Abstract: Nucleotide sequences encoding proteins of interest are isolated from DNA libraries using bacteriophage to link the protein to the sequence which encodes it. DNA libraries are prepared from cells encoding the protein of interest and inserted into or adjacent to a coat protein of a bacteriophage vector, or into a sequence encoding a protein which may be linked by means of a ligand to a phage coat protein. By employing affinity purification techniques the phage particles containing sequences encoding the desired protein may be selected and the desired nucleotide sequences obtained therefrom. Thus, for example, novel proteins such as monoclonal antibodies may be produced and conventional hybridoma technology avoided.

Abstract: A method for synthesizing oligonucleotides on a solid substrate. The method provides for the irradiation of a first predefined region of the substrate without irradiation of a first predefined region of the substrate. The irradiation of a second predefined region of the substrate. The irradiation step removes a protecting group therefrom. The substrate is contacted with a first nucleotide to couple the nucleotide to the substrate in the first predefined region. By repeating these steps, an array of diverse oligonucleotides is formed on the substrate.

Abstract: Phsophonate esters can be synthesized in high yields by condensations of alcohols with methyl phosphonates followed by selective demethylation. The reaction is general, relativly insensitive to steric constraints of hindered phosphonic acids, and can also be carried out on a solid support to synthesize large collections of compounds to screen for pharmacological activity.

Abstract: Substrates with surfaces comprising compounds with thiol functional groups protected with a photoremovable protecting group can be used to construct arrays of immobilized anti-ligands, such as oligonucleotide probes or other biological polymers. The arrays can be used in assays to detect the presence of complementary nucleic acids in a sample. Spatially addressed irradiation of predefined regions on the surface permits immobilization of oligonucleotides and other biological polymers at the activated regions on the surface. Cycles of irradiation on different regions of the surface and immobilization of different anti-ligands allow formation of an immobilized matrix of anti-ligands at defined sites on the surface. The immobilized matrix of anti-ligands permits simultaneous screenings of a liquid sample for ligands having high affinities for certain anti-ligands of the matrix.

Abstract: A technique for the synthesis of arrays of diverse polymers such as polypeptides and nucleic acids. The technique beneficially utilizes solid-phase chemistry techniques. Preferred embodiments utilize photolabile protecting groups, and photolithography. The technique forms polymers with monomer sequences and locations determined by the order of addition of monomers and the activation patterns formed on the substrate.

Abstract: A method and device for forming large arrays of polymers on a substrate (401). According to a preferred aspect of the invention, the substrate is contacted by a channel block (407) having channels (409) therein. Selected reagents are flowed through the channels, the substrate is rotated by a rotating stage (403), and the process is repeated to form arrays of polymers on the substrate. The method may be combined with light-directed methodolgies.

Abstract: A stereospecific method of preparing alpha-aminophosphonic acids and derivatives thereof is provided. A protected amino acid is converted to a acyl aroyl or diacyl peroxide which spontaneously rearranges to form an alpha-amino ester. This rearrangement occurs stereospecifically with retention of configuration. The ester is subsequently converted to an appropriate leaving group and displaced with a phosphite yielding a chiral alpha-aminophosphonic acid or derivative.Alpha-aminophosphonic acids are useful for the synthesis of peptide analogs that possess a phosphonate linkage in the place of an amide linkage. This substitution can impart protease resistance in therapeutic peptides thereby increasing the serum half-life.

Abstract: Phosphonate esters can be synthesized in high yields by condensations of alcohols with methyl phosphonates followed by selective demethylation. The reaction is general, relatively insensitive to steric constraints of hindered phosphonic acids, and can also be carried out on a solid support to synthesize large collections of compounds to screen for pharmacological activity.

Abstract: A random peptide library constructed by transforming host cells with a collection of recombinant vectors that encode a fusion protein comprised of a DNA binding protein and a random peptide and also contain a binding site for the DNA binding protein can be used to screen for novel ligands. The screening method results in the formation of a complex comprising the fusion protein bound to a receptor through the random peptide ligand and to the recombinant DNA vector through the DNA binding protein.

Abstract: A method and device for measuring the binding affinity of a receptor to a ligand. According to one aspect of the invention, arrays of polymers are synthesized or immobilized on a substrate (212). The array of polymers is exposed to a fluorescently-labelled receptor in solutions of varying concentration. The fluorescence intensity of the labelled receptor is measured by way of, e.g., a photon counter using a confocal microscope (316). Binding affinity is determined through analysis of the relationship between fluorescence intensity and the solution concentration of the receptor. On-rates are measured as a kinetic increase in surface fluorescence intensity, and the on-rate constant rate extracted from fits to the data.

Abstract: Compositions and methods for producing the activating moiety of a site-directed catalytic antibody are provided. The activating moiety serves to enhance the rate of chemical reactions involving the conversion of the prodrug to one or more active substrates or drugs. The activating moiety typically comprises a catalytic antibody. Compositions and methods for producing the catalytic antibodies, as well as the haptens which are used to generate the catalytic antibodies, are provided. Compositions and methods for producing the prodrugs are also provided.

Abstract: A random peptide library constructed by transforming host cells with a collection of recombinant vectors that encode a fusion protein comprised of a DNA binding protein and a random peptide and also encode a binding site for the DNA binding protein can be used to screen for novel ligands. The screening method results in the formation of a complex comprising the fusion protein bound to a receptor through the random peptide ligand and to the recombinant DNA vector through the DNA binding protein.

Abstract: Chimeric G-protein linked receptors are constructed which retain ligand binding specificity yet gain the ability to elevate intracellular free calcium as a result of agonist binding. This easily assayed function is provided by the insertion of or replacement with sequences substantially homologous to the i3 loop of a second G-protein-linked receptor. Such receptors are employed, for example, in methods of screening for compounds capable of acting as agonists or antagonists of G-protein-linked receptors.

Abstract: Methods and compositions are described for immobilizing anti-ligands, such as antibodies or antigens, hormones or hormone receptors, oligonucleotides, and polysaccharides on surfaces of solid substrates for various uses. The methods provide surfaces covered with caged binding members which comprise protecting groups capable of being removed upon application of a suitable energy source. Spatially addressed irradiation of predefined regions on the surface permits immobilization of anti-ligands at the activated regions on the surface. Cycles of irradiation on different regions of the surface and immobilization of different anti-ligands allows formation of an immobilized matrix of anti-ligands at defined sites on the surface. The immobilized matrix of anti-ligands permits simultaneous screenings of a liquid sample for ligands having high affinities for certain anti-ligands of the matrix. A preferred embodiment of the invention involves attaching photoactivatable biotin derivatives to a surface.

Abstract: A method for cyclization and reversal of the polarity of polymers on a substrate. The method provides for the formation of a polymer on a substrate (2) with a tether molecule (4). Through unmasking of a protective group (PG.sub.2) a cyclic polymer (6) is formed. Through cleavage of an appropriate bond, a polarity reversed polymer (8) is formed. The method finds particular application in the formation of, for example, peptides and oligonucleotides.

Abstract: Polypeptide arrays can be synthesized on a substrate by attaching photoremovable groups to the surface of a substrate, exposing selected regions of the substrate to light to activate those regions, attaching an amino acid monomer with a photoremovable group to the activated regions, and repeating the steps of activation and attachment until polypeptides of the desired length and sequences are synthesized. The resulting array can be used to determine which peptides on the array can bind to a receptor.