Selection of aptamers based on geometry
First Claim
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1. A method, comprising:
- geometrically enriching a plurality of aptamers of a given length or a range of aptamer lengths, wherein said geometric enrichment comprises formulating a set of possible aptamer geometries, wherein the aptamer geometries in the set share a common format defined by the number of stems, loops, and pockets present in the aptamer structure, and wherein the format comprises one or more stems, one or more loops, and one or more pockets, and;
each loop in the common format has a size of no less than 3 nucleotides and no more than 21 nucleotides,each pocket in the common format has a size of no less than 1 nucleotide and no more than 8 nucleotides, andeach stem in the common format has a size of no less than 2 nucleotides and no more than 7 nucleotides;
further enriching the set of possible aptamer geometries by formulating a library of aptamer sequences from the set of geometries, wherein the library is formulated by excluding sequences that do not satisfy one or more selected aptamer statistics relating to sequence(s) of stems, loops, and/or pockets, wherein the aptamer statistics are derived from data on pre-existing apatmers, and wherein the library comprises more than 1% of all possible geometries for a given aptamer length;
affixing at least one candidate aptamer from the library of aptamer sequences to a substrate.
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Abstract
Disclosed are methods for performing aptamer preselection based on unique geometry and the content of stems or loops of the aptamer, which methods are capable of providing suitable binders and also permit selection of aptamers performed essentially entirely on a chip or other device. Also disclosed are kits for aptamer selection.
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Citations
61 Claims
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1. A method, comprising:
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geometrically enriching a plurality of aptamers of a given length or a range of aptamer lengths, wherein said geometric enrichment comprises formulating a set of possible aptamer geometries, wherein the aptamer geometries in the set share a common format defined by the number of stems, loops, and pockets present in the aptamer structure, and wherein the format comprises one or more stems, one or more loops, and one or more pockets, and; each loop in the common format has a size of no less than 3 nucleotides and no more than 21 nucleotides, each pocket in the common format has a size of no less than 1 nucleotide and no more than 8 nucleotides, and each stem in the common format has a size of no less than 2 nucleotides and no more than 7 nucleotides; further enriching the set of possible aptamer geometries by formulating a library of aptamer sequences from the set of geometries, wherein the library is formulated by excluding sequences that do not satisfy one or more selected aptamer statistics relating to sequence(s) of stems, loops, and/or pockets, wherein the aptamer statistics are derived from data on pre-existing apatmers, and wherein the library comprises more than 1% of all possible geometries for a given aptamer length;
affixing at least one candidate aptamer from the library of aptamer sequences to a substrate. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61)
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Specification