NanoBioSensor Initiative

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DNA microarrays are powerful tools for high throughput monitoring of gene expression at the transcription level, determining genome wide DNA copy number changes, identifying targets of transcription factors, sequencing and more recently for profiling the micro RNA (miRNA) levels in cancer. The first reported DNA microarray was fabricated on nylon membranes using cDNA clones and used radioactively labeled targets for detection. Since then, many large-scale DNA microarray platforms have been developed, which includes, double-stranded cDNA, single stranded short 25mers (Affymetrix), mid-sized 30mer (Combimatrix) or long 50-70mers (Nimblegen or Agilent) oligonucleotides. All these methods rely upon various combinations of enzymatic amplification of the nucleic acid and fluorescently labeling of targets, hybridization, and amplification of signal followed by detection by optical scanners. While significant strides have been made in fluorescent-based DNA microarray technology, the methodologies are often time-consuming and in addition rely on the determination of fluorescence intensity and the sensitivity is thus limited by the ability to detect small numbers of photons. To overcome these barriers, we propose a highly sensitive system, based on transistors for the electronic detection of nucleic acid (NA) hybridization. The technique is analogous to the microarray concept, in which each transistor is associated with a distinct oligonucleotide, and is projected to far surpass existing technology in sensitivity, ease of use and in the capability toward miniaturization. Another significant advantage is that the method proposed does not require chemical or enzymatic manipulation of the nucleic acid being detected. In field effect transistors, the current versus voltage characteristics or transconductance between the source and drain electrodes are strongly dependent upon the total charge accumulated at the base (B) terminal. This effect is well understood and one can accurately estimate the amount of charge at the base from measurement of the transconductance curve. In the absence of bound charges at the base, as shown in the first panel, no current will flow at any voltage so that the transconductance curve traces a horizontal line. In the middle panel, we assume that single stranded DNA oligomers are immobilized at the base. This will cause a net negative charge from the phosphate backbone to accumulate at the base. The resulting transconductance curve will exhibit slight but measurable departure from horizontal linearity. Finally, if the single stranded DNA were hybridized with its complementary sequence, a net doubling of charge will occur at the base. This will drive the transistor into forward biased full operation and will produce large amplitude and highly nonlinear transconductance curves. The primary method that will be developed are transistors that utilize carbon nanotubes (CNTs). In parallel, a pilot study will be performed in collaboration with Dr. Stephanie Getty and Dr Gunter Kletetschka (NASA and Catholic University) to develop silicon nanowire (SiNW) transistors. Both operate very similar to silicon based metal oxide field effect transistors (MOSFETS). Notably, it has been shown that CNTs have a higher intrinsic mobility than silicon, leading to much higher charge sensitivity when used as a transistor. The geometry of these nanomaterials (cylinders) can better focus electric field than the planar (planks) geometry used in conventional MOSFETs, adding to the sensitivity of the nanodevice. The CNT system, however, presents challenges such as inter-nanotube variation in electronic properties and high temperature processing, which can be mitigated using SiNWs.DNA microarrays are powerful tools for high throughput monitoring of gene expression at the transcription level, determining genome wide DNA copy number changes, identifying targets of transcription factors, sequencing and more recently for profiling the micro RNA (miRNA) levels in cancer. The first reported DNA microarray was fabricated on nylon membranes using cDNA clones and used radioactively labeled targets for detection. Since then, many large-scale DNA microarray platforms have been developed, which includes, double-stranded cDNA, single stranded short 25mers (Affymetrix), mid-sized 30mer (Combimatrix) or long 50-70mers (Nimblegen or Agilent) oligonucleotides. All these methods rely upon various combinations of enzymatic amplification of the nucleic acid and fluorescently labeling of targets, hybridization, and amplification of signal followed by detection by optical scanners. While significant strides have been made in fluorescent-based DNA microarray technology, the methodologies are often time-consuming and in addition rely on the determination of fluorescence intensity and the sensitivity is thus limited by the ability to detect small numbers of photons. To overcome these barriers, we propose a highly sensitive system, based on transistors for the electronic detection of nucleic acid (NA) hybridization. The technique is analogous to the microarray concept, in which each transistor is associated with a distinct oligonucleotide, and is projected to far surpass existing technology in sensitivity, ease of use and in the capability toward miniaturization. Another significant advantage is that the method proposed does not require chemical or enzymatic manipulation of the nucleic acid being detected. In field effect transistors, the current versus voltage characteristics or transconductance between the source and drain electrodes are strongly dependent upon the total charge accumulated at the base (B) terminal. This effect is well understood and one can accurately estimate the amount of charge at the base from measurement of the transconductance curve. In the absence of bound charges at the base, as shown in the first panel, no current will flow at any voltage so that the transconductance curve traces a horizontal line. In the middle panel, we assume that single stranded DNA oligomers are immobilized at the base. This will cause a net negative charge from the phosphate backbone to accumulate at the base. The resulting transconductance curve will exhibit slight but measurable departure from horizontal linearity. Finally, if the single stranded DNA were hybridized with its complementary sequence, a net doubling of charge will occur at the base. This will drive the transistor into forward biased full operation and will produce large amplitude and highly nonlinear transconductance curves. The primary method that will be developed are transistors that utilize carbon nanotubes (CNTs). In parallel, a pilot study will be performed in collaboration with Dr. Stephanie Getty and Dr Gunter Kletetschka (NASA and Catholic University) to develop silicon nanowire (SiNW) transistors. Both operate very similar to silicon based metal oxide field effect transistors (MOSFETS). Notably, it has been shown that CNTs have a higher intrinsic mobility than silicon, leading to much higher charge sensitivity when used as a transistor. The geometry of these nanomaterials (cylinders) can better focus electric field than the planar (planks) geometry used in conventional MOSFETs, adding to the sensitivity of the nanodevice. The CNT sys [summary truncated at 7800 characters]