Nucleic acid binding oligonucleotides
OwnerGregory Verdine, Webster Santosinventors
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Abstract
The present application pertains to products and methods related to the ability of short nucleotide oligomers to bind the tertiary or globular structure of nucleic acids. This application discloses libraries of short oligomers and methods for using these libraries.
Claims127
A library of nucleic acid oligomers or nucleotide analog oligomers, wherein:
- each oligomer is a 15mer or shorter;
- and
- each oligomer is immobilized on a support.
An array comprising:
- a substrate comprising a plurality of addresses, wherein each address is associated with at least one nucleic acid oligomer, or one nucleotide analog oligomer, that is a 9mer or shorter.
The array of any one of claims 6-26, wherein the array further comprises a target nucleic acid molecule comprising a tertiary or globular structure bound to one or more selected addresses of the array.
A method of making a substrate suitable for evaluating oligomers, said method comprising:
- providing a substrate comprising a plurality of addresses;
- attaching at least one nucleic acid oligomer at each address, wherein the oligomer is a 9mer or shorter;
- and
- wherein the substrate provides an address for at least 10% of all permutations of four nucleotides at each position of an oligomer of a particular length.
A method of making a substrate suitable for evaluating oligomers, said method comprising:
- providing a substrate comprising a plurality of addresses;
- atlaching at least one nucleic acid oligomer at each address, wherein the oligomer is a 5mer or shorter;
- and
- wherein the substrate provides an address for at least 10% of all permutations of four nucleotide bases at each position of a nucleic acid oligomer of a particular length.
A method of identifying at least one nucleic acid oligomer that non-canonically binds a target RNA molecule, said method comprising:
- providing an array that comprises a substrate comprising a plurality of addresses, wherein each address comprises at least one nucleic acid oligomer,
- wherein the oligomer is from a 2mer to a 15mer, inclusive;
- and
- contacting the array with a target molecule that comprises a folded RNA.
A method of identifying a candidate therapeutic target sequence within an RNA molecule, comprising:
- providing an array comprising a substrate having a plurality of addresses, each address comprising at least one nucleic acid oligomer, and wherein the oligomer is from a 2mer to a 15mer, inclusive;
- contacting the array with a candidate RNA molecule;
- and
- detecting whether the candidate RNA molecule has bound the array;
- thereby identifying whether or not the RNA molecule comprises a candidate therapeutic target for a non-canonically binding oligomer.
A method of designing a nucleic acid oligomer that binds non-canonically to a target RNA molecule, comprising:
- providing an array comprising a substrate having a plurality of addresses, each address comprising at least one nucleic acid oligomer, and wherein the oligomer is from a 2mer to a 15mer, inclusive;
- contacting the array with the target RNA molecule;
- detecting whether the candidate RNA molecule binds the array;
- identifying the address to which the RNA molecule binds;
- correlating the address to the structural features of an oligomer comprised by the address;
- and
- using the structural features to design an oligomer that binds non-canonically to the target RNA molecule.
A kit for identifying oligomers that bind non-canonically to target nucleic acid molecules comprising:
- a container;
- and
- within that container is packaged an array comprising a substrate having a plurality of addresses, each address comprising at least one nucleic acid oligomer, and wherein the oligomer is from a 2mer to a 15mer, inclusive.
Dependencies are inferred from the claim text.