Data processing: measuring – calibrating – or testing – Measurement system in a specific environment – Chemical analysis
Reexamination Certificate
2000-04-24
2003-07-22
Barlow, John (Department: 2863)
Data processing: measuring, calibrating, or testing
Measurement system in a specific environment
Chemical analysis
Reexamination Certificate
active
06597996
ABSTRACT:
BACKGROUND
Various notational systems have been used to encode classes of chemical units by assigning a unique code to each chemical unit in the class. For example, a conventional notational system for encoding amino acids assigns a single letter of the alphabet to each known amino acid. A polymer of chemical units may be represented using such a notational system using a set of codes corresponding to the chemical units. Such notational systems have been used to encode polymers, such as proteins, in a computer-readable format. A polymer that has been represented in such a computer-readable format according to a notational system may be stored and processed by a computer.
Conventional notational schemes for representing chemical units have represented the chemical units as characters (e.g., A, T, G, and C for nucleic acids), and have represented polymers of chemical units as sequences or sets of characters. Various operations may be performed on such a notational representation of a chemical unit or a polymer comprised of chemical units. For example, a user may search a database of chemical units for a query sequence of chemical units. In such a case, the user typically provides a character-based notational representation of the sequence in the form of a sequence of characters, which is compared against the character-based notational representations of sequences of chemical units stored in the database. Character-based searching algorithms, however, are typically slow because such algorithms search by comparing individual characters in the query sequence against individual characters in the sequences of chemical units stored in the database. The spread of such algorithms is therefore related to the length of the query sequence, resulting in particularly poor performance for long query sequences.
The study of molecular and cellular biology is focused on the macroscopic structure of cells. We now know that cells have a complex microstructure that determine the functionality of the cell. Much of the diversity associated with cellular structure and function is due to the ability of a cell to assemble various building blocks into diverse chemical compounds. The cell accomplishes this task by assembling polymers from a limited set of building blocks referred to as monomers. The key to the diverse functionality of polymers is based in the primary sequence of the monomers within the polymer and is integral to understanding the basis for cellular function, such as why a cell differentiates in a particular manner or how a cell will respond to treatment with a particular drug.
The ability to identify the structure of polymers by identifying their sequence of monomers is integral to the understanding of each active component and the role that component plays within a cell. By determining the sequences of polymers it is possible to generate expression maps, to determine what proteins are expressed, to understand where mutations occur in a disease state, and to determine whether a polysaccharide has better function or loses function when a particular monomer is absent or mutated.
SUMMARY
Polymers may be characterized by identifying properties of the polymers and comparing those properties to reference polymers, a process referred to herein as property encoded nomenclature (PEN). In one embodiment, the properties are encoded using a binary notation system, and the comparison is accomplished by comparing the binary representations of polymers. For instance, in one aspect a sample polymer is subjected to an experimental constraint to modify the polymer, the modified polymer is compared to a reference database of polymers to identify a population of polymers having a property that is the same as or similar to a property of the sample polymer. The method may be repeated until the population of polymers in the reference database is reduced to one and the identity of the sample polymer is known.
In a system including a database of properties of polymers of chemical units a method for determining the composition of a sample polymer of chemical units having a known molecular weight and length is provided according to one aspect of the invention. The method includes the steps of
(A) selecting, from the database, candidate polymers of chemical units having the same length as the sample polymer of chemical units and having molecular weights similar to the molecular weight of the sample polymer of chemical units;
(B) performing an experiment on the sample polymer of chemical units;
(C) measuring properties of the sample polymer of chemical units resulting from the experiment; and
(D) eliminating, from the candidate polymers of chemical units, polymers of chemical units having properties that do not correspond to the experimental results.
In some embodiments the method also includes the step of:
(E) repeatedly performing the step (D) until the number of candidate polymers of chemical units falls below a predetermined threshold.
In other aspects the invention is a method for identifying a population of polymers of chemical units having the same property as a sample polymer of chemical units. The method includes the steps of determining a property of a sample polymer of chemical units, and comparing the property of the sample polymer to a reference database of polymers of known sequence and known properties to identify a population of polymers of chemical units having the same property as a sample polymer of chemical units, wherein the reference database of polymers includes identifiers corresponding to the chemical units of the polymers, each of the identifiers including a field storing a value corresponding to the property.
In one embodiment the step of determining a property of the sample polymer involves the use of mass spectrometry, such as for example, matrix assisted laser desorption ionization mass spectrometry (MALDI-MS), electron spray-MS, fast atom bombardment mass spectrometry (FAB-MS) and collision-activated dissociation mass spectrometry (CAD) to determine the molecular weight of the polymer. MALDI-MS, for instance, may be used to determine the molecular weight of the polymer with an accuracy of approximately one Dalton.
The step of identifying a property of the polymer in other embodiments may involve the reduction in size of the polymer into pieces of several units in length that may be detected by strong ion exchange chromatography. The fragments of the polymer may be compared to the reference database polymers.
According to other aspects, the invention is a method for identifying a subpopulation of polymers having a property in common with a sample polymer of chemical units. The method involves the steps of applying an experimental constraint to the polymer to modify the polymer, detecting a property of the modified polymer, identifying a population of polymers of chemical units having the same molecular length as the sample polymer, and identifying a subpopulation of the identified population of polymers having the same property as the modified polymer by eliminating, from the identified population of polymers, polymers having properties that do not correspond to the modified polymer. The steps may be repeated on the modified polymer to identify a second subpopulation within the subpopulation of polymers having a second property in common with the twice modified polymer. Each of the steps may then be repeated until the number of polymers within the subpopulation falls below a predetermined threshold. The method may be performed to identify the sequence of the polymer. In this case the predetermined threshold of polymers within the subpopulation is two polymers.
In yet another aspect, the invention is a method for identifying a subpopulation of polymers having a property in common with a sample polymer of chemical units. The method involves the steps of applying an experimental constraint to the polymer to modify the polymer, detecting a first property of the modified polymer, identifying a population of polymers of chemical units having a second property in common with the sample polymer
Keiser Nishla
Raman Rahul
Sasisekharan Ram
Shriver Zachary
Venkataraman Ganesh
Barlow John
Lau Tung S
Massachusetts Institute of Technology
Wolf Greenfield & Sacks PC
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