NanoBioSensor Initiative

纳米生物传感器计划

• 批准号: 7733435
• 负责人: Javed Khan
• 金额: $ 18.13万
• 依托单位: DIVISION OF BASIC SCIENCES - NCI
• 依托单位国家: 美国
• 资助国家: 美国
• 起止时间: 至
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/7733435
• 关键词: Base Pairing; Binding; Carbon; Carbon Nanotubes; Characteristics; Charge; Chemicals; Collaborations; Complementary DNA; Computer software; DNA; DNA Microarray Chip; DNA Microarray format; DNA copy number; Detection; Development; Devices; Diagnosis; Electrodes; Electronics; Exhibits; Fluorescence; Gene Expression Profiling; Genetic Transcription; Genome; High temperature of physical object; Label; Malignant Neoplasms; Measurable; Measurement; Membrane; Messenger RNA; Methodology; Methods; MicroRNAs; Microarray Analysis; Miniaturization; Nanotubes; Nucleic Acid Hybridization; Nucleic Acid Probes; Nucleic Acids; Numbers; Nylons; Oligonucleotide Probes; Oligonucleotides; Operative Surgical Procedures; Optics; Output; Pattern Recognition; Peptide Nucleic Acids; Personal Satisfaction; Photons; Pilot Projects; Process; Property; Purpose; Reporting; Signal Transduction; Silicon; Single-Stranded DNA; Source; System; Techniques; Technology; Testing; Time; Transistors; United States National Aeronautics and Space Administration; Universities; Variant; Vertebral column; base; concept; electric field; inorganic phosphate; locked nucleic acid; metal oxide; multiplex detection; nanobiosensor; nanodevice; nanomaterials; nanowire; nucleic acid detection; size; tool; transcription factor; voltage

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]

DNA 微阵列是强大的工具，可用于高通量监测转录水平的基因表达、确定全基因组 DNA 拷贝数变化、识别转录因子的靶标、测序以及最近用于分析癌症中的微小 RNA (miRNA) 水平。第一个报道的 DNA 微阵列是使用 cDNA 克隆在尼龙膜上制造的，并使用放射性标记的靶标进行检测。此后，许多大规模DNA微阵列平台被开发出来，其中包括双链cDNA、单链短25mer (Affymetrix)、中型30mer (Combimatrix) 或长50-70mer (Nimblegen 或Agilent) 寡核苷酸。所有这些方法都依赖于核酸酶扩增和靶标荧光标记、杂交和信号放大以及随后通过光学扫描仪检测的各种组合。虽然基于荧光的 DNA 微阵列技术已经取得了重大进展，但这些方法通常非常耗时，而且依赖于荧光强度的确定，因此灵敏度受到检测少量光子的能力的限制。为了克服这些障碍，我们提出了一种基于晶体管的高灵敏度系统，用于核酸（NA）杂交的电子检测。该技术类似于微阵列概念，其中每个晶体管都与不同的寡核苷酸相关联，预计在灵敏度、易用性和小型化能力方面将远远超过现有技术。另一个显着优点是所提出的方法不需要对被检测的核酸进行化学或酶操作。在场效应晶体管中，源极和漏极之间的电流与电压特性或跨导很大程度上取决于基极 (B) 端子处积累的总电荷。这种效应很好理解，人们可以根据跨导曲线的测量准确估计基极的电荷量。在基极没有束缚电荷的情况下，如第一幅图所示，在任何电压下都不会流过电流，因此跨导曲线描绘一条水平线。在中间的图中，我们假设单链 DNA 寡聚体固定在碱基上。这将导致磷酸盐主链的净负电荷在底部积聚。由此产生的跨导曲线将表现出与水平线性度的轻微但可测量的偏离。最后，如果单链 DNA 与其互补序列杂交，碱基处将发生净电荷加倍。这将驱动晶体管进入正向偏置的完全运行状态，并产生大幅度和高度非线性的跨导曲线。将开发的主要方法是利用碳纳米管（CNT）的晶体管。与此同时，我们将与 Stephanie Getty 博士和 Gunter Kletetschka 博士（NASA 和天主教大学）合作进行一项试点研究，以开发硅纳米线 (SiNW) 晶体管。两者的工作原理都与硅基金属氧化物场效应晶体管 (MOSFET) 非常相似。值得注意的是，事实证明，碳纳米管具有比硅更高的本征迁移率，因此在用作晶体管时具有更高的电荷灵敏度。这些纳米材料（圆柱体）的几何形状比传统 MOSFET 中使用的平面（板状）几何形状能够更好地聚焦电场，从而提高了纳米器件的灵敏度。然而，CNT 系统面临着电子特性和高温处理方面的纳米管间变化等挑战，而使用 SiNW 可以缓解这些挑战。DNA 微阵列是在转录水平上高通量监测基因表达、确定全基因组 DNA 拷贝数变化、识别转录因子目标、测序以及最近用于分析癌症中微小 RNA (miRNA) 水平的强大工具。第一个报道的 DNA 微阵列是使用 cDNA 克隆在尼龙膜上制造的，并使用放射性标记的靶标进行检测。此后，许多大规模DNA微阵列平台被开发出来，其中包括双链cDNA、单链短25mer (Affymetrix)、中型30mer (Combimatrix) 或长50-70mer (Nimblegen 或Agilent) 寡核苷酸。所有这些方法都依赖于核酸酶扩增和靶标荧光标记、杂交和信号放大以及随后通过光学扫描仪检测的各种组合。虽然基于荧光的 DNA 微阵列技术已经取得了重大进展，但这些方法通常非常耗时，而且依赖于荧光强度的确定，因此灵敏度受到检测少量光子的能力的限制。为了克服这些障碍，我们提出了一种基于晶体管的高灵敏度系统，用于核酸（NA）杂交的电子检测。该技术类似于微阵列概念，其中每个晶体管都与不同的寡核苷酸相关联，预计在灵敏度、易用性和小型化能力方面将远远超过现有技术。另一个显着优点是所提出的方法不需要对被检测的核酸进行化学或酶操作。在场效应晶体管中，源极和漏极之间的电流与电压特性或跨导很大程度上取决于基极 (B) 端子处积累的总电荷。这种效应很好理解，人们可以根据跨导曲线的测量准确估计基极的电荷量。在基极没有束缚电荷的情况下，如第一幅图所示，在任何电压下都不会流过电流，因此跨导曲线描绘一条水平线。在中间的图中，我们假设单链 DNA 寡聚体固定在碱基上。这将导致磷酸盐主链的净负电荷在底部积聚。由此产生的跨导曲线将表现出与水平线性度的轻微但可测量的偏离。最后，如果单链 DNA 与其互补序列杂交，碱基处将发生净电荷加倍。这将驱动晶体管进入正向偏置的完全运行状态，并产生大幅度和高度非线性的跨导曲线。将开发的主要方法是利用碳纳米管（CNT）的晶体管。与此同时，我们将与 Stephanie Getty 博士和 Gunter Kletetschka 博士（NASA 和天主教大学）合作进行一项试点研究，以开发硅纳米线 (SiNW) 晶体管。两者的工作原理都与硅基金属氧化物场效应晶体管 (MOSFET) 非常相似。值得注意的是，事实证明，碳纳米管具有比硅更高的本征迁移率，因此在用作晶体管时具有更高的电荷灵敏度。这些纳米材料（圆柱体）的几何形状比传统 MOSFET 中使用的平面（板状）几何形状能够更好地聚焦电场，从而提高了纳米器件的灵敏度。 CNT 系统 [摘要被截断为 7800 个字符]