Identification of DNA basepairing via tunnel-current decay.

@article{He2007IdentificationOD,
  title={Identification of DNA basepairing via tunnel-current decay.},
  author={Jin He and Lisha Lin and Peiming Zhang and Stuart Lindsay},
  journal={Nano letters},
  year={2007},
  volume={7 12},
  pages={
          3854-8
        }
}
We propose a new approach for reading the sequence of a DNA molecule passing between electrodes on a nanopore, using hydrogen bond-mediated tunneling signals. The base-electrode interaction is modeled using a nucleo-base-functionalized STM probe that is pulled away from a nucleoside monolayer. Watson-Crick recognition results in slow decay of the tunnel current, which is uniquely characteristic of the basepair in over half the reads. Thirteen independent reads would yield the desired 99.99… 

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References

SHOWING 1-10 OF 25 REFERENCES
Electronic signature of DNA nucleotides via transverse transport.
TLDR
It is found that, if the electrodes which sandwich the DNA have the appropriate spatial width, each nucleotide carries a unique signature due to the different electronic and chemical structure of the four bases, independent of the nearest-neighbor nucleotides.
Complementary base-pair-facilitated electron tunneling for electrically pinpointing complementary nucleobases.
  • T. Ohshiro, Y. Umezawa
  • Chemistry, Physics
    Proceedings of the National Academy of Sciences of the United States of America
  • 2006
TLDR
The electron tunneling between a sampleucleobase and its complementary nucleobase molecular tip was much facilitated compared with its noncomplementary counterpart and the complementary nucleOBase tip was thereby capable of electrically pinpointing each nucleobases.
Influence of the environment and probes on rapid DNA sequencing via transverse electronic transport.
TLDR
It is found that the intrinsic measurement bandwidth of the electrodes helps the detection of single bases by averaging over the current distributions of each base, and the intrinsic distinguishability of the bases is not significantly affected by pore size and transverse field strength.
First-principles transversal DNA conductance deconstructed.
First-principles calculation of the transverse conductance across DNA fragments placed between gold nanoelectrodes reveals that such conductance describes electron tunneling that depends critically
Base pairing structure in the poly d(G-T) double helix: wobble base pairs.
High resolution nuclear magnetic resonance (NMR) and ethidium bromide binding studies are used to demonstrate that poly d(G-T) forms an ordered double helical structure at low temperatures (below 24
Self-assembly of molecular superstructures studied by in situ scanning tunneling microscopy: DNA bases on gold (111)
Wc have studied the DNA bases adenine, thymine, guanine, and cytosine adsorbed onto Au(111) using in situ scanning tunneling microscopy (STM), atomic force microscopy (AFM), and cyclic voltammetry.
Graphite: a mimic for DNA and other biomolecules in scanning tunneling microscope studies.
TLDR
These images illustrate features previously thought to be due to biological molecules, such as periodicity and meandering of "molecules" over steps, that can no longer be used to distinguish real molecules from features of the native substrate.
Thermodynamics of internal C.T mismatches in DNA.
TLDR
The data show that the nearest-neighbor model is adequate for predicting thermodynamics of oligonucleotides with internal C.T mismatches, which destabilize the duplex in all sequence contexts and varies weakly depending on the orientation of the mismatch and its context.
High-resolution STM imaging of novel poly(G)-poly(C) DNA molecules.
TLDR
STM imaging of single double-stranded poly(G)-poly(C) DNA molecules, made by a novel synthesis method, shows the molecules morphology, revealing a periodic structure of approximately 4 nm, seen as repeating "bulbs" along the molecules.
Alteration of DNA Primary Structure by DNA Topoisomerase I. Isolation of the Covalent Topoisomerase I−DNA Binary Complex in Enzymatically Competent Form
TLDR
DNA ligation by DNA topoisomerase I was investigated employing synthetic DNA substrates containing a single strand nick, finding that site-specific cleavage resulted in uncoupling of the cleavage and ligation reactions of the enzyme, thereby trapping the covalent enzyme−DNA intermediate.
...
...