Methods and systems to generate target-binding oligonucleotides
AssigneesPresident and Fellows of Harvard College, Massachusetts Institute of Technology
InventorsPardis Sabeti, Hayden Metsky, Sreekar Mantena
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Abstract
Current machine learning methods for target binding oligonucleotides design are limited to considering natural sequences in the targets. Here, Applicants generated novel target binding oligonucleotides—with multiple mismatches to any natural sequence—that are optimized for desired properties. These novel target binding oligonucleotides offer more sensitive and specific detection of, for example, pathogen genome variation than baseline design methods, and they illuminate a new, interpretable design rule that broadens nucleic acid sequence targeting.
Claims59
A computer-implemented method to generate one or more target binding oligonucleotides, comprising:
- a) processing one or more target nucleic acid sequences with a deployed oligonucleotide generating network and
- b) generating, by the deployed oligonucleotide generating network, one or more engineered target binding oligonucleotides, wherein the one or more engineered target binding oligonucleotides comprise one or more mismatches.
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A system to generate one or more engineered target binding oligonucleotides, comprising:
- a storage device;
- and
- a processor communicatively coupled to the storage device, wherein the processor executes application code instructions that are stored in the storage device to cause the system to:
- a) process one or more target nucleic acid sequences with a deployed oligonucleotide generating network and
- b) generate one or more engineered target binding oligonucleotides with the deployed oligonucleotide generating network, wherein the one or more engineered target binding oligonucleotides comprise one or more mismatches.
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A computer program product, comprising:
- a non-transitory computer-readable storage device having computer-executable program instructions embodied thereon that when executed by a computer cause the computer to generate one or more engineered target binding oligonucleotides, the computer-executable program instructions comprising:
- a) computer-executable program instructions to process one or more target nucleic acid sequences with a deployed oligonucleotide generating network and
- b) computer-executable program instructions to generate one or more engineered target binding oligonucleotides with the deployed oligonucleotide generating network, wherein the one or more engineered target binding oligonucleotides comprise one or more mismatches.
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Dependencies are inferred from the claim text.