Data processing: database and file management or data structures – Database design – Data structure types
Reexamination Certificate
2000-01-10
2001-08-28
Lintz, Paul R. (Department: 2771)
Data processing: database and file management or data structures
Database design
Data structure types
C707S793000, C705S026640
Reexamination Certificate
active
06282550
ABSTRACT:
FIELD OF THE INVENTION
The medical and biological arenas have undergone significant development in research and many researchers require custom synthesis of polymers, including but not limited to oligonucleotides, peptides, peptide nucleic acids, polysaccharides and antibodies. The invention described herein is for use in the health, medical, medical research, biological and biotechnical fields.
BACKGROUND OF THE INVENTION
Researchers in the medical and biological fields often require custom synthesis of polymers, including but not limited to oligonucleotides, peptides, peptide nucleic acids, polysaccharides and antibodies. There are millions of permutations of oligonucleotides, peptides, peptide nucleic acids, polysaccharides and antibodies that can be synthesized, and researchers currently must contact numerous suppliers in an effort to find a supplier that is able to and will produce specific oligonucleotides, peptides, peptide nucleic acids, polysaccharides and antibodies. This is a time consuming, inefficient and not always productive process, which rarely reveals the lowest available price for the requested product.
SUMMARY OF THE INVENTION
The present invention eliminates the need to make multiple phonecalls or contacts to multiple suppliers. By requesting the specific oligonucleotide, peptide, peptide nucleic acid, polysaccharide or antibody through the inventive system maintained by the provider, the customer makes one request and multiple suppliers' synthesis capabilities are searched. A list of capable suppliers and their prices are generated for the customer. The customer chooses a supplier and the synthesized oligonucleotide, peptide, peptide nucleic acid, polysaccharide or antibody is prepared and shipped to the customer. The provider bills the customer and pays the supplier.
As will be demonstrated herein, the invention is directed to an apparatus and method for storing the capabilities and pricing (collectively “Capabilities”) of suppliers (“Supplier” or “Suppliers”) of synthesized strands in any form, including but not limited to linear, cyclic or branched formations; providing access to the stored Capabilities; receiving a request (“Request”) from a customer (“Customer”) including a desired synthesized strand; automatically searching the stored Capabilities for one or more Suppliers that has the ability to fulfill the Request; and automatically generating a list of Suppliers who can fulfill the Request, and the prices at which each Supplier can fulfill the Request. Although the system utilized herein may take any appropriate form, preferably, the system is implemented using a global computerized network.
In a preferred embodiment of the invention (“First Embodiment”), a provider (“Provider”) enters into one or more agreements with one or more Suppliers of synthesized oligonucleotides (“ON”), peptides (“PT”) or peptide nucleic acids (“PNA”) (the group of ON, PT and PNA are defined as “Strand” or “Strands”). (Other embodiments may include polysaccharides or antibodies in the definition of Strands.) The synthesized ON are defined as any one of dioxyribonucleic acid (“DNA”), ribonucleic acid (“RNA”) or any modified nucleotides. Nucleotides comprise a nitrogenous base moiety, sugar moiety, and phosphate moiety or modifications of any of the three moieties. Synthesized PTs include Strands comprised of amino acids or modified amino acids. Synthesized PNAs include analogs of DNA with peptide-like backbones, for example made from N-(2-aminoethyl)-glycine with amino bonds and A, C,G and/or T monomers attached by methylene carbonyl bonds. The Suppliers provide information including the Supplier's capabilities (“Supplier's Capabilities” or “Capabilities” or “Supplier Capability Information”) for synthesizing Strands to the Provider. The Supplier's Capabilities may include one or more of the following: backbones, nucleotides, modified nucleotides, amino acids, modified amino acids, scales of synthesis, 5′ tags, 3′ tags, internal tags, amino terminals, carboxyl terminals, relevant modifications, relevant conjugates, and the possible locations of said conjugates, dyes and the possible placement of said dyes, purification methods, branch points, synthesis limitations, and pricing algorithms for the Supplier's Strands. It should be understood that all of the Supplier Capabilities do not apply to all types of Strands, for example peptides do not utilize 5′ tags or 3′ tags. Additionally, any nucleotide modifications are only limited by the actual synthesizing abilities of each Supplier. Synthesis Limitations may include the maximum or minimum number of nucleotides in a Strand. The purification requirements may be limited by the other capabilities enumerated in the Customer's Request. A matrix may be created in the Database comprising all of the unique combinations of Supplier, backbone and scale of synthesis. The Pricing Algorithm preferably comprises a logical entity which relates each Supplier Capability to a cost and may limit a specific Supplier Capability to a given number of instances per Strand (e.g. each Strand may only have zero or one of each of the 3′ or 5′ tags due to the nature of these tags). Further, the Pricing Algorithm may include threshold discounts, which prices the Strand by the number of nucleotides and if a specified number is exceeded, all the nucleotides are discounted, or graduated discounts, which prices the Strand by the number of nucleotides and if a specified number is exceeded, all additional nucleotides are discounted.
Further in this First Embodiment, Customers who are in the market for synthesized Strands will access a database (“Database”) through a network (“Network”), most preferably a global computer network. The Database preferably includes all of the Capabilities of each Supplier. The Customer places a Request for one or more synthesized Strands. The Customer may enter the Request as a customer generated sequence or may use the System's stock sequences stored in the Database for building Strands quickly. The Request may include one or more of the following: the specification of the sequence of one or more of: nucleotides, modified nucleotides, amino acids and modified amino acids; backbones (which may include, but are not limited to DNA, RNA or 2′-o-Me-RNA); nucleotides; modified nucleotides; amino acids; modified amino acids; scale of synthesis; 5′ tags; 3′ tags; internal tags; amino terminals; carboxyl terminals; relevant modifications; relevant conjugates; and the placement of said conjugates; dyes and placement thereof; purification requirements; a purification method, branch points and synthesis limitations (“Requested Strand” or “Desired Product Information”). It should be understood that all of the Desired Product Information do not apply to all types of Strands, for example peptides do not utilize 5′ tags or 3′ tags. The Customer's Request must include backbones, however, additional information is helpful for accurate pricing but is not required for the process to continue. The Database is automatically searched, preferably with iterative logic, to correlate the Request with each Supplier who has the requisite Capabilities to synthesize the Requested Strand. A list of one or more Suppliers with said capability (“List”) is generated from the Database, and the Customer has the ability to access the List. The List may include the price generated by the Pricing Algorithm for each Matching Supplier and may correlate the price to the scale of synthesis.
The Customer then selects a Supplier (“Selected Supplier”) from the list. If the price cannot be generated, then the customer is informed that a price quote (“Price Quote”) will be sent to the Customer preferably via electronic mail. Supplier sends a Price Quote to Customer, preferably via the Provider. If the Customer accepts the price, the Network transmits the Request to the Selected Supplier. Then, the Selected Supplier accepts, rejects or modifies the Request (“Selected Supplie
Johnson Todd Riley
Lynn Joshua David
Parkinson Eric Christopher
Venkatesan Jay Raman
Feehery Maryellen
Lintz Paul R.
Reed Smith LLP
Tangerine Technologies, Inc.
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