Photochemical modification and patterning of SU-8 using anthraquinone photolinkers

Bioactive protein patterns and microarrays achieved by selective localization of biomolecules find various applications in biosensors, bio-microelectromechanical systems (bio-MEMS), and in basic protein studies. In this paper we describe simple photochemical methods to fabricate two-dimensional patterns on a Novolac A derivative polymer (SU-8) and, subsequently, their functionalization with biomolecules. Anthraquinone (AQ) derivatives are used to chemically modify and pattern SU-8 surfaces. Features as small as 20 mum are obtained when using uncollimated light. The X-Y spatial resolution of micropatterned AQ molecules is improved to 1.5 mum when a collimated light source is used. This micropatterning process will be important for the functionalization of MEMS-based biosensors. The method saves several processing steps and can be integrated in cleanroom fabrication thus avoiding contamination of the sensor surfaces.     

Conformational structures and vibrational spectra of isolated pyrimidine nucleosides: Fourier transform infrared matrix isolation study of 2-deoxyuridine

The conformational structures of 2-deoxyuridine (dU) were investigated using Fourier transform infrared (FTIR) matrix isolation spectroscopy. For the first time the FTIR spectra of dU in Ar matrices were obtained in the range 4000-200 cm(-1). The stabilities of conformers were estimated by the methods HF/3-21G (p), HF/6-31G (d,p) and MP2/6-31G (d,p). Ab initio calculations of the infrared spectra were performed by the methods HF/3-21G (p) and HF/6-31G (d,p). The actual occupancy of conformational isomers in matrix samples was determined. It was shown that anti-conformers of dU are dominant. The ribose rings of the main anti-conformers dU _a0, dU _a1 are in the C2'-endo conformation, but the ribose rings of minor anti-conformers dU_a2, dU_a3 have the C3'-endo conformation, stabilized by intramolecular hydrogen bonds O3'H...O5' and O5'H...O3', accordingly. Syn-conformers of dU are stabilized by the intramolecular hydrogen bond O5'H...O2 and the dominant conformation of the ribose ring is C2'-endo.     

Surface Functionalization of Micro Mechanical Cantilever Sensors by Organic Capped TiO2 and Fe2O3 Nanocrystals

A convenient and rapid procedure has been achieved to immobilize densely packed nanoporous 3D arrays of oleic acid (OLEA)-capped rod-shaped TiO₂ nanocrystals (NCs) and nearly spherical Fe₂O₃ NCs on the surface of micro mechanical cantilever sensors on SU-8. The NCs have been immobilized at room temperature and in the dark on the micro cantilevers before their release. AFM, SEM and XPS investigations attest for an effective and attachment of the NCs on the SU-8 which occurs with not modifying the original morphology and chemical composition of the nano-objects allowing for an effective accomplishment of the cantilever fabrication.     

6-Thioguanine luminescence probe to study DNA and low-molecular-weight systems

6-Thioguanine, an antitumor drug, has been tested as a luminescence probe to study DNA and cryoprotector solutions at temperatures between 4.2 and 273 K. The electronic structure of the tautomeric and ionic forms of 6-thioguanine is studied comprehensively both theoretically and experimentally. An excited-state diagram of 6-thioguanine N9H tautomer is proposed. The temperature behavior of 6-thioguanosine is examined in different cryoprotector solutions and with different aggregate states of solvents. Structure and phase transitions in low-molecular-weight cryoprotectors (glycerol, ethanol, propanediol, DMSO) and their water solution are investigated in the 4.2–273 K temperature range. New structural transitions in propanediol-water solutions are found in the temperature interval 10–180 K. DNA solutions are investigated by using 6-thioguanine incorporated in DNA by the method of biosynthesis. Phosphorescence intensity curves for 6-thioguanosine in native DNA manifest peculiarities at 21, 64, 87, 140, 180, and 268 K.     

Effect of Mg2+ Ions on the Stability of PolyA/2PolyU Three-Stranded Helices in Aqueous Solutions

The influence of Mg²⁺, Na⁺ and temperature on the conformational state of three-stranded helical polyA/2polyU (A2U) has been studied by the thermal denaturation method. At Na⁺ concentrations of 0.01–0.1 M , on heating the transition A2U→AU+U (the 3→2 transition) and then AU→A+U transition (the 2→1 transition) are observed. (AU is double helix polyA/polyU; A and U are single-stranded polyA and polyU, respectively.) With 0.01 M and 0.03 M Na⁺ these transitions occur at Mg²⁺ concentrations within (0 ÷ 0.003) M . At these ionic concentrations, there is a narrow temperature region (3 ÷ 5°C) at which double-helical AU formed by the 3→2 transition is resistant to heating. In 0.1 M Na⁺, a rise in the Mg²⁺ concentration leads to a continuous decrease in the temperature range of this region, and above a critical concentration of Mg²⁺ (ca. 3.6×10^–5 M )_cr there is only one transition (the 3→1 transition) instead of the successive transitions 3→2→1. The constants of Mg²⁺ ion association with polyU, polyA and A2U were calculated using equilibrium binding theory. The data obtained helped explain the reasons for the different phase diagrams for A2U + Mg²⁺ complexes in solution at high and low Na⁺ concentrations.     

Electrical characteristics of HTS/manganite double layers

Superconductor/ferromagnetic (SC/FM) Y₁Ba₂Cu₃O_7−δ /La_0.7Sr_0.3MnO₃ (YBCO/LSMO) double layers were prepared on LaAlO₃ substrates by magnetron sputtering and their electrical and microwave parameters were investigated at 77 K. In the theoretical plan, simple formulas for estimation of the sensitivity of the SC surface impedance to the concentration changes of normal charge carriers were proposed and the surface resistance R _S peculiarities of both SC and FM surfaces were described. Thinner YBCO/LSMO structure was characterized by lower SC parameters and higher surface resistance R _S at ∼ 4 GHz. The difference of R _S of sample SC surfaces was interpreted as due to a difference between the normal charge carrier densities in these samples. R _S of the FM surface was higher than that of the SC surface due to the microwave losses of the magnetic subsystem. A peak of the microwave losses, observed in the thicker double layer, was assumed to be caused by uniform FMR in the LSMO film. Presented at 5-th International Conference Solid State Surfaces and Interfaces, November 19–24, 2006, Smolenice Castle, Slovakia.     

Ni2+ Ion Effect of Conformations on Single‐, Double‐ and Three‐Stranded Homopolynucleotides Containing Adenine and Uracil

Differential UV and visible spectroscopy and thermal denaturation were used to study the interaction of Ni²⁺ ions with adenosine 5′‐monophosphate (AMP), uridine 5′‐monophosphate (UMP), single‐stranded polyadenylic acid (polyA) and polyuridylic (polyU), double‐stranded polyA/polyU (AU) and three‐stranded polyA/2 polyU (A2U). The coil → helix transition observed in polyA, AU and A2U at room temperature is induced by Ni²⁺ binding to the oxygen atoms of the phosphate groups which belong to the disordered single‐stranded parts of the polynucleotides. Ni²⁺ ions coordinate with bases only in individual AMP and single‐stranded polyA. This coordination causes disordering of the helical parts of the strands. The disordered single strands form thermally stable compact particles with effective radii of ˜100 Å. Diagrams of the phase equilibrium between single‐, double‐ and three‐stranded conformations as a function of temperature and Ni²⁺ concentration have been obtained. The melting ranges of A2U and AU differ considerably, mainly due to different enthalpies of their helix–coil transitions. The behaviour of the transition parameters in the presence of Ni²⁺ ions agrees with the data obtained from the theory of equilibrium binding. The constants of the Ni²⁺ binding to AU and A2U are found. The effect of Ni²⁺ ions upon the thermal stability of AU and A2U is connected mainly with their different binding to multi‐stranded helices and polyU. The end of melting of the double‐stranded AU formed due to the A2U → AU + U transition has the character of a second‐order phase transition.     

Na+ and Mg2+ ion effect on the stability of a poly I . poly A . poly I triple helix

Differential UV spectroscopy was used to study the temperature dependence of the conformational equilibrium in aqueous poly I . poly A . poly I (A2I) solutions containing Na+ (0.1-2 M) and Mg2+ (10(-5)-0.005 M) ions. Over the whole range of the studied Na+ and Mg2+ concentrations, the heating-induced destruction of the triple A2I helix is actually the A2I --> A + I + I (3 --> 1) transition. The rise of the transition temperature with increasing Na+ and Mg2+ contents is well described by Manning's and the "ligand" theories, which makes it possible to estimate the linear charge density on the single-stranded poly I (xi = 1.9 +/- 0.1) and the Mg2+-A2I binding constant (K = 1,250 M(-1) for the zero degree of binding). An analytical expression has been obtained, which correlates the constants of Mg2+ binding to three- and single-stranded polynucleotides (K3 and K1, respectively) and the linear charge density on them. There are only minor distinctions between the K3 values for A2U and A2I because these polynucleotides have similar structures. The difference in the K1 values is also slight as single-stranded poly U, poly I, and poly A have similar conformations. Dependence of the conformational transition temperatures of two triple helices with changing Mg2+ concentration.