Molecular Analysis

• US 20080003566A1
• Filed: 01/26/2005
• Published: 01/03/2008
• Est. Priority Date: 01/26/2004
• Status: Abandoned Application

• Current Assignee: David Vaux
• Original Assignee: David Vaux
• Inventors: Vaux, David
• Application Number:
  US10/587,387
• Publication Number:
  US 20080003566A1
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: C12Q 1/6811 Selection methods for production or design of target specific oligonucleotides or binding molecules
• CPC Class Codes: C12Q 2525/151 repeat or repeated sequences, e.g. VNTR, microsatellite, concatemer
• CPC Class Codes: C12Q 2531/113 PCR
• CPC Class Codes: C12Q 2539/103 Serial analysis of gene expression [SAGE]

Abstract

The present invention relates to a method of determining the sequence and/or occurrence frequency of a number of variable gene inserts from a gene library, which inserts exhibit a desired specific characteristic, wherein each variable gene insert is flanked (5′) and (3′) by known sequences, the method comprising; selecting the number of inserts by their ability to exhibit the desired specific characteristic, conducting polymerase chain reaction to amplify the selected number of variable gene inserts to produce components of a mixed PCR product, ligating the components of the mixed PCR product to produce a concatenated sequence and sequencing or determining the occurrence of the gene inserts in the concatenated sequence.

Claims

1. A method of determining the sequence and/or occurrence frequency of a number of variable gene inserts from a gene library which inserts exhibit a desired specific characteristic, wherein each variable gene insert is flanked 5′

and 3′

adjacent known sequences, the method comprising;

selecting the number of inserts by their ability to exhibit the desired specific characteristic, conducting polymerase chain reaction to amplify the selected number of variable gene inserts to produce components of a mixed PCR product;

litigating the components of the mixed PCR product to produce a concatenated sequence; and

sequencing or determining the occurrence of the gene inserts in the concatenated sequence.

2. A method as claimed in claim 1 wherein the gene library is a peptide phage display library.

15. The method as claimed in claim 1, wherein the components of the mixed PCR product are digested with a restriction endonuclease before ligation to produce the concatenated sequence.

16. The method as claimed in claim 1, wherein the concatenated sequence is cloned into a plasmid before sequencing.

17. The method as claimed in claim 16, wherein the concatenated sequence is size selected to from about 500 to about 1.5 kilobases in length before cloning into the plasmid.

18. The method as claimed in claim 2, wherein the length of each variable gene inserts is from about 18 to about 36 nucleotides.

19. The method as claimed in claim 18, wherein the specific characteristic is one or more of protein binding or occurrence only in one state of tissue in a comparison with the same tissue in a different state.

20. The method as claimed in claim 2, wherein the number of variable gene inserts are from phage which do not exhibit a specific characteristic.

21. The method as claimed in claim 1, wherein selecting the number of inserts by their ability to exhibit the desired specific characteristic comprises two or more rounds of selection based on the ability of the variable gene inserts to exhibit the desired characteristic.

22. The method as claimed in claim 1, wherein when more than one round of selection by the ability of the insert to exhibit the desired characteristic is carried out, then the different rounds of selection may be of more than one desired specific characteristic.

23. The method as claimed in claim 1, further comprising characterisation of a target molecule.

24. The method as claimed in claim 1, further comprising quantitation of a target molecule.

25. The method as claimed in claim 23, wherein characterisation comprises using fluorescence resonant energy transfer.

26. The method as claimed in claim 24, wherein quantitation comprises using fluorescence resonant energy transfer.

27. A dataset of a sub-library resulting from the method of claim 1.

28. A determination of the sequence or occurrence frequency of a number of variable gene inserts from a gene library obtained by the method of claim 1.

3-14. -14. (canceled)