Stretching and unzipping nucleic acid hairpins using a synthetic nanopore

We have explored the electromechanical properties of DNA by using an electric field to force single hairpin molecules to translocate through a synthetic pore in a silicon nitride membrane. We observe a threshold voltage for translocation of the hairpin through the pore that depends sensitively on the diameter and the secondary structure of the DNA. The threshold for a diameter 1.5 < d < 2.3 nm is V > 1.5 V, which corresponds to the force required to stretch the stem of the hairpin, according to molecular dynamics simulations. On the other hand, for 1.0 < d < 1.5 nm, the threshold voltage collapses to V < 0.5 V because the stem unzips with a lower force than required for stretching. The data indicate that a synthetic nanopore can be used like a molecular gate to discriminate between the secondary structures in DNA

Molecular Modeling of Peroxidase and Polyphenol Oxidase: Substrate Specificity and Active Site Comparison

Peroxidases (POD) and polyphenol oxidase (PPO) are enzymes that are well known to be involved in the enzymatic browning reaction of fruits and vegetables with different catalytic mechanisms. Both enzymes have some common substrates, but each also has its specific substrates. In our computational study, the amino acid sequence of grape peroxidase (ABX) was used for the construction of models employing homology modeling method based on the X-ray structure of cytosolic ascorbate peroxidase from pea (PDB ID:1APX), whereas the model of grape polyphenol oxidase was obtained directly from the available X-ray structure (PDB ID:2P3X). Molecular docking of common substrates of these two enzymes was subsequently studied. It was found that epicatechin and catechin exhibited high affinity with both enzymes, even though POD and PPO have different binding pockets regarding the size and the key amino acids involved in binding. Predicted binding modes of substrates with both enzymes were also compared. The calculated docking interaction energy of trihydroxybenzoic acid related compounds shows high affinity, suggesting specificity and potential use as common inhibitor to grape ascorbate peroxidase and polyphenol oxidase

Sustainable Electronics Based on Crop Plant Extracts and Graphene: A “Bioadvantaged” Approach

In today’s fast-paced and well-connected world, consumer electronics are evolving rapidly. As a result, the amount of discarded electronic devices is becoming a major health and environmental concern. The rapid expansion of flexible electronics has the potential to transform consumer electronic devices from rigid phones and tablets to robust wearable devices. This means increased use of plastics in consumer electronics and the potential to generate more persistent plastic waste for the environment. Hence, today, the need for flexible biodegradable electronics is at the forefront of minimizing the mounting pile of global electronic waste. A “bioadvantaged” approach to develop a biodegradable, flexible, and application-adaptable electronic components based on crop components and graphene is reported. More specifically, by combining zein, a corn-derived protein, and aleuritic acid, a major monomer of tomato cuticles and sheellac, along with graphene, biocomposite conductors having low electrical resistance (≈10 Ω sq−1) with exceptional mechanical and fatigue resilience are fabricated. Further, a number of high-performance electronic applications, such as THz electromagnetic shielding, flexible GHz antenna construction, and flexible solar cell electrode, are demonstrated. Excellent performance results are measured from each application comparable to conventional nondegrading counterparts, thus paving the way for the concept of “plant-e-tronics” towards sustainability

Stability and bandwidth investigation of alternative structures for nanopore sensors

The genetic information carriers, DNA molecules can be thought of as the blueprints of living organisms. This crucial functionality of the DNA mole- cules may explain the drive and momentum for DNA sequencing research. The commonly used parallel sequencing methods require extensive sample preparation, long processing times and expensive chemical reagents. In or- der to realize the goal of $1000 genome sequencing, many alternative meth- ods are proposed. One of the most promising technologies among these is nanopore sequencing. Nanopore sequencing involves the threading of a DNA molecule between two electrolytic reservoirs through a nanometer-sized pore on a synthetic or an organic platform by means of electrophoresis and/or mag- netism. During the threading of DNA molecules, various electrical aspects of the bases are investigated. The minimal label-free sample preparation, possibility of parallelizability and high throughput are the factors that make this method a very promising solution for low-cost, robust and fast DNA se- quencing. In the nanopore sequencing eld, the synthetic platforms have the advantage of durability and mass production value due to the existing sili- con device fabrication technologies. This thesis work focuses on the stability and bandwidth investigation of alternative structures for nanopore sensing. Membranes with various thicknesses of Al2O3, Si3N4 and SiO2 stack con gu- rations were fabricated. The fabricated membranes were analyzed and drilled through by focused e-beam sputtering in TEM. The membranes were tested in 0.1 M and 1 M KCl solutions for IV characteristics, noise level and AC response. The membranes with desirable noise and IV characteristics were further tested for DNA sensing purposes. The membranes featuring Al2O3 insulating layer con gurations yielded low noise, high bandwidth and lim- ited durability in KCl solutions. The low yield in DNA sensing in 1 M KCl solutions using these architectures forms the background and motivation for next generation structures for DNA sensing

Nano to Micro Scale Coulter Counters

As biotechnology advances, personalized medicine has become one of the prominent trends. It can be briefly described as an effort to provide preventative, diagnostic and treatment measures for health problems implemented on an individual basis. Resistive pulse technique is a measurement scheme that has found a wide range of applications in this field. In this dissertation, research on devices that are based on resistive pulse technique from nano to micro scale are presented. Nanopore sensing, one of the major candidate technologies for next-generation DNA sequencing is an example of nano-scale application of this technique. It is a promising technology due to its potential to provide label-free, robust and rapid DNA sequencing. However, there are several challenges in reaching this ultimate goal. We present an architecture for solving the aggregate base detection problem through ubiquitous, cost-effective CMOS fabrication. We describe the challenges and advantages of this approach. Beyond DNA sequencing, there are many exciting potential applications of synthetic nanopores, such as sizing and investigating polymer based constructs. Due to its well understood properties, DNA can be used to build functional nano-mechanical structures. However, DNA nano-structures usually lack a robust validation and quality control method, leading to populations that are poorly characterized in terms of shape and size. In this dissertation, the feasibility of utilizing synthetic nanopores to characterize a high volume of DNA nanotubes is investigated. Next, a micro scale application of resistive pulse technique for cancer diagnosis is explored. Particularly, Circulating Tumor Cells(CTCs) have recently emerged as indicators of cancer metastasis. Thus, efficient detection of CTCs can provide non-invasive biopsy, enable personalized medicine and help understand cancer biology. Currently used immunoassay based CTC detection techniques are inefficient and insufficient to classify extremely heterogeneous CTCs such as Circulating Melanoma Cells(CMCs). Cancer cells have markedly different physical attributes, such as size and stiffness, and can be used to distinguish tumor cells from normal cells. We report a micro-fluidic chip potentially meeting the urgent need to detect individual CTCs in a label-free, fast and inexpensive fashion while maintaining cell viability. We present the design, fabrication and modeling of microfluidic channels that enable the classification of CTCs based on their size and stiffness. We use the device was to classify melanoma (MNT1)and breast cancer (MCF-7) cells both alone and in the presence of blood cells

Partial purification and kinetic characterization of mushroom stem polyphenoloxidase and determination of its storage stability in different lyophilized forms

WOS: 000247084000003Monophenolase (1011 +/- 626 U/g AP) and diphenolase activities (5163 +/- 3059 U/g AP) of PPO in acetone powders (APs) of different mushroom stems varied considerably. However, the limited variation of average dipenolase (L-DOPA) to monophenolase (L-tyrosine) activity ratio (5.4 +/- 0.7) in crude extracts showed the homogeneity of PPO from different mushroom stems. The change in extraction material or partial purification method (ammonium sulfate or acetone precipitation) did not affect the temperature stability, temperature and pH dependency and K-m of monophenolase activity considerably. However, some changes were observed in pH stability and substrate specificity of PPO in different parties of mushroom stems. The most important aspects of mushroom stem PPO are its lower diphenolase to monophenolase activity ratio than mushroom cap PPO, low temperature dependency of activity between 25 and 40 degrees C (Ea = 30 kJ/mol), broad optimum pH between 6 and 8, but lack of activity pH <= 5, and ability to use phloridzin as substrate. The mushroom stem PPOs partially purified and lyophilized by using sucrose, dextran or alginate showed moderate to high stability at -18 degrees C for 6-6.5 months. Thus, the mushroom stems obtained as a waste material during mushroom processing may be used as a more homogenous source than whole mushrooms to obtain PPO used for different industrial, clinical or research purposes. (C) 2007 Elsevier Ltd. All rights reserved

Commercially suitable pectin methylesterase from Valencia orange peels [Valencia portakal kabuklari{dotless}ndan ticari olabilecek pektin metilesteraz eldesi]

A simple and effective procedure was developed to extract pectin methylesterase (PME) from Valencia orange peels. Orange peels contain 25-34 µmol of COOH min-1 g-1 of peel PME activity. The enzyme was ionically bound to cell walls and could not be extracted with water. This enables removal of water soluble pectic substances and oils from peels via homogenization and washing with water before enzyme extraction. Enzyme extraction can be conducted simply by addition of suitable amounts of NaCl (optimum: 10 g of NaCl 100 g-1 of extraction mixture) to peel homogenate and stirring (optimum: 30 min at 200 rpm). The PME extracted from orange peels contains almost the same amount of heat-stable and heat-labile fraction, and the enzymes cannot be activated by mild heating. A slight activation of enzyme (almost 20%) was achieved by adding 1 mM CaCl2 to enzyme extracts, but this agent was inhibitory at higher concentrations. The extracts stabilized by Na-benzoate and K-sorbate maintained more than 90% of their PME activity at 4 °C for at least 5 months. The obtained PME was successfully used to prepare low-methoxyl citrus pectin used in edible film formation in the presence of CaCl2. This study shows the potential of using Valencia orange peels as a source of commercial PME. © TÜBİTAK

TRACE-METAL CHARACTERIZATION OF AIRBORNE PARTICLES FROM THE NORTHEASTERN MEDITERRANEAN

Data from 24 airborne dust samples collected on a land-based atmospheric collection tower at the southeastern coast of Turkey and analyzed for Al, Fe, Mn, Cr, Ni, V, Co, Na, Ca, Mg, Zn, Pb and Cd are presented

Transport of heavy metals within a two-layered system: the Marmara-Mediterranean-Black Seas system

The concentration of heavy metals (Zn, Cy Ni, Cr, Cd, and Hg) in sea water was determined along the Turkish Straits (Dardanelles and Bosphorus) and in the Marmara Sea. The concentrations are ranging between 13.26-144.9 mu g/L for Zn, 0.23-0.77 mu g/L for Cu, 0.41-5.42 mu g/L for Ni, 0.26-2.56 mu g/L for Cr, 0.67-12.67 ng/L for Cd and 2.0-5.3 ng/L for Hg