preparation-mica-silicon-substrates-for-dna-origami-analysis

Preparation of Mica and Silicon Substrates for DNA Origami Analysis and Experimentation

The designed nature and controlled, one-pot synthesis of DNA origami provides exciting opportunities in many fields, particularly nanoelectronics. Many of ...

University of Notre Dame

Molecular electronics is commonly conceived as reproducing diode or transistor action at the molecular level. The quantum-dot cellular automata (QCA) approach offers an attractive alternative in which binary information is encoded in the configuration of charge among redox-active molecular sites. The Coulomb interaction between neighboring molecules provides device-device coupling. No current flow between molecules is required. We present an ab initio analysis of a simple molecular system which acts as a molecular QCA cell. The intrinsic bistability of the charge configuration results in dipole or quadrupole fields which couple strongly to the state of neighboring molecules. We show how logic gates can be implemented. We examine the role of the relaxation of nuclear coordinates in the molecular charge reconfiguration.

Molecular quantum-dot cellular automata.

For quantum-dot cellular automata molecular electronic devices, one of the fundamental tasks is to arrange the molecules on a surface in a controlled manner. In this report, we discuss a molecular lift off technique to form nanopatterns toward the development of molecular circuits. In our molecular lift off technique, we use electron beam lithography to form nano-trenches on a polymethylmethacrylate (PMMA) film on a SiO2 wafer. This wafer is soaked in a Creutz-Taube ion [(NH3)5Ru(pyrazine)Ru(NH3)5](o-toluenesulfonate)5 (CT5) aqueous solution. After residual PMMA removal, atomic force microscopy is used to investigate the resulting surface. Thirty-five nanometer CT5 lines are demonstrated on a SiO2 surface. Compared with other molecular nanopatterning techniques, ours is both economical and capable of high-resolution.

A liftoff technique for molecular nanopatterning.

We demonstrate a guided self-assembly approach to the fabrication of DNA nanostructures on silicon substrates. DNA oligonucleotides self-assemble into "rafts" 8 x 37 x 2 nm in size. The rafts bind to cationic SAMs on silicon wafers. Electron-beam lithography of a thin poly(methyl methacrylate) (PMMA) resist layer was used to define trenches, and (3-aminopropyl)triethoxysilane (APTES), a cationic SAM precursor, was deposited from aqueous solution onto the exposed silicon dioxide at the trench bottoms. The remaining PMMA can be cleanly stripped off with dichloromethane, leaving APTES layers 0.7-1.2 nm in thickness and 110 nm in width. DNA rafts bind selectively to the resulting APTES stripes. The coverage of DNA rafts on adjacent areas of silicon dioxide is 20 times lower than on the APTES stripes. The topographic features of the rafts, measured by AFM, are identical to those of rafts deposited on wide-area SAMs. Binding to the APTES stripes appears to be very strong as indicated by "jamming" of the rafts at a saturation coverage of 42% and the stability to repeated AFM scanning in air.

Deposition of DNA rafts on cationic SAMs on silicon [100].

The surface attachment properties of the Creutz-Taube ion, i.e., [(NH(3))(5)Ru(pyrazine)Ru(NH(3))(5)](5+), on both hydrophilic and hydrophobic types of surfaces were investigated using X-ray photoelectron spectroscopy (XPS). The results indicated that the Creutz-Taube ions only bound to hydrophilic surfaces, such as SiO(2) and -OH terminated organic SAMs on gold substrates. No attachment of the ions on hydrophobic surfaces such as -CH(3) terminated organic SAMs and poly(methylmethacrylate) (PMMA) thin films covered gold or SiO(2) substrates was observed. Further ellipsometric, atomic force microscopy (AFM) and time-dependent XPS studies suggested that the attached cations could form an inorganic analog of the self-assembled monolayer on SiO(2) substrate with a "lying-down" orientation. The strong electrostatic interaction between the highly charged cations and the anionic SiO(2) surface was believed to account for these observations. Based on its selective binding property, patterning of wide ( approximately 200 nm) and narrow ( approximately 35 nm) lines of the Creutz-Taube ions on SiO(2) surface were demonstrated through PMMA electron resist masks written by electron beam lithography (EBL).

Selective binding, self-assembly and nanopatterning of the Creutz-Taube ion on surfaces.

We demonstrate immobilization of DNA nanostructures (37 nm x 8 nm) on silicon by a combination of "top-down" fabrication and "bottom-up" self-assembly. Anchor lines and pads were defined using electron beam lithography and a cationic molecular monolayer. Individual DNA nanostructures bind in 85% yield onto the anchor pads and can be washed and imaged in air. The strength of the binding interaction between a DNA nanostructure and its anchor pad is at least -43 kJ/mol.

Guided deposition of individual DNA nanostructures on silicon substrates.

The World Health Organization has called for an effort to eliminate Lymphatic Filariasis (LF) around the world. In regions where the disease is endemic, local production and distribution of medicated salt dosed with diethylcarbamazine (DEC) has been an effective method for eradicating LF. A partner of the Notre Dame Haiti program, Group SPES in Port-au-Prince, Haiti, produces a medicated salt called Bon Sel. Coarse salt is pre-washed and sprayed with a solution of DEC citrate and potassium iodate. Iodine levels are routinely monitored on site by a titrimetric method. However, the factory had no method for monitoring DEC. Critical analytical issues include 1) determining whether the amount of DEC in each lot of Bon Sel is within safe and therapeutically useful limits, 2) monitoring variability within and between production runs, and 3) determining the effect of a common local practice (washing salt before use) on the availability of DEC. This paper describes a novel titrimetric method for analysis of DEC citrate in medicated salt. The analysis needs no electrical power and requires only a balance, volumetric glassware, and burets that most salt production programs have on hand for monitoring iodine levels. The staff of the factory used this analysis method on site to detect underloading of DEC on the salt by their sprayer and to test a process change that fixed the problem.

A low-tech analytical method for diethylcarbamazine citrate in medicated salt.

DNA origami nanopatterning on chemically modified graphene.

Gallium nitride, with a thin passivating layer of Ga2O3, has been functionalized with octadecyltrichlorosilane (OTS) and aminopropyltriethoxysilane (APTES) self-assembled monolayers (SAMs). Water contact angles, atomic force microscopy, and X-ray photoelectron spectroscopy were used for characterization of the bare and functionalized surfaces. The SAMs are stable in acetonitrile, but both the hydrophobic OTS SAM and the hydrophilic APTES SAM completely desorb after 1-24 h of immersion in water and common buffers. The concentration of gallium in solution after a clean GaN chip is immersed in water is consistent with dissolution of roughly one monolayer of interfacial gallium oxide. Dissolution of this oxide layer could account for the loss of SAMs from GaN surfaces.

Loss of siloxane monolayers from GaN surfaces in water.

Reports of low-quality pharmaceuticals have been on the rise in the past decade, with the greatest prevalence of substandard medicines in developing countries, where lapses in manufacturing quality control or breaches in the supply chain allow substandard medicines to reach the marketplace. Here, we describe inexpensive test cards for fast field screening of pharmaceutical dosage forms containing beta lactam antibiotics or combinations of the four first-line antituberculosis (TB) drugs. The devices detect the active pharmaceutical ingredients (APIs) ampicillin, amoxicillin, rifampicin, isoniazid, ethambutol, and pyrazinamide and also screen for substitute pharmaceuticals, such as acetaminophen and chloroquine that may be found in counterfeit pharmaceuticals. The tests can detect binders and fillers such as chalk, talc, and starch not revealed by traditional chromatographic methods. These paper devices contain 12 lanes, separated by hydrophobic barriers, with different reagents deposited in the lanes. The user rubs some of the solid pharmaceutical across the lanes and dips the edge of the paper into water. As water climbs up the lanes by capillary action, it triggers a library of different chemical tests and a timer to indicate when the tests are completed. The reactions in each lane generate colors to form a "color bar code" which can be analyzed visually by comparison with standard outcomes. Although quantification of the APIs is poor compared with conventional analytical methods, the sensitivity and selectivity for the analytes is high enough to pick out suspicious formulations containing no API or a substitute API as well as formulations containing APIs that have been "cut" with inactive ingredients.

Paper analytical devices for fast field screening of beta lactam antibiotics and antituberculosis pharmaceuticals.

CONSPECTUS: Our work on lithographic patterning of DNA nanostructures was inspired by a collaboration on molecular electronic devices known as quantum-dot cellular automata or QCA. QCA is a paradigm for computation in which information is transmitted and processed through the interaction of coupled electrical charges or magnetic dipoles. We began to explore the idea of molecular scale QCA and found that ab initio methods, a thermodynamic Ising model, and larger scale circuit design work suggested that circuits that did computationally interesting things could function at room temperature if made from molecular QCA cells of chemically reasonable design. But how could the QCA cells be patterned to form the complex arrays needed for computationally interesting circuitry, and how could those arrays of molecular circuitry be integrated with conventional electronic inputs and outputs? Top-down methods lacked the spatial resolution and high level of parallelism needed to make molecular circuits. Bottom-up chemical synthesis lacked the ability to fabricate arbitrary and heterogeneous structures tens to hundreds of nanometers in size. Chemical self-assembly at the time could produce structures in the right size scale, but was limited to homogeneous arrays. A potential solution to this conundrum was just being demonstrated in the late 1990s and early 2000s: DNA nanostructures self-assembled from oligonucleotides, whose high information density could handle the creation of arbitrary structures and chemical inhomogeneity. Our group became interested in whether DNA nanostructures could function as self-assembling circuit boards for electrical or magnetic QCA systems. This Account focuses on what we learned about the interactions of DNA nanostructures with silicon substrates and, particularly, on how electron-beam lithography could be used to direct the binding of DNA nanostructures on a variety of functional substrates.

Electron-beam lithography and molecular liftoff for directed attachment of DNA nanostructures on silicon: top-down meets bottom-up.

Paper-based devices serve to address many analytical questions both inside and outside of the laboratory setting. For the first time, yeast is used to construct a whole-cell, paper-based biosensor device. This biologically based paper analytical device (BioPAD) is sensitive to antibiotics in the tetracycline family, and it could potentially address questions of pharmaceutical quality as well as antibiotic contamination in liquids. Our BioPAD can qualitatively discriminate the presence/absence of doxycycline over a range of 30-10,000 μg/mL. In an analysis of a doxycycline dosage form (tablet) commonly used for malaria prophylaxis, BioPADs identified the presence of antibiotic with 92 and 95 % sensitivity, evaluated by eye and computer-assisted image analysis, respectively, with no false positives by either method. BioPADs were found to remain viable for at least 415 days when stored at 4 °C. This research demonstrates the utility of whole yeast cells in paper-based pharmaceutical testing, and it highlights the potential for the development of yeast-based BioPADs to address a range of qualitative analytical questions, especially in low resource settings.

Incorporating yeast biosensors into paper-based analytical tools for pharmaceutical analysis.

A paper test card has been engineered to perform an iodometric titration, an application that requires storage and mixing on demand of several mutually incompatible reagents. The titration is activated when a user applies a test solution to the test card: the dried reagents are reconstituted and combined through a surface-tension-enabled mixing (STEM) mechanism. The device quantifies 0.8-15 ppm of iodine atoms from iodate in aqueous solutions. This is useful, for example, to quantify iodine levels in fortified salt. A blinded internal laboratory validation established the accuracy as 1.4 ppm I and the precision as 0.9 ppm I when the test card was read by newly trained users. Using computer software to process images, the accuracy and precision both improved to 0.9 ppm I. The paper card can also detect substandard β lactam antibiotics using an iodometric back-titration. When used to quantify amoxicillin, good distinction is achieved between solutions that differ by 0.15 mg/mL over a working range of 0-0.9 mg/mL. The test card was designed to meet the World Health Organization ASSURED criteria for use in low resource settings, where laboratory-based analytical procedures are often not available.

Lab on paper: iodometric titration on a printed card.

Carrying out chemical analysis of antimalarials to detect low-quality medications before they reach a patient is a costly venture. Here, we show that a library of chemical color tests embedded on a paper card can presumptively identify formulations corresponding to very low quality antimalarial drugs. The presence or absence of chloroquine (CQ), doxycycline (DOX), quinine, sulfadoxine, pyrimethamine, and primaquine antimalarial medications, in addition to fillers used in low-quality pharmaceuticals, are indicated by patterns of colors that are generated on the test cards. Test card sensitivity for detection of these pure components ranges from 90% to 100% with no false positives in the absence of pharmaceutical. The color intensities from reactions characteristic of CQ or DOX allowed visual detection of formulations of these medications cut with 60% or 100% filler, although samples cut with 30% filler could not be reliably detected colorimetrically. However, the addition of unexpected fillers, even in 30% quantities, or substitute pharmaceuticals, could sometimes be detected by other color reactions on the test cards. Tests are simple and inexpensive enough to be carried out in clinics, pharmacies, and ports of entry and could provide a screening method to presumptively indicate very low quality medicines throughout the supply chain.

Article	Year
Molecular quantum-dot cellular automata. Journal of the American Chemical Society\| PubMed ID: 12537505	2003
A liftoff technique for molecular nanopatterning. Journal of nanoscience and nanotechnology\| PubMed ID: 14598444	2003
Deposition of DNA rafts on cationic SAMs on silicon [100]. Langmuir : the ACS journal of surfaces and colloids\| PubMed ID: 17154616	2006
Selective binding, self-assembly and nanopatterning of the Creutz-Taube ion on surfaces. International journal of molecular sciences\| PubMed ID: 19333420	2009
Guided deposition of individual DNA nanostructures on silicon substrates. Langmuir : the ACS journal of surfaces and colloids\| PubMed ID: 20590122	2010
A low-tech analytical method for diethylcarbamazine citrate in medicated salt. PLoS neglected tropical diseases\| PubMed ID: 21347443	2011
DNA origami nanopatterning on chemically modified graphene. Angewandte Chemie (International ed. in English)\| PubMed ID: 22034171	2012
Loss of siloxane monolayers from GaN surfaces in water. Langmuir : the ACS journal of surfaces and colloids\| PubMed ID: 23534848	2013
Paper analytical devices for fast field screening of beta lactam antibiotics and antituberculosis pharmaceuticals. Analytical chemistry\| PubMed ID: 23725012	2013
Electron-beam lithography and molecular liftoff for directed attachment of DNA nanostructures on silicon: top-down meets bottom-up. Accounts of chemical research\| PubMed ID: 24716716	2014
Incorporating yeast biosensors into paper-based analytical tools for pharmaceutical analysis. Analytical and bioanalytical chemistry\| PubMed ID: 25381614	2015
Lab on paper: iodometric titration on a printed card. Analytical chemistry\| PubMed ID: 25711696	2015
Paper test cards for presumptive testing of very low quality antimalarial medications. The American journal of tropical medicine and hygiene\| PubMed ID: 25897064	2015
Enabling the Development and Deployment of Next Generation Point-of-Care Diagnostics. PLoS neglected tropical diseases\| PubMed ID: 25973602	2015

Marya Lieberman

Biography

JoVE Journal Publications

Other Publications