An efficient binding chemistry for glass polynucleotide microarrays.

A variety of methods have been described for making synthetic polynucleotide microarrays. These include in situ synthesis directly on the array surface, for example, by photolithography or ink-jet printing technologies, and the application of presynthesized polynucleotides that are derivatized with various nucleophiles or electrophiles. In the latter case, a variety of surface chemistries have been developed, and several are available commercially. These chemistries must be compatible with nanoliter-scale volumes of polynucleotide reagents, which contact the array over a small portion of their surface. We reasoned that a three-dimensional polymer coating could potentially offer greater surface contact and higher binding efficiency. Here we describe a polyethylenimine-based coating chemistry that provides exceptional binding and hybridization characteristics. In our preferred process, size-fractionated polyethylenimine polymers are cross-linked onto an aminopropylsilanated glass surface in the presence of cyanuric chloride. The resulting three-dimensional coating binds polynucleotides through a mixture of covalent and noncovalent interactions as evidenced by comparisons between 5'-aminoalkyl modified and unmodified polynucleotides. Binding and hybridization comparisons are presented including analogous two-dimensional electrophilic and electrostatic chemistries.     

Optimizing the immobilization of single-stranded DNA onto glass beads

The attachment of single-stranded DNA to a solid support has many biotechnology and molecular biology applications. This paper compares different immobilization chemistries to covalently link single-stranded DNA (20 base pairs), oligo(1), onto glass beads via a 5'-amino terminal end. Immobilization methods included a one-step 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide (EDC) and a two-step EDC reaction to succinylated and PEG-modified glass beads. The third method used 1,4-phenylene diisothiocyanate to immobilize oligo(1) to aminopropyl glass beads. The influence of coupling buffer, oligo(1) concentration, and EDC concentration was also investigated. The one-step EDC-mediated procedure with succinylated or PEG-modified beads in 0.1 M MES buffer, pH 4.5, resulted in the highest immobilization efficiency, 82-89%. EDC concentrations greater than 50 mM and oligo(1) concentrations of 3 microg/g bead were required for effective immobilization. A complementary oligonucleotide, oligo(2), was able to hybridize to the immobilized oligo(1) with a 58% efficiency. This oligonucleotide was subsequently released at 70 degrees C. The relationship between the surface density of oligo(1) and the hybridization efficiency of the complementary oligonucleotide is described.     

Fabrication of DNA microarrays using unmodified oligonucleotide probes

Microarrays printed on glass slides are often constructed by covalently linking oligonucleotide probes to a derivatized surface. These procedures typically require relatively expensive amine- or thiol-modified oligonucleotide probes that add considerable expense to larger arrays. We describe a system by which unmodified oligonucleotide probes are bound to either nonderivatized or epoxy-silane-derivatized glass slides. Biotinylated PCR products are heat denatured, hybridized to the arrays, and detected using an enzymatic amplification system. Unmodified probes appear to detach from the slide surface at high pH (> 10.0), suggesting that hydrogen bonding plays a significant role in probe attachment. Regardless of surface preparation, high temperature (up to 65 degrees C) and low ionic strength (deionized water) do not disturb probe attachment; hence, the fabrication method described here is suitable for a wide range of hybridization stringencies and conditions. We illustrate kinetics of room temperature hybridizations for probes attached to nonderivatized slides, and we demonstrate that unmodified probes produce hybridization signals equal to amine-modified, covalently bound probes. Our method provides a cost-effective alternative to conventional attachment strategies that is particularly suitable for genotyping PCR products with nucleic acid microarrays.     

Assay of adenylate cyclase by use of polyacrylamide-boronate gel columns

A method is described for covalent attachment of up to 1.1 mmol of m-aminobenzeneboronic acid/g dry weight of polyacrylamide beads. Small (4 ml) columns of the derivatized beads have been used to separate quantitatively cyclic AMP from ATP in a single-step procedure. Columns of the polyacrylamide-boronate gel have been used as the basis of a convenient new assay of the soluble adenylate cyclase prepared from nuclei of Physarum polycephalum.     

Assessment of methods for covalent binding of nucleic acids to magnetic beads, Dynabeads, and the characteristics of the bound nucleic acids in hybridization reactions.

Dynabeads are magnetic monosized beads with high stability, high uniformity, unique paramagnetic properties, low particle-particle interaction, and high dispersibility. Different reactive groups; hydroxyl, carboxyl and amino groups can be attached to the surface. Several methods for covalent attachment of DNA or oligonucleotides to the beads were investigated. Best coupling yields were obtained by carbodiimide-mediated end-attachment of 5'-phosphate and 5'-NH2 modified nucleic acids to respectively amino and carboxyl beads. The carboxyl beads showed a low degree of non-specific binding, while a better yield of end-attached nucleic acids was obtained using the amino beads. The DNA-beads worked efficiently in hybridization experiments, and the kinetics of hybridization approach those of solution hybridization.     

Factors affecting cell attachment, spreading, and growth on derivatized microcarriers. I. Establishment of working system and effect of the type of the amino-charged groups

A working system for studying the effects of factors involved in the chemical nature of microcarriers on cell attachment, spreading, and growth was established. The system is based on polyacrylamide beads, prepared by the emulsion polymerization technique. Sieved beads of desirable mean diameter were derivatized to generate controlled amounts of primary and tertiary amino groups. These microcarriers were used for the propagation of four different cell strains: BHK, MDCK, CEF, and MRC-5. It was found that BHK cells attach and spread significantly faster on primary amino-derivatized beads than those with tertiary amino groups, and at a lower degree of charging. Cell yields of MDCK cells (with pronounced epithelial morphology) propagated on primary amino-derivatized beads were higher than that obtained for the tertiary amino-derivatized microcarriers. On the other hand, CEF and MRC-5 cells (with pronounced fibroblast morphology) achieved higher cell yields on the tertiary amino-derivatized microcarriers.     

Phosphomannosyl-derivatized beads detect a receptor involved in lymphocyte homing

Recirculating lymphocytes initiate extravasation from the blood stream by binding to specialized high endothelial venules (HEV) within peripheral lymph nodes (PN) and other secondary lymphoid organs. We have previously reported that lymphocyte attachment to PN HEV is selectively inhibited by mannose-6-phosphate (M6P) and related carbohydrates (Stoolman, L. M., T. S. Tenforde, and S. D. Rosen, 1984, J. Cell Biol., 99:1535-1540). In the present study, we employ a novel cell-surface probe consisting of fluorescent beads derivatized with PPME, a M6P-rich polysaccharide. PPME beads directly identify a carbohydrate-binding receptor on the surface of mouse lymphocytes. In every way examined, lymphocyte attachment to PPME beads (measured by flow cytofluorometry) mimics the interaction of lymphocytes with PN HEV (measured in the Stamper-Woodruff in vitro assay): both interactions are selectively inhibited by the same panel of structurally related carbohydrates, are calcium-dependent, and are sensitive to mild treatment of the lymphocytes with trypsin. In addition, thymocytes and a thymic lymphoma, S49, bind poorly to PPME beads in correspondence to their weak ability to bind to HEV. When the S49 cell line was subjected to a selection procedure with PPME beads, the ability of the cells to bind PPME beads, as well as their ability to bind to PN HEV, increased six- to eightfold. We conclude that a carbohydrate-binding receptor on mouse lymphocytes, detected by PPME beads, is involved in lymphocyte attachment to PN HEV.     

High-performance liquid chromatography of proteins on deformed nonporous agarose beads: immuno-affinity chromatography, exemplified with human growth hormone as ligand and a combination of ethylene glycol and salt for desorption of the antibodies

An affinity chromatography column packed with nonporous agarose beads derivatized with human growth hormone via carbonyldiimidazol was used for the purification of antibodies against human growth hormone from antiserum. Desorption with 1 M sodium chloride in 60% ethylene glycol at pH 9.8 gave 100% total recovery of the antibodies, as measured by radioimmunoassay. The adsorption/desorption process is discussed in terms of hydrophobic and electrostatic interaction (these interactions may be involved in the bond between antibody and antigen in a cooperative fashion). The binding capacity of the column was estimated at about 50 micrograms of antibodies per gram sedimented agarose beads.     

Differential adhesion of microspheres mediated by DNA hybridization I: experiment

We have developed a novel method to study collective behavior of multiple hybridized DNA chains by measuring the adhesion of DNA-coated micron-scale beads under hydrodynamic flow. Beads coated with single-stranded DNA probes are linked to surfaces coated with single target strands through DNA hybridization, and hydrodynamic shear forces are used to discriminate between strongly and weakly bound beads. The adhesiveness of microspheres depends on the strength of interaction between DNA chains on the bead and substrate surfaces, which is a function of the degree of DNA chain overlap, the fidelity of the match between hybridizing pairs, and other factors that affect the hybridization energy, such as the salt concentration in the hybridization buffer. The force for bead detachment is linearly proportional to the degree of chain overlap. There is a detectable drop in adhesion strength when there is a single base mismatch in one of the hybridizing chains. The effect of single nucleotide mismatch was tested with two different strand chemistries, with mutations placed at several different locations. All mutations were detectable, but there was no comprehensive rule relating the drop in adhesive strength to the location of the defect. Since adhesiveness can be coupled to the strength of overlap, the method holds promise to be a novel methodology for oligonucleotide detection.     

Attachment of marine sponge cells of Hymeniacidon perleve on microcarriers

Toward the development of an in vitro cultivation of marine sponge cells for sustainable production of bioactive metabolites, the attachment characteristics of marine sponge cells of Hymeniacidon perleve on three types of microcarriers, Hillex, Cytodex 3, and glass beads, were studied. Mixed cell population and enriched cell fractions of specific cell types by Ficoll gradient centrifugation (6%/8%/15%/20%) were also assessed. Cell attachment ratio (defined as the ratio of cells attached on microcarrier to the total number of cells in the culture) on glass beads is much higher than that on Cytodex 3 and Hillex for both mixed cell population and cell fraction at Ficoll 15-20% interface. The highest attachment ratio of 41% was obtained for the cell fraction at Ficoll 15-20% interface on glass beads, which was significantly higher than that of a mixed cell population (18%). The attachment kinetics on glass beads indicated that the attachment was completed within 1 h. Cell attachment ratio decreases with increase in cell-to-microcarrier ratio (3-30 cells/bead) and pH (7.6-9.0). The addition of serum and BSA (bovine serum albumin) reduced the cell attachment on glass beads.     

Immunoassays and sequence-specific DNA detection on a microchip using enzyme amplified electrochemical detection

A CMOS fabricated silicon microchip was used as a platform for immunoassays and DNA synthesis and hybridization. The chip is covered with a biofriendly matrix wherein the chemistries occur. The active silicon chip has over 1000 active electrodes that can be individually addressed for both synthesis of DNA and protein attachment to a membrane on the chip surface. Additionally, the active chip can be further used for the detection of various analytes at the chip surface via digital read out resulting from the redox enzymes on the captured oligonucleotide or antibody.     

X-ray micro analyses of cations (Na, K, Ca) and anions (S, P, Cl) in uterine secretions during blastocyst implantation in the rat

The mass changes of sodium, potassium, and calcium ions in the rat uterine secretion at blastocyst delay, activation, and attachment have been estimated with X-ray microanalyses of samples of uterine secretions absorbed by small Sephadex beads. A quantification of the ions was attempted by using a standardized coat of gold on the beads as a reference element for normalization of the ion peaks and by fitting the normalized values into corresponding linear regression equations obtained from measurements of step-wise dilutions of a control rat serum. The concentrations of sodium observed at delay, activation, and attachment were 117, 201, and 203 mEq/l, respectively, and those of potassium were 6, 18, and 19 mEq/l, respectively. Calcium values were about 2 mEq/l and decreased at attachment. Among the anions, only the chloride concentration increased at activation and attachment.     

High-Performance Liquid Chromatography of Proteins on Deformed Nonporous Agarose Beads. Affinity Chromatography of Dehydrogenases Based on Cibacron Blue-Derivatized Agarose

Nonporous agarose beads, prepared by shrinkage and cross-linking in organic solvents, were derivatized with Cibacron Blue F3G-A. A compressed bed of these beads was used for purification of dehydrogenases (glucose-6-phosphate dehydrogenase, lactate dehydrogenase and alcohol dehydrogenase). The chromatographic conditions for the purification of glucose-6-phosphate dehydrogenase were optimized by varying the pH of the buffer; the concentrations of eluting agents, i.e. NADP (specific elution) and sodium chloride (nonspecific elution); flow rate; residence time of the protein on the column bed; and protein load. Specific elution with NADP (2 mM in 0.025 M Tris-HCl, pH 8.0) gave the highest recovery (140%) and highest purification factor (200-fold) of the enzyme. The ability of the compressed bed of nonporous agarose beads to tolerate high flow rates was essential, since the recovery of the enzyme activity increased with an increase in flow rate.     

High-performance liquid chromatography of proteins on deformed nonporous agarose beads. Affinity chromatography of dehydrogenases based on cibacron blue-derivatized agarose

Nonporous agarose beads, prepared by shrinkage and cross-linking in organic solvents, were derivatized with Cibacron Blue F3G-A. A compressed bed of these beads was used for purification of dehydrogenases (glucose-6-phosphate dehydrogenase, lactate dehydrogenase and alcohol dehydrogenase). The chromatographic conditions for the purification of glucose-6-phosphate dehydrogenase were optimized by varying the pH of the buffer; the concentrations of eluting agents, i.e. NADP (specific elution) and sodium chloride (nonspecific elution); flow rate; residence time of the protein on the column bed; and protein load. Specific elution with NADP (2 mM in 0.025 M Tris-HCl, pH 8.0) gave the highest recovery (140%) and highest purification factor (200-fold) of the enzyme. The ability of the compressed bed of nonporous agarose beads to tolerate high flow rates was essential, since the recovery of the enzyme activity increased with an increase in flow rate.     

Laminin-2/4 from human placenta is a better adhesion agent for primary keratinocytes than laminin-1 from EHS sarcoma

A comparison of the adhesion of human primary keratinocytes to laminin-1 from murine EHS sarcoma and laminin-2/4 from human placenta was carried out using two methods, cell adhesion to substrates covered with the laminin isoforms, and interaction of keratinocytes from suspension with latex beads coated with the proteins. Laminin-2/4 was considerably more potent as a promoter of attachment of primary human keratinocytes than laminin-1 (and fibronectin), with increased attachment of cells correlating well with the number of latex bead binding sites. Only small cells of diameter of less than 20 microm bound more than 5 beads. Staining of keratinocytes with involucrin antibodies confirmed the existence of an inverse relationship between laminin-2/4-coated bead binding and differentiation.     

Structural transitions of soluble and immobilized chymotrypsinogen A in urea and guanidinium chloride as measured by fluorescence

A cylindrical flow-through quartz cell was designed for measuring fluorescence changes associated with structural transitions in proteins immobilized by covalent attachment to insoluble matrices. Chymotrypsinogen A was immobilized by covalent attachment to derivatized porous glass beads. Conformational transitions in both native, soluble chymotrypsinogen and glass-bound chymotrypsinogen were assessed from fluorescence emission spectra obtained in 0 to 8 m urea and in 0 to 7 m guanidinium chloride. Evidence for the complete reversibility of such transitions in this zymogen was provided by comparing spectra generated by the native zymogen exposed to a given concentration of denaturant with spectra recorded for a mixture of the native zymogen and completely denatured zymogen at the same final concentration of denaturant. The observed transition appeared to follow a two-state mechanism. First order kinetics of unfolding and of refolding were observed in the transition region of the immobilized protein by monitoring fluorescence changes after rapidly adjusting the concentration of denaturant; apparent first order rate constants at pH 7 and 25 °C averaged 0.016 min^?1. Neither the chemistry of the immobilization reactions nor the microenvironment of the surface appears to affect the stability of the native zymogen or the refolding of denatured chymotrypsinogen. Thus, it appears that immobilization of proteins can provide a means for investigating conformational transitions which, due to such complicating secondary reactions as protein-protein interactions and autolysis, cannot otherwise be examined.     

Design and synthesis of polyacrylamide-based oligonucleotide supports for use in nucleic acid diagnostics.

Polyacrylamide supports, in a range of pore sizes, were investigated as nucleic acid affinity matrices for the detection of target DNA or RNA sequences using a sandwich hybridization format. Bromoacetyl and thiol oligonucleotide derivatives were covalently linked to sulfhydryl- and bromoacetyl-polyacrylamide supports with greater than 95% end-attachment efficiencies. These polyacrylamide-oligonucleotide supports were further derivatized with anionic residues to provide multi-functional supports which show low non-specific binding for non-complementary nucleic acids. While all the polyacrylamide-oligonucleotide supports capture complementary oligonucleotides with high affinity, the pore size was found to be a critical parameter in sandwich hybridization reactions. The superior hybridization characteristics of the Trisacryl support was ascribed to a combination of its macroporous nature, hydrophilicity and the terminal attachment of its capture oligonucleotides.     

Cyclodextrin-polyethylenimine conjugates for targeted in vitro gene delivery

Many human gene therapies will require cell-specific targeting. Though recombinant viruses are much more efficient than nonviral vectors, the latter, especially polymers, have the advantage of being targetable via conjugation of cell-specific ligands, including sugars, peptides, and antibodies, which can be covalently attached to the polymer using a variety of chemistries. Cyclodextrin, which forms inclusion complexes with small hydrophobic molecules, has been incorporated into a gene-delivery polymer and may provide a facile and versatile attachment site for targeting ligands. Polyethylenimine (PEI) was derivatized with beta-cyclodextrin on approximately 10% of the polymer's amines (termed CD-PEI). Human insulin was also derivatized with a hydrophobic palmitate group (pal-HI), which could anchor the protein to CD-PEI/DNA polyplexes. CD-PEI was essentially nontoxic to HEK293 cells at concentrations optimal for gene delivery and mediated nearly 4-fold higher gene expression than unmodified PEI, which is relatively toxic to these cells. More importantly, addition of the pal-HI to CD-PEI enhanced gene expression by more than an order of magnitude compared to unmodified PEI, either with or without the pal-HI. Because of the relative ease with which CD-binding moieties may be attached to various types of ligands, CD-PEI may be a generally useful material for testing novel cell-specific targeting compounds.