Method of determining a cellular response to a biological agent
First Claim
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1. A method of determining a cellular response to a biological agent, the method comprising:
- providing a well plate in a sealed, sterile package, the well plate being storable at a temperature of up to at least about 37°
C. while maintaining functionality of a dried siRNA deposited therein, the well plate having a plurality of wells, including;
a first control well with a dried control composition, wherein the dried control composition includes at least one of no siRNA, a positive control siRNA that is capable of targeting a known gene, a non-targeting negative control siRNA, an siRNA having at least one toxic motif, a non-functional siRNA, an siRNA that inhibits being taken in and processed by RISC, or a control siRNA that includes a fluorescent marker, the dried control composition being capable of being solublized or resuspended in an aqueous medium; and
a first test well with a dried test gene silencing composition deposited therein that includes a test siRNA that is capable of silencing a first target gene, the dried test gene silencing composition being capable of being solublized or resuspended in the aqueous medium, the test siRNA comprising;
a sense strand having 2′
-O-methyl modifications on the first and second 5′
nucleotides; and
an antisense strand having a 2′
-O-methyl modification on the second 5′
nucleotide and a 5′
end phosphate;
wherein the sense region and the antisense region are capable of forming a duplex of 18-26 base pairs of nucleotides that has at least 80% complementarity over the range of the duplex, and wherein nucleotides of the sense strand and antisense strand other than the first 5′
sense nucleotide, the second 5′
sense nucleotide, and the second 5′
antisense nucleotide include a 2′
-OH;
unsealing the package to expose the plurality of wells;
adding the aqueous medium to the first control well and the first test well;
solublizing or resuspending the dried test gene silencing composition and the dried control composition in the aqueous medium;
adding cells to the first test well under conditions that permit transfection;
adding cells to a first control well under conditions that permit transfection;
adding a biological agent to the first test well and first control well, the biological agent being at least one of a known drug, a pro-drug, a candidate drug, a nucleic acid, a plasmid DNA, a polypeptide, a protein, an enzyme, a cytokine, a hormone, a polymer, a known cellular toxin, a suspected toxin, a microorganism, a virus, a bacterium, a yeast, a protozoan, or a sensitizing agent; and
determining whether a first response to the biological agent by the cells in the first test well is different from a first control response to the biological agent by the cells in the first control well, wherein a condition of the first response being different from the first control response is an indication that the first target gene is involved in the response by the cell to the biological agent.
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Abstract
A method of determining a cellular response to a biological agent can be preformed in the presence of gene silencing. Such a method can include the use of siRNA in order to silence various genes in the cell in order to monitor the cellular response to the biological agent when a gene has been silenced. Accordingly, the response of a cell having a silenced gene to a biological agent can be indicative of which genes may be responsible for normal or abnormal cellular responses to various synthetic and natural biological agents such as active agents or pathogens.
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Citations
23 Claims
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1. A method of determining a cellular response to a biological agent, the method comprising:
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providing a well plate in a sealed, sterile package, the well plate being storable at a temperature of up to at least about 37°
C. while maintaining functionality of a dried siRNA deposited therein, the well plate having a plurality of wells, including;a first control well with a dried control composition, wherein the dried control composition includes at least one of no siRNA, a positive control siRNA that is capable of targeting a known gene, a non-targeting negative control siRNA, an siRNA having at least one toxic motif, a non-functional siRNA, an siRNA that inhibits being taken in and processed by RISC, or a control siRNA that includes a fluorescent marker, the dried control composition being capable of being solublized or resuspended in an aqueous medium; and a first test well with a dried test gene silencing composition deposited therein that includes a test siRNA that is capable of silencing a first target gene, the dried test gene silencing composition being capable of being solublized or resuspended in the aqueous medium, the test siRNA comprising; a sense strand having 2′
-O-methyl modifications on the first and second 5′
nucleotides; andan antisense strand having a 2′
-O-methyl modification on the second 5′
nucleotide and a 5′
end phosphate;wherein the sense region and the antisense region are capable of forming a duplex of 18-26 base pairs of nucleotides that has at least 80% complementarity over the range of the duplex, and wherein nucleotides of the sense strand and antisense strand other than the first 5′
sense nucleotide, the second 5′
sense nucleotide, and the second 5′
antisense nucleotide include a 2′
-OH;unsealing the package to expose the plurality of wells; adding the aqueous medium to the first control well and the first test well; solublizing or resuspending the dried test gene silencing composition and the dried control composition in the aqueous medium; adding cells to the first test well under conditions that permit transfection; adding cells to a first control well under conditions that permit transfection; adding a biological agent to the first test well and first control well, the biological agent being at least one of a known drug, a pro-drug, a candidate drug, a nucleic acid, a plasmid DNA, a polypeptide, a protein, an enzyme, a cytokine, a hormone, a polymer, a known cellular toxin, a suspected toxin, a microorganism, a virus, a bacterium, a yeast, a protozoan, or a sensitizing agent; and determining whether a first response to the biological agent by the cells in the first test well is different from a first control response to the biological agent by the cells in the first control well, wherein a condition of the first response being different from the first control response is an indication that the first target gene is involved in the response by the cell to the biological agent. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19)
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17. A method of determining a cellular response to an siRNA, the method comprising:
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adding an aqueous medium to a first test well in a well plate having a substantially dry gene silencing composition, the gene silencing composition having a test siRNA that is capable of silencing a first target gene, the dried test gene silencing composition being capable of being solublized or suspended in the aqueous medium in an amount sufficient for transfecting cells in the first test well, the test siRNA comprising; a sense strand having 2′
-O-methyl modifications on the first and second 5′
nucleotides; andan antisense strand having a 2′
-O-methyl modification on the second 5′
nucleotide and a 5′
end phosphate;wherein the sense region and the antisense region are capable of forming a duplex of 18-26 base pairs of nucleotides that has at least 80% complementarity over the range of the duplex, and wherein nucleotides of the sense strand and antisense strand other than the first 5′
sense nucleotide, the second 5′
sense nucleotide, and the second 5′
antisense nucleotide include a 2′
-OH;solublizing or resuspending the dried test gene silencing composition in the aqueous medium; adding cells to the first test well under conditions that permit transfection; adding cells to a first control well with a dried control composition under conditions that permit transfection, wherein, the dried control composition in the first control well includes at least one of no siRNA, a positive control siRNA that is capable of targeting a known gene, a non-targeting negative control siRNA, an siRNA having at least one toxic motif, a non-functional siRNA, an siRNA that inhibits being taken in and processed by RISC, or a control siRNA that includes a fluorescent marker, the dried control composition being capable of being solublized or resuspended in an aqueous medium; comparing the effect of the control composition and the test siRNAs on the cells in the first test well and the first control well. - View Dependent Claims (20, 21, 22, 23)
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Specification