DNA molecules and configurations in a solid-state nanopore microscope

Levene, M.J. et al. Zero-mode waveguides for single-molecule analysis at high concentrations. Science 299, 682–686 ( 2003).

Rees, W.A., Keller, R.W., Vesenka, J.P., Yang, G. & Bustamante, C. Evidence of DNA bending in transcription complexes imaged by scanning force microscopy. Science 260, 1646–1649 ( 1993).

Hansma, H.G. et al. Properties of biomolecules measured from atomic force microscope images: A review. J. Struct. Biol. 119, 99–108 ( 1997).

Quake, S.R., Babcock, H. & Chu, S. The dynamics of partially extended single molecules of DNA. Nature 388, 151–154 ( 1997).

Smith, S.B., Cui, Y. & Bustamante, C. Overstretching b-DNA: The elastic response of individual double-stranded and single-stranded DNA molecules. Science 271, 795–799 ( 1996).

Hille, B. Ionic Channels and Excitable Membranes (Sinauer, Sunderland, Massachusetts, 1992).

Bezrukov, S.M., Vodyanoy, I. & Parasegian, V.A. Counting polymers moving through a single ion channel. Nature 370, 279–281 ( 1994).

Kasianowicz, J.J., Brandin, E., Branton, D. & Deamer, D.W. Characterization of individual polynucleotide molecules using a membrane channel. Proc. Natl Acad. Sci. USA 93, 13770–13773 ( 1996).

Akeson, M., Branton, D., Kasianowicz, J.J., Brandin, E. & Deamer, D.W. Microsecond time-scale discrimination among polycytidylic acid, polyadenylic acid, and polyuridylic acid as homopolymers or as segments within single RNA molecules. Biophys. J. 77, 3227–3233 ( 1999).

Mellor, A., Nivon, L., Brandin, E., Golovchenko, J. & Branton, D. Rapid nanopore discrimination between single polynucleotide molecules. Proc. Natl Acad. Sci. USA 97, 1079–1084 ( 2000).

Li, J. et al. Ion-beam sculpting at nanometre length scales. Nature 412, 166–169 ( 2001).

Sauer-Budge, A.F. Unzipping Double-Stranded DNA Molecule by Molecule in a Nanopore Thesis, Harvard Univ. ( 2002).

Muthukumar, M. Dynamics of polyelctrolyte solutions. J. Chem. Phys. 107, 2619–2635 ( 1997).

Muthukumar, M. Polymer translocation through a hole. J. Chem. Phys. 111, 10371–10374 ( 1999).

Muthukumar, M. Polymer escape through a nanopore. J. Chem. Phys. 118, 5174–5184 ( 2003).

Lee, N. & Obukhov, S. Diffusion of a polymer chain through a thin membrane. J. Physique II 6, 195–204 ( 1996).

Evans, D.F. & Wennerström, H. The Colloidal Domain 361 (Wiley-VCH, New York, 1999).

Han, J. & Craighead, H.G. Separation of long DNA molecules in a microfabricated trap array. Science 288, 1026–1029 ( 2000).

Saleh, O.A. & Sohn, L.L. An artificial nanopore for molecular sensing. Nano Lett. 3, 37–38 ( 2003).

Kasianowicz, J.J., Henrickson, S.E., Weetall H.H. & Robertson, B. Simultaneous multianalyte detection with a nanopore. Anal. Chem. 73, 2268–2272 ( 2001).

Vercoutere, W. et al. Rapid discrimination among individual DNA hairpin molecules at single-nucleotide resolution using an ion channel. Nature Biotechnol. 19, 248–252 ( 2001).

Byers, T.J., Husain-Chishti, A., Dubreuil, R.R., Branton, D., & Goldstein, L.S. Sequence similarity of the amino-terminal domain of Drosophila β-spectrin to α-actinin and dystrophin. J. Cell Biol. 109, 1633–1641 ( 1989).

Sambrook, J., Fritsch, E.F. & Maniatis, T. Molecular Cloning: A Laboratory Manual 2nd edn (Cold Spring Harbor Laboratory, New York, 1989).