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US 5,672,472 AGranted
Synthetic unrandomization of oligomer fragments
AssigneeIsis Pharmaceuticals, Inc.
InventorsDavid J. Ecker, Jacqueline Wyatt, Thomas W. Bruice, Kevin Anderson, Ronnie C. Hanecak, Timothy Vickers, Peter Davis
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Abstract
Methods useful for the determination of oligomers which have specific activity for a target molecule from a pool of primarily randomly assembled subunits are provided. The disclosed methods involve repeated syntheses of increasingly simplified sets of oligomers coupled with selection procedures for determining oligomers having the highest activity. Freedom from the use of enzymes allows the application of these methods to any molecules which can be oligomerized in a controlled fashion.
Claims64
A method for determining an oligonucleotide having specific, assayable activity for a target comprising the steps of:
- (a) preparing a group of sets of oligonucleotides each oligonucleotide comprising at least four nucleotide units by:
- (i) defining a common position in the oligonucleotides of the sets, and
- (ii) synthesizing said sets of oligonucleotides such that each set has a different base unit in said common position, the base units which are not in said common position being randomized;
- (b) assaying each of the sets for activity against the target;
- (c) selecting a set based upon its activity against the target;
- (d) preparing a further group of sets of oligonucleotides, each of the sets of said further group of sets having in the previously defined common position the base unit appearing in that position in the set selected in step (c);
- each set of said further group of sets having a different base unit in an additional, defined common position, the base units in the positions of the oligonucleotides which are not in a defined common position being randomized;
- (e) assaying each of the sets of said further group of sets specific activity for the target;
- (f) selecting a set based upon its activity in said assay;
- and
- (g) performing steps (d), (e) and (f) iteratively until all positions of said oligonucleotide are identified, thereby determining an oligonucleotide having said specific assayable activity.
8 more elements
A method for determining an oligonucleotide cassette having specific, assayable activity for a target comprising the steps of:
- (a) preparing a group of sets of oligonucleotides, each oligonucleotide comprising at least four base units by:
- (i) defining a common position in the oligonucleotides of the sets, and
- (ii) synthesizing said sets of oligonucleotides such that each set has a different base unit in said common position, the base units which are not in said common position being randomized;
- (b) assaying each of the sets for activity against the target;
- (c) selecting a set based upon its activity in said assay;
- (d) preparing a further group of sets of oligonucleotides, each of the sets of said further group of sets having in the previously defined common position the base unit appearing in the previously defined common position in the previously selected set;
- each set of said further group of sets having a different base unit in an additional, defined common position, the base units in the positions of the oligonucleotides which are not in a defined common position being randomized;
- (e) assaying each of the sets of said further group of sets for specific activity for the target;
- (f) selecting a set based upon its activity in said assay;
- and (g) performing steps (d), (e), and (f) iteratively to provide said cassette having each position defined.
7 more elements
A method for determining an oligonucleotide having specific, assayable activity for a non-antibody target comprising the steps of:
- (a) preparing a group of sets of oligonucleotides, each oligonucleotide comprising at least four nucleotide units by:
- (i) defining a common position in the oligonucleotides of the sets, and
- (ii) synthesizing said sets of oligonucleotides such that each set has a different base unit in said common position, the base units which are not in said common position being randomized;
- (b) assaying each of the sets for activity against the target;
- (c) selecting a set based upon its activity against the target;
- (d) preparing a further group of sets of oligonucleotides;
- each of the sets of said further group of sets having in the previously defined common position the base unit appearing in that position in the set selected in step (c);
- each set of said further group of sets having a different base unit in an additional, defined common position, the base units in the positions of the oligonucleotides which are not in a defined common position being randomized;
- (e) assaying each of the sets of said further group of sets for specific activity for the target;
- (f) selecting a set based upon its activity in said assay;
- and
- (g) performing steps (d), (e) and (f) iteratively until all positions of said oligonucleotide are identified, thereby determining an oligonucleotide having said specific, assayable activity.
9 more elements
A method for determining an oligonucleotide cassette having specific, assayable activity for a non-antibody target comprising the steps of:
- (a) preparing a group of sets of oligonucleotides, each oligonucleotide comprising at least four base units by;
- (i) defining a common position in the oligonucleotides of the sets, and
- (ii) synthesizing said sets of oligonucleotides such that each set has a different base unit in said common position, the base units which are not in said common position being randomized;
- (b) assaying each of the sets for activity against the target;
- (c) selecting a set based upon its activity in said assay;
- (d) preparing a further group of sets of oligonucleotides, each of the sets of said further group of sets having in the previously defined common position the base unit appearing in the previously defined common position in the previously selected set;
- each set of said further group of sets having a different base unit in an additional, defined common position, the base units in the positions of the oligonucleotides which are not in a defined common position being randomized;
- (e) assaying each of the sets of said further group of sets for specific activity for the target;
- and
- (f) selecting a set based upon its activity in said assay;
- and
- (g) performing steps (d), (e), and (f) iteratively to provide said cassette having each position defined.
9 more elements
Dependencies are inferred from the claim text.