Colloquium: Physical approaches to DNA sequencing and detection

Abstract

With the continued improvement of sequencing technologies, the prospect of genome-based medicine is now at the forefront of scientific research. To realize this potential, however, a revolutionary sequencing method is needed for the cost-effective and rapid interrogation of individual genomes. This capability is likely to be provided by a physical approach to probing DNA at the single-nucleotide level. This is in sharp contrast to current techniques and instruments that probe ͑through chemical elongation, electrophoresis, and optical detection͒ length differences and terminating bases of strands of DNA. Several physical approaches to DNA detection have the potential to deliver fast and low-cost sequencing. Central to these approaches is the concept of nanochannels or nanopores, which allow for the spatial confinement of DNA molecules. In addition to their possible impact in medicine and biology, the methods offer ideal test beds to study open scientific issues and challenges in the relatively unexplored area at the interface between solids, liquids, and biomolecules at the nanometer length scale. This Colloquium emphasizes the physics behind these methods and ideas, critically describes their advantages and drawbacks, and discusses future research opportunities in the field.

Electrical Conductance in Biological Molecules

“…The physical-chemical modalities of the above-mentioned sensors are hot topic for the present, they are systematically studied by several groups using theoretical approaches and cause vivid debates in the literature (see, for example, works [124][125][126][127][128][129][130][131] and the references therein).…”

Single-Molecule Analysis Methods Using Nanogap Electrodes and Their Application to DNA Sequencing Technologies

“…As a result, we predicted that single-base molecules between nanoelectrodes will have conformations that are energetically stable, and as a result, the single-molecule conductance measurements will obtain only single peaks for them. 31,32,102,103 The conductance histograms of all of the base molecules tested by us were found to have large dispersions. The tunneling current flowing through a molecule strongly depends on the distance between the molecule and the electrodes and the conformation of the molecule.…”

“…Theoretical calculations support this prediction. 31,32,102,103 However, because the degrees of freedom of base molecules in DNA are limited by chemical bonds, the variance of the histograms of base molecules in DNA is actually smaller than the variance for individual base molecules. 37 As is shown in Figure 21, there is an order in the various values of the peak conductance of each conductance histogram.…”

“…Furthermore, because the base molecules are asymmetrically charged molecules composed of π electron systems, sugar, and phosphoric acid, they have dipole moments. 102 These dipole moments are subjected to forces when electric fields are generated across them. As a result, we predicted that single-base molecules between nanoelectrodes will have conformations that are energetically stable, and as a result, the single-molecule conductance measurements will obtain only single peaks for them.…”

Nanopore Integrated Nanogaps for DNA Detection

“…Thanks to this property, a signal specific to the base residing in the nanogap will not interfere with the signals from neighboring bases. 2 This approach overcomes nanopore spatial resolution limit imposed by the typical silicon nitride membrane thickness of 10−50 nm, through which it is impossible to distinguish signals in ionic current between adjacent nucleotides on the DNA strand. Although the thickness of membrane embedding the nanopore was recently addressed by using a 0.34 nm thick graphene sheet, 3−5 DNA sequencing using direct ionic current measurements has not been fully realized.…”