Stuart Linsay, director of Arisona State University’s Centre for Single Molecule Biophysics at the Biodesign Institute, along with his colleagues, demonstrates a novel method known as translocation, in the current issue of Science. This method mainly involves threading a single stranded ribbon of DNA through a carbon nanotube, which provides voltage spikes that provide information about the passage of DNA bases as they pass through the tube.
Carbon nanotubes(CNTs) are the allotropes of carbon with a cylindrical nanostructure, carried arrangements of carbon atoms, exhibiting unique properties of strength and electrical conductivity. Nanotubes are members of fullerene structural family, which also includes the spherical buckyballs. These cylindrical carbon molecules have novel properties that make them potentially useful in medical applications.
Knowledge of DNA sequences has become indispensable for basic biological research, and other research branches utilizing DNA sequencing, and in numerous applied fields such as diagnostic, biotechnology, forensic biology and biological systematics. The advent of DNA sequencing has significantly accelerated biological research and discovery. Traditional methods for reading the genetic script, made up of four nucleotide bases, adenine, thymine, cytosine and guanine (labeled A,T,C,&G), typically rely on shredding the DNA molecule into hundreds of thousands of pieces, reading these abbreviated sections and finally, reconstructing the full genetic sequence with the aid of massive computing power. A decade ago, the first human genome — a sequence of over 3 billion chemical base pairs -was successfully decoded, in a biological tour de force.
The current study deals with single walled carbon nanotubes, 1-2 nm in diameter. These single walled carbon nanotubes were used for the conducting channels. When a current was induced through the nanotube, segments of single-stranded DNA (known as oligomeres) made up of either 60 or 120 nucleotides, were drawn into the opening of the nanotube and translocated from the anode side of the nanotube to the output cathode side, due to the negative charge carried by the DNA molecule. The velocity of DNA translocation is dependent on both the nucleotide structure and molecular weight of the DNA sample. The carbon nanotubes were grown on an oxidized silicon wafer. Results indicate that among the successfully formed nanotubes — those fully opened and without leakage along their length — a sharp spike in electrical activity is detected during the process of DNA translocation. Further, reversing the bias of the electrodes causes the current spikes to disappear; restoring the original bias caused the spikes to reappear.
Lindsay stresses that the transient current pulses, each containing roughly 10x7charges, represent an enormous amplification of the translocated charge. A technique known as quantitative polymerase chain reaction (qPCR) was used to verify that the particular carbon nanotubes displaying these anomalously sharp current spikes — around 20 percent of the total sample, were indeed those through which DNA translocation had occurred.
qPCR is a laboratory technique based on PCR, which is used to amplify and simultaneously quantify a targeted DNA molecule. It enables both detection and quantification of one or more specific sequences in a DNA sample.
The team carried out molecular simulations to try to determine the mechanism for the anomalously large ionic currents detected in the nanotubes. Observation of current-voltage curves registered at varying ionic concentrations showed that ion movement through some of the tubes is very unusual, though understanding the precise mechanism by which DNA translocation gives rise to the observed current spikes will require further modeling. Nevertheless, the characteristic electrical signal of DNA translocation through tubes with high ionic conductance may provide a further refinement in ongoing efforts to apply nanopore technology for rapid DNA sequencing.
If the process can be perfected, Lindsay emphasizes, DNA sequencing could be carried out thousands of times faster than through existing methods, at a fraction of the cost. Realizing the one-patient-one-genome goal of personalized medicine would provide essential diagnostic information and help pioneer individualized treatments for a wide range of diseases.
Thus the emergence of coupled play of high speed genetic sequencing and carbon nanotubes helps in unlocking the mysteries of human diseases, particularly for personalized medicine at a faster rate.