Charge-Perturbation Signature (CPS): a new bio-electrical method for nucleic acid detection

Direct detection of electric charge perturbations during polymerase-catalyzed reactions by the electrode system with immobilized DNA can uniquely identify a DNA sequence. The polymerization process generates local perturbations of charge in the solution near the electrode surface and induces a charge in a polarazible gold electrode. This event is detected as a transient current by a differential amplifier. Dispensing individual dNTPs to the electrode solution and detecting the charge alterations can determine single nucleotides in a sequence. Alternatively, multiple bases can be determined at the same time using a mix of all dNTPs with subsequent analysis of the resulting signal. The initial enzyme attachment to the DNA molecule can be detected prior to polymerization with electrode capacitance measurement. This technique thus enables also the detection of enzyme-DNA interactions at the electrode surface.

Sensitivity of detection in the macro-scale system (with millimeter-sized electrodes) is in the low femtomol range. Through additional development, this technology has the potential to be scaled down inside a compact device that is simple and easy to use with the capability of uniquely identifying microbial pathogens in environmental, food, research, and clinical samples. Furthermore, efforts are under way to develop an integrated array version of this platform and demonstrate its application to pathogen detection, gene expression and short DNA sequencing for target detection and validation. This multidisciplinary approach will involve researchers from molecular biology, chemistry, computer science and electrical engineering. The project is a collaborative effort between the Stanford Genome Technology Center (SGTC) and two different groups at the Stanford Center for Integrated System (CIS), circuit design and signal processing groups.

 

Relevant publications & patents:
  1. Direct electrical detection of DNA synthesis.
    Pourmand N., Karhanek M., Persson H. J., Webb C. B., Lee T. H. , Zahradníková A., Davis R. W., PNAS2006, 103(17):6466-70

    [PNAS]

  2. Pourmand N., Hassibi A. US Patent Application 20020155476 (2003).
  3. Pourmand N., Hassibi A. US Patent Application US 20030152985 (2003).
  4. Pourmand N., Karhanek M., Davis R.W. U.S PTO No. 60/627,192, and Stanford Docket S04-291 (2004)