Hesaam Esfandyarpour

Gate-Controlled Microfluidic Chamber With Magnetic Bead for DNA Sequencing-by-Synthesis Technology

In this paper we present a novel microfluidic platform for DNA sequencing-by-synthesis methods (e.g. pyrosequencing). The proposed platform is based on the valve-controllable PDMS channel technology with DNA-coated magnetic beads. The encapsulation of the reaction of DNA polymerization in picoliter-sized wells provides for excellent isolation and control for detection. This separation prevents cross-talk amongst neighbor reactors which is one of the most limitations for higher integration of the current technologies. Through application of an external magnetic field the beads can be allocated with better accuracy. In addition this property can help mixing for the reaction. The proposed system is useful for a number of other bio-species detection and sorting templates. This paper illustrates the design and experimental results of a primary template as well as different advantages and potential applications of the Gate-Controlled Magnetic Bead (GCMB) platform in the world of DNA sequencing and genetics.Copyright

Label-free electronic probing of nucleic acids and proteins at the nanoscale using the nanoneedle biosensor

Detection of proteins and nucleic acids is dominantly performed using optical fluorescence based techniques, which are more costly and timely than electrical detection due to the need for expensive and bulky optical equipment and the process of fluorescent tagging. In this paper, we discuss our study of the electrical properties of nucleic acids and proteins at the nanoscale using a nanoelectronic probe we have developed, which we refer to as the Nanoneedle biosensor. The nanoneedle consists of four thin film layers: a conductive layer at the bottom acting as an electrode, an oxide layer on top, and another conductive layer on top of that, with a protective oxide above. The presence of proteins and nucleic acids near the tip results in a decrease in impedance across the sensing electrodes. There are three basic mechanisms behind the electrical response of DNA and protein molecules in solution under an applied alternating electrical field. The first change stems from modulation of the relative permittivity at the interface. The second mechanism is the formation and relaxation of the induced dipole moment. The third mechanism is the tunneling of electrons through the biomolecules. The results presented in this paper can be extended to develop low cost point-of-care diagnostic assays for the clinical setting.

Electrical Detection of Proteins and DNA using Bioactivated Microfluidic Channels: Theoretical and Experimental Considerations

In order to detect diseases like cancer at an early stage while it still may be curable, its necessary to develop a diagnostic technique which can rapidly and inexpensively detect protein and nucleic acid biomarkers, without making any sacrifice in the sensitivity. We have developed a technique, based on the use of bioactivated microfluidic channels integrated with electrodes for electrical sensing, which can be used to detect protein biomarkers, target cells, and DNA hybridization. In this paper, we discuss the theoretical detection limits of this kind of sensor, and also discuss various experimental considerations in the electrical characterization of our device. In particular, we discuss the temperature dependence, the impedance drift, the noise sources, and various methods for optimizing the signal to noise ratio.

Picocalorimetric method for DNA sequencinga)

In this article, the authors present a new method for DNA sequencing based on direct measurement of heat incorporation in the DNA polymerization reaction. This picocalorimetry assay that the authors call thermosequencing is a label-free, direct, and simple technique that enables inexpensive DNA sequencing envisioned to reduce the cost of DNA sequencing by three to four orders of magnitude. The authors discuss some advantages and potentials of this real-time method and its effect on the DNA sequencing market.

Publisher's Note: “Label-free electronic probing of nucleic acids and proteins at the nanoscale using the nanoneedle biosensor” [Biomicrofluidics 7, 044114 (2013)]

[This corrects the article on p. 044114 in vol. 7.].

Structural Optimization of Microfluidic Gate Controlled Magnetic Bead System for DNA Sequencing-by-Synthesis

In this paper we present a structural and geometrical optimization of a microfluidic gate-controlled magnetic bead system for DNA Sequencing by Synthesis technology. To optimize the efficiency of the technology, we designed, fabricated and tested several structures of the GCMB platform. Different designs of the system were created to study the effects of the pressure, structure, geometry, materials, thickness of intermediate layer between flow and control lines; Toward optimization of the system for a better sensing and to concentrate signal (e.g. heat in Thermosequencing [4–9]) into specific regions for detection in the real system, we recommend an optimized modified gated structure for the microfluidic detection platform and show how this new platform could improve the detection efficiency.Copyright