using PNA probes

The ability to rapidly tag and identify trace amounts of DNA without the need for costly and time-consuming amplification can lead to cheaper and faster pathogen and mutation diagnostics platforms. Low-cost and high-speed platforms are essential for an effective response to emerging infection threats and will ultimately result in a more accurate treatment, as well as an overall decrease in morbidity and mortality.

To this end we have developed a nanopore-based DNA bar-coding method, which employs a purely electrical detection of individual Peptide Nucleic Acid (PNA)-tagged double-stranded DNA molecules. The PNA probes are designed to hybridize to specific sequences in the target genomes, thus creating unique 'bar-code' pattern for the target, as shown schematically in Figure 1. Then single DNA molecules are threaded through a sub-5 nm solid-state pores, which reads that pattern, as illustrated in Figure 2. Sensing of individual DNA molecules tagged with PNA probes, proceeds with high-throughput (>1 molecule/second at sub-nM DNA concentrations), enabling rapid single-molecule identification of specific dsDNA sequences.

Our current result already demonstrated the ability to probe one or two PNA probes hybridized specifically to a ~3,000bp DNA, as shown in Figure 3. The bare DNA result in a reduction of ~1nA in the open-pore current. In contrast, the PNA/DNA hybrid results in a reduction of 1.5nA in the current, which is readily detectable using our system. Read more about this method in our Nano Letters paper.


  1. Singer A, Wanunu M, Morrison W, Kuhn H, Frank-Kamenetskii M and A. Meller.(2010) Nanopore-based sequence-specific detection of duplex DNA for genomic profiling. Nano Letters. 10(2), 738-42.


DNA barcoding

Figure 1


Figure 2

2 PNA signal

Figure 3