Methods and compositions for rna-guided treatment of hiv infection

Abstract

A method of preventing transmission of a retrovirus from a mother to her offspring, by administering to the mother a therapeutically effective amount of a composition comprising a Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)-associated endonuclease, and the two or more different multiplex gRNAs, wherein each of the at least two gRNAs is complementary to a different target nucleic acid sequence in a long terminal repeat (LTR) of proviral DNA of the virus that is unique from the genome of the host cell, cleaving a double strand of the proviral DNA at a first target protospacer sequence with the CRISPR-associated endonuclease, cleaving a double strand of the proviral DNA at a second target protospacer sequence with the CRISPR-associated endonuclease, excising an entire HIV-I proviral genome, eradicating the HIV-I proviral DNA from the host cell, and preventing transmission of the proviral DNA to the offspring.

What is claimed is: 
     
         1 . A method of excising part or all of a retroviral sequence from a genome of a cell, the method comprising contacting the cell with:
 a. a CRISPR-associated endonuclease or a nucleic acid encoding the CRISPR-associated endonuclease;   b. a first guide RNA (gRNA) or a nucleic acid encoding the first gRNA, the first gRNA being complementary to a first target nucleic acid site within the retroviral sequence; and   c. a second gRNA or nucleic acid encoding the second gRNA, the second gRNA being complementary to a second target nucleic acid site within the retroviral sequence.   
     
     
         2 . The method of  claim 1 , wherein the first target nucleic acid site is within section U3, R, or U5 region of a 5′ long terminal repeat (LTR). 
     
     
         3 . The method of  claim 1 , wherein the first target nucleic acid site is within section U3, R, or U5 region of a 3′ LTR. 
     
     
         4 . The method of  claim 1 , wherein the second target nucleic acid site is within section U3, R, or U5 region of a 5′ long terminal repeat (LTR). 
     
     
         5 . The method of  claim 1 , wherein the second target nucleic acid site is within section U3, R, or U5 region of a 3′ LTR. 
     
     
         6 . A method of excising part or all of a retroviral sequence from a genome of a cell, the method comprising contacting the cell with:
 a. a CRISPR-associated endonuclease or a nucleic acid encoding the CRISPR-associated endonuclease; and   b. at least one guide RNA (gRNA) or a nucleic acid encoding the at least one gRNA, one or more of the at least one gRNA being complementary to a first target nucleic acid site within a retroviral sequence and one or more of the at least one gRNA being complementary to a second target nucleic acid site within the retroviral sequence.   
     
     
         7 . The method of  claim 6 , wherein the first target nucleic acid site is within section U3, R, or U5 region of a 5′ long terminal repeat (LTR). 
     
     
         8 . The method of  claim 6 , wherein the first target nucleic acid site is within section U3, R, or U5 region of a 3′ LTR. 
     
     
         9 . The method of  claim 6 , wherein the second target nucleic acid site is within section U3, R, or U5 region of a 5′ long terminal repeat (LTR). 
     
     
         10 . The method of  claim 6 , wherein the second target nucleic acid site is within section U3, R, or U5 region of a 3′ LTR. 
     
     
         11 . A composition:
 a. a CRISPR-associated endonuclease or a nucleic acid encoding the CRISPR-associated endonuclease;   b. a first guide RNA (gRNA) or a nucleic acid encoding the first gRNA, the first gRNA being complementary to a first target nucleic acid site within a retroviral sequence;   c. a second gRNA or nucleic acid encoding the second gRNA, the second gRNA being complementary to a second target nucleic acid site within the retroviral sequence; and   d. an excipient.   
     
     
         12 . The composition of  claim 11 , wherein the first target nucleic acid site is within section U3, R, or U5 region of a 5′ long terminal repeat (LTR). 
     
     
         13 . The composition of  claim 11 , wherein the first target nucleic acid site is within section U3, R, or U5 region of a 3′ LTR. 
     
     
         14 . The composition of  claim 11 , wherein the second target nucleic acid site is within section U3, R, or U5 region of a 5′ long terminal repeat (LTR). 
     
     
         15 . The composition of  claim 11 , wherein the second target nucleic acid site is within section U3, R, or U5 region of a 3′ LTR. 
     
     
         16 . The composition of  claim 11 , wherein the nucleic acid sequence encoding the CRISPR-associated endonuclease, the nucleic acid sequence encoding the first gRNA, and the nucleic acid sequence encoding the second gRNA are in a same expression vector. 
     
     
         17 . The composition of  claim 11 , wherein the nucleic acid sequence encoding the CRISPR-associated endonuclease, the nucleic acid sequence encoding the first gRNA, and the nucleic acid sequence encoding the second gRNA are in different expression vectors.