Synthesis of "Porphyrin-linker-Thiol" molecules with diverse linkers for studies of molecular-based information storage

The attachment of redox-active molecules such as porphyrins to an electroactive surface provides an attractive approach for electrically addressable molecular-based information storage. Porphyrins are readily attached to a gold surface via thiol linkers. The rate of electron transfer between the electroactive surface and the porphyrin is one of the key factors that dictates suitability for molecular-based memory storage. This rate depends on the type and length of the linker connecting the thiol unit to the porphyrin. We have developed different routes for the preparation of thiol-derivatized porphyrins with eight different linkers. Two sets of linkers explore the effects of linker length and conjugation, with one set comprising phenylethyne units and one set comprising alkyl units. One electron-deficient linker has four fluorine atoms attached directly to a thiophenyl unit. To facilitate the synthesis of the porphyrins, convenient routes have been developed to a wide range of aldehydes possessing a protected S-acetylthio group. An efficient synthesis of 1-(S-acetylthio)-4-iodobenzene also has been developed. A set of porphyrins, each bearing one S-acetyl-derivatized linker at one meso position and mesityl moieties at the three remaining meso positions, has been synthesized. Altogether seven new aldehydes, eight free base porphyrins and eight zinc porphyrins have been prepared. The zinc porphyrins bearing the different linkers all form self-assembled monolayers (SAMs) on gold via in situ cleavage of the S-acetyl protecting group. The SAM of each porphyrin is electrochemically robust and exhibits two reversible oxidation waves.

Synthesis of thiol-derivatized porphyrin dimers and trimers for studies of architectural effects on multibit information storage

We present the rational design and synthesis of multiporphyrin arrays containing thiol-derivatized linkers for the purpose of multibit molecular information storage. Porphyrin dimers and trimers were synthesized by the Pd-mediated coupling of iodo-substituted and ethynyl-substituted porphyrin building blocks in 5-51% yields. Each porphyrin dimer bears one S-acetylthio group. The architecture of the trimers incorporates a trans-substituted porphyrin (central) bearing two S-acetylthio groups and two diphenylethyne-linked porphyrins (wings) in a trans geometry. The central porphyrin and the wing porphyrins bear distinct substituents and central metals, thereby affording different oxidation potentials. The S-acetylthio groups provide a means for attachment of the arrays to an electroactive surface. The dimers are designed for vertical orientation on an electroactive surface while the trimers are designed for horizontal orientation of the central porphyrin. Altogether seven different arrays were synthesized. Each array forms a self-assembled monolayer (SAM) on gold via in situ cleavage of the S-acetyl protecting group. The SAM of each array is electrochemically robust and exhibits multiple, reversible oxidation waves. In general, however, the trimeric arrays appear to form more highly ordered monolayers that exhibit sharper, better-defined redox features.

Laser interference pattern ablation of a carbon fiber microelectrode: biosensor signal enhancement after enzyme attachment.

Fluorescence microscopy was used to visualize the accumulated fluorescent product of the enzyme alkaline phosphatase to indicate where active covalently bound enzyme remained on the surface after application of a Nd: YAG laser interference pattern to a surface that was first globally derivatized with the covalently bound enzyme. The electrochemical kinetics of the same carbon fiber surface were examined through the electrogenerated chemiluminescence of Ru(bpy)(3)2+ to determine that electron-transfer sites were indeed segregated from the enzyme-binding sites. The enzyme-derivatized areas are determined to be separate and distinct from the areas of enhanced electron transfer. Two other enzymes, glucose oxidase and malic dehydrogenase, were then covalently bound to carbon fiber microelectrode surfaces in order to verify the change in detection limit of their respective cofactors, NADH or H2O2, under a variety of surface conditions. The S/N of an enzyme-modified electrode after laser interference pattern photoablation and electrocatalytic treatment is improved by more than 1 order of magnitude over that observed at an electrode that is globally enzyme modified.

Segregation of micrometer-dimension biosensor elements on a variety of substrate surfaces.

With the rapid development of micro total analysis systems and sensitive biosensing technologies, it is often desirable to immobilize biomolecules to small areas of surfaces other than silicon. To this end, photolithographic techniques were used to derivatize micrometer-sized, spatially segregated biosensing elements on several different substrate surfaces. Both an interference pattern and a dynamic confocal patterning apparatus were used to control the dimensions and positions of immobilized regions. In both of these methods, a UV laser was used to initiate attachment of a photoactive biotin molecule to the substrate surfaces. Once biotin was attached to a substrate, biotin/avidin/biotin chemistry was used to attach fluorescently labeled or nonlabeled avidin and biotinylated sensing elements such as biotinylated antibodies. Dimensions of 2-10 microm were achievable with these methods. A wide variety of materials, including glassy carbon, quartz, acrylic, polystyrene, acetonitrile-butadiene-styrene, polycarbonate, and poly(dimethylsiloxane), were used as substrates. Nitrene- and carbene-generating photolinkers were investigated to achieve the most homogeneous films. These techniques were applied to create a prototype microfluidic sensor device that was used to separate fluorescently labeled secondary antibodies.

Development of sub-micron patterned carbon electrodes for immunoassays.

Sub-micron sized domains of a carbon surface are derivatized with antibodies using biotin/avidin technology. These sites are spatially-segregated from, and directly adjacent to, electron transfer sites on the same electrode surface. The distance between these electron transfer sites and enzyme-loaded domains are kept to a minimum (e.g. less than a micron) to maintain the high sensitivity required for the measurement of enzyme-linked cofactors in an enzyme-linked immunoassay (ELISA). This is accomplished through the use of photolithographic attachment of photobiotin using an interference pattern from a UV laser generated at the electrode surface. This allows the construction of microscopic arrays of active ELISA sites on a carbon substrate while leaving other sites underivatized to facilitate electron transfer reactions of redox mediators; thus maximizing sensitivity and detection of the enzyme mediator. The carbon electrode surface is characterized with respect to its chemical structure and electron transfer properties following each step of the antibody immobilization process. The characterization of specific modifications of micron regions of the carbon surface requires analytical methodology that has both high spatial resolution and sensitivity. We have used fluorescence microscopy with a cooled CCD imaging system to visualize the spatial distribution of enzyme immobilization sites (indicated by fluorescence from Texas-Red labeled antibody) across the carbon surface. The viability of the enzyme attached to the surface in this manner was demonstrated by imaging the distribution of an insoluble, fluorescent product.

A laser ablation method for the spatial segregation of enzyme and redox sites on carbon fiber microelectrodes.

A laser-generated interference pattern was used to remove enzyme from micrometer-wide stripes on an enzyme-covered carbon fiber microelectrode surface to create regions of facile electron transfer. Fluorescence microscopy was used to visualize fluorophore-tagged enzyme to indicate where the adsorbed enzyme remained on the surface. The electrochemical kinetics of the carbon fiber surface were examined to see if electron-transfer sites could indeed be segregated from enzyme adsorbed across the entire surface. CCD imaging of the electrochemical luminescence of Ru(bpy)3(2+) was used to verify the segregation between photoablated sites (with facile electron-transfer kinetics) and surfaces with adsorbed enzyme (which exhibit slow electron-transfer kinetics). The laser-ablated surface could also be distinguished from the enzyme-covered carbon surface with atomic force microscopy. Thus, photoablation of the surface of a protein-covered carbon fiber microelectrode with an interference pattern generated by a Nd:YAG laser allows the activation of 1.7-micron-wide bands of the electrode surface (available for facile electron transfer) while leaving 2.6-micron-wide enzyme-modified areas intact, thereby producing electroactive regions directly adjacent to enzyme modified regions of the same surface.

Electron transfer kinetics at a biotin/avidin patterned glassy carbon electrode.

Photolithographic techniques using a laser interference pattern were used to attach photobiotin to micron-sized stripes on the surface of a carbon electrode. Fluorophore-tagged avidin was attached to this spatially-patterned biotin with essentially no loss in spatial resolution. The kinetics of the glassy carbon surface were examined to see if electron transfer sites could indeed be segregated from the attachment sites of photobiotin-immobilized avidin. The ECL of luminol and SECM were used to verify the segregation between underivatized sites (which exhibit normal electron transfer kinetics) and extensively derivatized biotin/avidin surfaces (which presumably exhibit slow electron transfer kinetics). Both techniques were found to be capable of differentiating the protein-covered surface from bare carbon with sufficient resolution to tell whether a significant portion of the carbon surface is still active and available to detect the product of an enzyme generated analyte. These results indicate that extensive biotin/avidin derivatization of the surface does decrease the electron transfer rate of a carbon electrode, and that the photolithographic approach was able to modify specific sections of the electrode surface, while leaving other regions untouched and available for facile electron transfer. This leads to a more general protocol for the construction of enzyme-based biosensors which utilize diffusable mediators.

Generation of biotin/avidin/enzyme nanostructures with maskless photolithography.

Micrometer-sized domains of a carbon surface are modified to allow derivatization to attach redox enzymes with biotin/avidin technology. These sites are spatially segregated from and directly adjacent to electron transfer sites on the same electrode surface. The distance between these electron transfer sites and enzyme-loaded domains must be kept to a minimum (e.g., less than 5 microns) to maintain the fast response time and high sensitivity required for the measurement of neurotransmitter dynamics. This is accomplished through the use of photolithographic attachment of photobiotin using an interference pattern from a UV laser generated at the electrode surface. This will allow the construction of microscopic arrays of active enzyme sites on a carbon fiber substrate while leaving other sites underivatized to facilitate electron transfer reactions of redox mediators, thus maximizing enzyme activity and detection of the enzyme mediator. The ultimate sensitivity of these sensors will be realized only through careful characterization of the carbon electrode surface with respect to its chemical structure and electron transfer properties following each step of the enzyme immobilization process. The characterization of specific modifications of micrometer regions of the carbon surface requires analytical methodology that has both high spatial resolution and sensitivity. We have used fluorescence microscopy with a cooled CCD imaging system to visualize the spatial distribution of enzyme immobilization sites (indicated by fluorescence from Texas Red-labeled avidin) across the carbon surface. The viability of the enzyme attached to the surface in this manner was demonstrated by imaging the distribution of an insoluble, fluorescent product. An atomic force microscope was used to obtain high-resolution images that probe the heterogeneity of the enzyme sites.

Nucleic-acid immobilization, recognition and detection at chronopotentiometric DNA chips.

Wide-scale DNA testing requires the development of fast, small, easy-to-use biosensing devices. Various synthetic oligonucleotides and DNA have thus been immobilized onto microfabricated thick-film carbon transducers for performing several new nucleic-acid assay protocols. These include hybridization detection of nucleic acid sequences, determination of small molecules (drugs, pollutants) based on their collection into the dsDNA layer or via monitoring their effect upon the intrinsic DNA oxidation signal, and direct adsorptive stripping measurements of ultratrace levels of nucleic acids. Transduction of these DNA recognition processes is accomplished by a new highly-sensitive constant-current stripping chronopotentiometric operation. Comparison to traditional electrodes indicates that the biosensing performance is not compromised by the use of mass-producible disposable transducers. Such thick-film DNA biosensors have been coupled to a compact, user-friendly, hand-held analyzer. Applicability for the detection of sequences from M. tuberculosis and HIV-1 DNAs is illustrated. Such activity in the author's laboratory, aimed at developing DNA-coated screen-printed electrodes, is reviewed.

DNA electrochemical biosensor for the detection of short DNA sequences related to the human immunodeficiency virus.

An electrochemical biosensor for the detection of short DNA sequences related to the human immunodeficiency virus type 1 (HIV-1) is described. The sensor relies on the immobilization and hybridization of the 21- or 42-mer single-stranded oligonucleotide from the HIV-1 U5 long terminal repeat (LTR) sequence at carbon paste or strip electrodes. The extent of hybridization between the complementary sequences is determined by the enhancement of the chronopotentiometric peak of the Co(phen)3(3+) indicator. Numerous factors affecting the probe immobilization, target hybridization, and indicator binding reactions are optimized to maximize the sensitivity and speed the assay time. A detection limit of 4 x 10(-9) M HIV-1 U5 LTR segment is reported following a 30 min hybridization. The hybridization biosensor format obviates the use of radioisotopes common in radioactive methods for the detection of HIV-1 DNA. We also report on the direct adsorptive chronopotentiometric stripping measurements of trace levels of various HIV-1 DNAs.

DNA biosensor for the detection of hydrazines.

A double-stranded (ds) DNA-coated carbon paste electrode is employed as a remarkably sensitive biosensor for the detection of hydrazine compounds. The sensor relies on monitoring changes in the intrinsic anodic response of the surface-confined DNA resulting from its interaction with hydrazine compounds and requires no label or indicator. Short reaction times (1-10 min) are sufficient for monitoring part-per-billion levels of different hydrazines. Applicability to untreated natural water samples is illustrated. The response mechanism is discussed, along with prospects of using DNA biosensors for quantitaing other important molecules and elucidating DNA interactions and damage.