Optical Detection of DNA Conformational Polymorphism on Single-Walled Carbon Nanotubes

The transition of DNA secondary structure from an analogous B to Z conformation modulates the dielectric environment of the single-walled carbon nanotube (SWNT) around which it is adsorbed. The SWNT band-gap fluorescence undergoes a red shift when an encapsulating 30-nucleotide oligomer is exposed to counter ions that screen the charged backbone. The transition is thermodynamically identical for DNA on and off the nanotube, except that the propagation length of the former is shorter by five-sixths. The magnitude of the energy shift is described by using an effective medium model and the DNA geometry on the nanotube sidewall. We demonstrate the detection of the B-Z change in whole blood, tissue, and from within living mammalian cells.

[1]  S. Louie,et al.  Electron-hole excitations and optical spectra from first principles , 2000 .

[2]  Thomas M. Jovin,et al.  The Transition Between B-DNA and Z-DNA , 1987 .

[3]  J. Duguid,et al.  Raman spectroscopy of DNA-metal complexes. I. Interactions and conformational effects of the divalent cations: Mg, Ca, Sr, Ba, Mn, Co, Ni, Cu, Pd, and Cd. , 1993, Biophysical journal.

[4]  M. Strano,et al.  Near-infrared optical sensors based on single-walled carbon nanotubes , 2004, Nature materials.

[5]  Thomas E. Eurell,et al.  Single‐Walled Carbon Nanotube Spectroscopy in Live Cells: Towards Long‐Term Labels and Optical Sensors , 2005 .

[6]  P. Lambin,et al.  Electron-phonon and electron-photon interactions and resonant Raman scattering from the radial-breathing mode of single-walled carbon nanotubes , 2005 .

[7]  J. Abascal,et al.  Computer simulation of the thermodynamics of the B → Z-DNA transition: effect of the ionic size and charge , 2004 .

[8]  M. Dresselhaus,et al.  Structure-Based Carbon Nanotube Sorting by Sequence-Dependent DNA Assembly , 2003, Science.

[9]  Phaedon Avouris,et al.  Scaling of excitons in carbon nanotubes. , 2004, Physical review letters.

[10]  F. Pohl.  Salt-induced transition between two double-helical forms of oligo (dC-dG). , 1983, Cold Spring Harbor symposia on quantitative biology.

[11]  H R Drew,et al.  The anatomy of A-, B-, and Z-DNA. , 1982, Science.

[12]  S. Harvey,et al.  A molecular mechanical model to predict the helix twist angles of B-DNA. , 1984, Nucleic acids research.

[13]  S. Zimmerman.  The three-dimensional structure of DNA. , 1982, Annual review of biochemistry.

[14]  V. C. Moore,et al.  Band Gap Fluorescence from Individual Single-Walled Carbon Nanotubes , 2002, Science.

[15]  A. Rich,et al.  A PKR-like eukaryotic initiation factor 2alpha kinase from zebrafish contains Z-DNA binding domains instead of dsRNA binding domains. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[16]  T M Jovin,et al.  Salt-induced co-operative conformational change of a synthetic DNA: equilibrium and kinetic studies with poly (dG-dC). , 1972, Journal of molecular biology.

[17]  Jacques H. van Boom,et al.  Molecular structure of a left-handed double helical DNA fragment at atomic resolution , 1979, Nature.

[18]  A. Rich,et al.  The Biology of Left-handed Z-DNA (*) , 1996, The Journal of Biological Chemistry.

[19]  Lukas Novotny,et al.  Single carbon nanotube optical spectroscopy. , 2005, Chemphyschem : a European journal of chemical physics and physical chemistry.