High Density Protein Microarrays via Addressing to Arrayed Peptide

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GSJ: Received June 2, 2005: http://wbabin.net/saba/saba46.htm

High Density Protein Microarrays via Addressing to Arrayed Peptide

James Saba

High densities of polynucleotides and peptides can be fabricated on biochips, for example with the use of photolithography.

Such high density microarrays of polynucleotides have found utility as capture probes, and as relevant here, in their ability to allow for addressing of conjugated complementary polynucleotides.

This invention is an analogous concept utilizing microarrayed peptides as capture probes. Preferably, addressed to these probes are proteins having two portions, an antibody portion which binds the arrayed peptide, and a second distal portion which can variously be another antibody, polypeptide, nucleic acid or other conjugated 'ligand'.

As a clear example of the invention, Figure 1 depicts the utilization of monoclonal bispecific antibodies.

Herein three different bispecific monoclonal antibodies (mAbs) are addressed to three arrayed peptides.

An "antibody" as used herein denotes either a single-chain or multi-chain protein with relatively strong and highly specific binding capacity. Molecules other than proteins, such as aptamers, which can be designed to bind arrayed peptides are also applicable.

In Figure 2 molecules addressed to the arrayed peptides are single-chain antibodies whose portions distal the peptide binding portions are different. Notice, various natural and unnatural molecules could be conjugated to single-stranded antibodies distal the peptide-binding portions, perhaps utilizing unnatural amino acids incorporated in the antibody.

Figure 3 is an interesting derivation wherein recombinant phage displaying antibody are utilized.

Finding highly efficient antibodies to address to arrayed peptides could readily be done with antibody-phage display libraries directed to the arrayed peptides.

Once a set of antibodies directed to a universal set of arrayed peptides was established, it could in a modulatorty fashion be coupled with various kinds of molecules.

The ability to for such an array of infectious viruses and even cells, with or without further derivations distal the peptide-binding antibodies, appears to have interesting utilities.

It may be desirable to covalently crosslink the addressed molecules to the the arrayed peptides or support, and various means of achieving this are possible. One perhaps uncommon method would be to incorporate one or more cross-linking amino acids into the arrayed peptides or antibodies.

Finally, very precise and complex supramolecular structures could be constructed in similar processes, for example using trispecific antibodies.

This invention is considered valuable and a US patent application is anticipated to be filed. However, it is hoped that others with laboratory facilities will investigate its full potential.

The following provisional claims are an attempt to encompass important aspects of this invention.

1) A process of addressing molecules, viruses or cells to an array of peptides.

2) The process of claim 1 wherein the molecules are antibodies.

3) The process of claim 2 wherein the antibodies are displayed by a phage or cell.

4) Any process above wherein the peptide array has been photolithographically produced.

5) An array resulting from any of the above processes.

Addendum 6/8/05 Epitope-targeted proteome analysis: towards a large-scale automated protein-protein-interaction mapping utilizing synthetic peptide arrays.
Bialek, et al Anal Bioanal Chem. 2003 Aug;376(7):1006-13

Multiplexed sorting of libraries on libraries: a novel method for empirical protein design by affinity-driven phage enrichment on synthetic peptide arrays.
Hultschig, et al Mol Divers. 2004;8(3):231-45

These highly relevant references describe in detail a means of establishing the combinations of molecular associations as the present invention requires.

However, from the abstracts the processes described appear be concerned with phage library screening technique, and have not have recognized the potential of the technique in fabricating high density protein arrays via addressing, particularly to a universal set of arrayed peptides.