Methods and Algorithms for Selecting Polynucleotides For Synthetic Assembly

• US 20110224086A1
• Filed: 03/09/2010
• Published: 09/15/2011
• Est. Priority Date: 03/09/2010
• Status: Abandoned Application

• Current Assignee: Centocor Ortho Biotech Incorporated (Johnson & Johnson)
• Original Assignee: Centocor Ortho Biotech Incorporated (Johnson & Johnson)
• Inventors: Zhao, Shanrong, Pardinas, Jose
• Application Number:
  US12/720,060
• Publication Number:
  US 20110224086A1
• Time in Patent Office: Days
• US Class Current: 506/2
• CPC Class Codes: C12N 15/1044 Preparation or screening of libraries displayed on scaffold proteins
• CPC Class Codes: C12N 15/1089 Design, preparation, screening or analysis of libraries using computer algorithms
• CPC Class Codes: C40B 40/08 Libraries containing RNA or DNA which encodes proteins, e.g. gene libraries
• CPC Class Codes: G16B 30/00 ICT specially adapted for sequence analysis involving nucleotides or amino acids
• CPC Class Codes: G16B 30/20 Sequence assembly
• CPC Class Codes: G16B 35/00 ICT specially adapted for in silico combinatorial libraries of nucleic acids, proteins or peptides
• CPC Class Codes: G16B 35/10 Design of libraries
• CPC Class Codes: G16C 20/60 In silico combinatorial chemistry

Abstract

The present invention relates to methods and algorithms for identifying, synthesizing and co-assembling combinatorial libraries of polynucleotide variants.

Claims

1. A method of identifying a combinatorial library of polynucleotide variants, comprising:

a. providing a collection of polynucleotide variants;

b. obtaining sequences of the polynucleotide variants;

c. parsing the polynucleotide variants into contiguous parsed oligonucleotides;

d. adding a first polynucleotide variant from the collection of polynucleotide variants into the combinatorial library;

e. comparing corresponding parsed oligonucleotides in the first polynucleotide variant and the collection of polynucleotide variants;

f. adding those polynucleotide variants from the collection of polynucleotide variants into an analyzed pool of polynucleotide variants that differ at only one corresponding parsed oligonucleotide from the first polynucleotide variant;

g. adding a second polynucleotide variant from the analyzed pool of polynucleotide variants into the combinatorial library;

h. comparing corresponding parsed oligonucleotides in the second polynucleotide variant and the collection of polynucleotide variants;

i. adding those polynucleotide variants from the collection of polynucleotide variants into the analyzed pool of polynucleotide variants that differ at only one corresponding parsed oligonucleotide from the second polynucleotide variant; and

j. repeating steps g-i until the analyzed pool of polynucleotide variants is empty.

2. A method of synthesizing a combinatorial library of polynucleotide variants, comprising:

a. providing a collection of polynucleotide variants;

b. obtaining sequences of the polynucleotide variants;

c. parsing the polynucleotide variants into contiguous parsed oligonucleotides;

d. adding a first polynucleotide variant from the collection of polynucleotide variants into the combinatorial library;

e. comparing corresponding parsed oligonucleotides in the first polynucleotide variant and the collection of polynucleotide variants;

f. adding those polynucleotide variants from the collection of polynucleotide variants into an analyzed pool of polynucleotide variants that differ at only one corresponding parsed oligonucleotide from the first polynucleotide variant;

g. adding a second polynucleotide variant from the analyzed pool of polynucleotide variants into the combinatorial library;

h. comparing corresponding parsed oligonucleotides in the second polynucleotide variant and the collection of polynucleotide variants;

i. adding those polynucleotide variants from the collection of polynucleotide variants into the analyzed pool of polynucleotide variants that differ at only one corresponding parsed oligonucleotide from the second polynucleotide variant;

j. repeating steps g-i until the analyzed pool of polynucleotide variants is empty, and

k. synthesizing the combinatorial library of polynucleotide variants using synthetic polynucleotide assembly.

5. The method of claim 2 or 3 wherein the fragments are between 16-32 nucleotides long.

6. The method of claim 2 or 3 wherein the fragments are at least 16 nucleotides long.

7. The method of claim 2 or 3 wherein the fragments are 24 nucleotides long.

3. A method of selecting combinatorial libraries that can form a co-assembly set, comprising:

a. identifying a first and a second combinatorial library according to methods of the invention;

b. parsing each sequence in the first and the second combinatorial library into contiguous oligonucleotides;

c. comparing a first pool of corresponding parsed oligonucleotides in the first library and a second pool of corresponding parsed oligonucleotides in the second library; and

d. selecting the first and the second combinatorial library when the first pool of corresponding parsed oligonucleotides and the second pool of corresponding parsed oligonucleotides share zero identical sequences at one or more adjacent corresponding fragments.

4. The method of claim 3, wherein the first and the second combinatorial library comprises one polynucleotide variant each.