Systems and methods for constructing frequency lookup tables for expression systems
a technology of expression system and frequency lookup table, which is applied in the field of coding protein expression, can solve the problems of no reliable strategy for selecting codons, and no current reliable algorithm
Inactive Publication Date: 2013-07-18
DNA TWOPOINTO
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Benefits of technology
The patent describes a method for designing and synthesizing polynucleotides that have modified expression characteristics. The method involves using computational biology and data mining techniques to map codon space for polynucleotides. This allows for the creation of modified polynucleotides that have desired expression properties. The method can be used to create new polynucleotides with improved expression characteristics for various applications. The patent also describes a system for modeling the relationship between polynucleotide sequence properties and expression properties to further improve the design of polynucleotides.
Problems solved by technology
A problem with these correlations is that protein expression is generally believed to be controlled at the level of initiation of transcription and translation, not translational velocity.
Thus there is currently no reliable strategy for selecting the codons in a synthetic gene to obtain high protein expression levels, nor is there currently a reliable algorithm with which to assess the likely level of protein expressed from a synthetic gene.
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[0048]Before the present invention is described in detail, it is to be understood that this invention is not limited to the particular methodology, devices, solutions or apparatuses described, as such methods, devices, solutions or apparatuses can, of course, vary. It is also to be understood that the terminology used herein is for the purpose of describing particular embodiments only, and is not intended to limit the scope of the present invention.
5.1 DEFINITIONS
[0049]Use of the singular forms “a,”“an,” and “the” include plural references unless the context clearly dictates otherwise. Thus, for example, reference to “a polynucleotide” includes a plurality of polynucleotides, reference to “a substrate” includes a plurality of such substrates, reference to “a variant” includes a plurality of variants, and the like.
[0050]Where a range of values is recited, it is to be understood that each intervening integer value, and each fraction thereof, between the recited upper and lower limits ...
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Methods for determining a property that affects expression of polynucleotides are provided. A plurality of polynucleotides each encoding a polypeptide sequence is constructed. A frequency that a sequence element is used in a first polynucleotide is different than in a second polynucleotide. Each polynucleotide is expressed in an expression system to obtain an expression property value thereby constructing a dataset that contains, for each respective polynucleotide, sequence element occurrence in the respective polynucleotide and the measured expression property value of the respective polynucleotide. A model is computed that describes variation in the measured expression property values as a function of a plurality of variables and weights. From the model, a property that affects expression of polynucleotides in the expression system is determined, where the property is an effect that the frequency of occurrence of one or more sequence elements has on the expression property of polynucleotides in the expression system.
Description
CROSS REFERENCE TO RELATED APPLICATION[0001]This application is a continuation under 37 C.F.R. §1.53(b) of copending U.S. patent application Ser. No. 12 / 184,233, filed Jul. 31, 2008, which claims priority under 35 U.S.C. §119(e) of U.S. Provisional Application No. 61 / 131,238, filed Jun. 6, 2008, and—of U.S. Provisional Application No. 61 / 132,892, filed on Jun. 24, 2008, the disclosures of which are hereby incorporated by reference in their entireties.STATEMENT AS TO RIGHTS TO INVENTIONS MADE UNDER FEDERALLY SPONSORED RESEARCH AND DEVELOPMENT[0002]The research described in this application was funded in part by NSF SBIR grant 0638333.1. FIELD OF THE INVENTION[0003]This invention relates to methods for designing nucleic acids with desired properties, particularly for the expression of encoded proteins.2. BACKGROUND OF THE INVENTION[0004]It is frequently desirable to express proteins encoded by nucleic acids, for example for production of the protein to be used in a therapeutic or bioc...
Claims
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IPC IPC(8): C12Q1/68G16B25/00G16B30/10G16B40/20G16B40/30
CPCG06F19/20C12Q1/68G06F19/24G06F19/22G16B25/00G16B30/00G16B40/00G16B40/30G16B30/10G16B40/20
InventorWELCH, MARKGUSTAFSSON, CLAES
OwnerDNA TWOPOINTO