Source: http://www.google.com/patents/US7771935?dq=5,960,411
Timestamp: 2015-11-26 14:54:59
Document Index: 170656473

Matched Legal Cases: ['Application No. 60', 'Application No. 60', 'Application No. 60', 'Application No. 60', 'Application No. 60', 'Application No. 60', 'Application No. 60']

Patent US7771935 - Evolving new molecular function - Google PatentsSearch Images Maps Play YouTube News Gmail Drive More »Sign inAdvanced Patent SearchPatentsNature evolves biological molecules such as proteins through iterated rounds of diversification, selection, and amplification. The power of Nature and the flexibility of organic synthesis are combined in nucleic acid-templated synthesis. The present invention provides a variety of template architectures...http://www.google.com/patents/US7771935?utm_source=gb-gplus-sharePatent US7771935 - Evolving new molecular functionAdvanced Patent SearchPublication numberUS7771935 B2Publication typeGrantApplication numberUS 10/950,367Publication dateAug 10, 2010Filing dateSep 24, 2004Priority dateAug 19, 2002Fee statusPaidAlso published asCA2495881A1, CA2495881C, EP1540013A2, EP1540013A4, EP1540013B1, US7491494, US8206914, US20040180412, US20050170376, US20110190141, WO2004016767A2, WO2004016767A3Publication number10950367, 950367, US 7771935 B2, US 7771935B2, US-B2-7771935, US7771935 B2, US7771935B2InventorsDavid R. Liu, Zev J. Gartner, Christopher T. CalderoneOriginal AssigneePresident And Fellows Of Harvard CollegeExport CitationBiBTeX, EndNote, RefManPatent Citations (106), Non-Patent Citations (289), Referenced by (17), Classifications (10), Legal Events (2) External Links: USPTO, USPTO Assignment, EspacenetEvolving new molecular function
US 7771935 B2Abstract
1. An in vitro method of inducing a reaction between first and second reactive units during a nucleic acid-templated chemical reaction, the method comprising the steps of:
(a) providing (i) a template comprising a first reactive unit covalently attached to a first oligonucleotide comprising a codon and (ii) a transfer unit comprising a second reactive unit covalently associated with a second oligonucleotide comprising an anti-codon capable of annealing to said codon, wherein said codon or said anti-codon comprise first and second spaced apart regions; and
(b) annealing said first and second oligonucleotides thereby to bring said first reactive unit and said second reaction unit into reactive proximity and produce a reaction product that is not a nucleic acid, wherein, upon annealing, said codon or said anti-codon having said first and second spaced apart regions anneal to the corresponding anti-codon or codon via said first and second spaced apart regions to produce a loop of oligonucleotides disposed between said first and second spaced apart regions that are not annealed to the corresponding anti-codon or codon, wherein the loop of oligonucleotides permits the codon to anneal to the corresponding anti-codon and bring the first and second reactive units into reactive proximity.
2. The method of claim 1, wherein at least one of said reactive units is attached adjacent a terminal region of its corresponding oligonucleotide.
3. The method of claim 2, wherein each of said reactive units is attached adjacent a terminal portion of its corresponding oligonucleotide.
4. The method of claim 1, 2, or 3, wherein said codon or said anti-codon is disposed at least 10 bases away from its corresponding reactive unit.
5. The method of claim 1, 2, or 3, wherein said codon or said anti-codon is disposed at least 20 bases away from its corresponding reactive unit.
6. The method of claim 1, 2, or 3, wherein said codon or said anti-codon is disposed directly adjacent its corresponding reactive unit.
7. The method of claim 1, wherein in said codon or said anti-codon comprising said first and second spaced apart regions, said first region is disposed directly adjacent a terminus of its corresponding oligonucleotide.
8. The method of claim 1 or 7, wherein said first region of said codon or said anti-codon comprises three, four or five adjacent nucleotides.
9. The method of claim 1 or 7, wherein said first region of said codon or said anti-codon comprises five adjacent nucleotides.
10. The method of claim 1 or 7, wherein said second region is disposed at least 20 bases away from said reactive unit.
11. The method of claim 1 or 7, wherein said second region is disposed at least 30 bases away from said reactive unit.
12. An in vitro method of inducing a reaction between first and second reactive units during a nucleic acid-templated chemical reaction, the method comprising the steps of:
(a) providing (i) a template comprising a first reactive unit covalently attached to a first oligonucleotide having a proximal end and a distal end and comprising a codon and (ii) a transfer unit comprising a second reactive unit associated with a second oligonucleotide comprising an anti-codon capable of annealing with said codon, wherein said first reactive unit is attached to an attachment site intermediate said proximal end and said distal end of said first oligonucleotide; and
(b) annealing said oligonucleotides together thereby to bring said first reactive unit and said second reactive unit into reactive proximity and produce a reaction product that is not a nucleic acid.
13. The method of claim 12, wherein said template comprises a second, different codon capable of annealing to a second, different anti-codon sequence.
14. The method of claim 13, wherein said first codon is located proximal to, and said second codon is located distal to, said attachment site of said first reactive unit.
15. The method of claim 13 or 14, further comprising providing a second transfer unit comprising a third reactive unit associated with a third oligonucleotide comprising a second, different anti-codon sequence capable of annealing with said second codon.
16. The method of claim 15, wherein said first anti-codon of said first transfer unit anneals to said first codon of said template and said second anti-codon of said second transfer unit anneals to said second codon of said template.
17. The method of claim 16, wherein said first transfer unit anneals with said template concurrently with said second transfer unit, so that said second reactive unit and said third reactive unit react with said first reactive unit.
18. The method of claim 12, wherein said second reactive unit is covalently attached to said second oligonucleotide.
19. The method of claim 15, wherein said third reactive unit is covalently attached to said third oligonucleotide.
20. The method of claim 12, wherein said first reactive unit is a scaffold molecule.
This application is a continuation of U.S. patent application 10/643,752, filed Aug. 19, 2003, which claims the benefit of (i) U.S. Provisional Patent Application No. 60/404,395, filed Aug. 19, 2002, (ii) U.S. Provisional Patent Application No. 60/419,667, filed Oct. 18, 2002, (iii) U.S. Provisional Patent Application No. 60/432,812, filed Dec. 11, 2002, (iv) U.S. Provisional Patent Application No. 60/444,770, filed Feb. 4, 2003, (v) U.S. Provisional Patent Application No. 60/457,789, filed Mar. 26, 2003, (vi) U.S. Provisional Patent Application No. 60/469,866, filed May 12, 2003, and (vii) U.S. Provisional Patent Application No. 60/479,494, filed Jun. 18, 2003, the disclosures of each of which are incorporated by reference herein. The application is also related to U.S. Provisional Patent Application Nos. 60/277,081 (filed Mar. 19, 2001), 60/277,094 (filed Mar. 19, 2001), 60/306,691 (filed Jul. 20, 2001), and 60/353,565 (filed Feb. 1, 2002), as well as to U.S. patent application Ser. Nos. 10/101,030 (filed Mar. 19, 2002) and 10/102,056 (filed Mar. 19, 2002), and to International Patent Application serial number US02/08546 (filed Mar. 19, 2002).
The research described in this application was sponsored, in part, by the Office for Naval Research under Contract No. N00014-00-1-0596 and Grant No. 00014-03-1-0749. The United States Government may have certain rights in the invention.
FIGS. 28A-28E depict strategies for DNA-templated synthesis using autocleaving linkers (FIGS. 28A, 28B and 28E), scarless linkers (FIG. 28C), and useful scar linkers (FIG. 28D).
FIG. 36 is a table showing the melting temperatures of selected template-reagent combinations using the omega (Ω) and end-of-helix (E) architectres.
FIG. 58 is a schematic representation of a method of creating a template used in the synthesis of a DNA-templated macrocyclic fumaramide library.
FIG. 59 is a schematic representation of an amine acylation and cyclization reaction useful in the synthesis of macrocyclic fumaramide library.
FIG. 60 depicts representative monomer structures that can be incorporated into a PNA polymer.
FIG. 61 is a schematic representation of a method for making functional polymers. As shown the polymer is still associated with the template.
FIG. 62 depicts a DNA-templated aldehyde polymerization reaction.
FIG. 63 depicts PNA polymerization reactions using a 40 base template with mismatched codons located at certain positions of the template.
FIG. 64 shows the specificity of DNA-templated polymerization reactions.
FIG. 65A is a schematic representation showing a method of using a nucleic acid to direct the synthesis of new polymers and plastics. FIG. 65B is a schematic representation showing the use of Grubbs' ring-opening metathesis polymerization catalysis to evolve plastics.
FIG. 66 is a schematic representation showing the evolution of plastics through iterative cycles of ligand diversification, selection, and amplification to create polymers with desired properties.
FIG. 67 depicts exemplary functionalized nucleotides that can be incorporated by DNA polymerase.
FIG. 68 depicts exemplary metal binding uridine and 7-deazaadenosine analogs.
FIG. 69 depicts an exemplary synthesis of analog 7 from FIG. 67.
FIG. 70 depicts an exemplary synthesis of compound 30, a precursor to compound 13 from FIG. 67.
FIG. 71 depicts an exemplary synthesis of compound 40, a precursor to compound 13 from FIG. 67.
FIG. 72 depicts an exemplary synthesis of compound 38, a precursor to compound 40 from FIG. 71.
FIG. 73 depicts exemplary deoxyadenosine derivatives.
FIG. 74 depicts an exemplary synthesis of modified deoxyadenosine triphosphates.
FIG. 75 depicts a summary of modified nucleotide