Back to results
US 2019/0055551 A1Published application
NOVEL pRNA THREE-WAY JUNCTIONS
AssigneeThe Board of Regents of the University of Oklahoma
InventorsAlyssa C. Hill, Susan J. Schroeder
Life of this patent
Estimating the term…
Abstract
Three-way junction (3WJ) RNA scaffolds derived from phi29, M2, SF5, and GA1 pRNAs and which have high stability are described. The pRNA 3WJ scaffolds can be used to form compounds, conjugates, compositions, and nanoparticles for delivery of active agents for therapeutic and/or diagnostic functions.
Claims28
An RNA junction scaffold, comprising:
- a three-way junction (3WJ) domain, the 3WJ domain comprising a 3WJa sequence comprising a first RNA polynucleotide, a 3WJb sequence comprising a second RNA polynucleotide, and a 3WJc sequence comprising a third RNA polynucleotide, wherein a first branch of the 3WJ domain is formed from a 5′ portion of the 3WJa sequence and a 3′ portion of the 3WJc sequence and comprises a first helical region, a second branch of the 3WJ domain is formed from a 3′ portion of the 3WJa sequence and a 5′ portion of the 3WJb sequence and comprises a second helical region, and a third branch of the 3WJ domain is formed from a 3′ portion of the 3WJb sequence and a 5′ portion of the 3WJc sequence and comprises a third helical region, wherein each of said helical regions comprises a plurality of RNA nucleotide pairs that form canonical Watson-Crick bonds, and wherein (i) the 3WJa sequence is absent an unpaired nucleotide positioned between the first helical region and the second helical region, and two unpaired nucleotides are positioned in the 3WJa sequence in the second branch, and (ii) two adjacent unpaired nucleotides are positioned in the 3WJc sequence between the first helical region and the third helical region, and one unpaired nucleotide is positioned in the 3WJb sequence between the second helical region and the third helical region.
An RNA junction scaffold, comprising:
- a three-way junction (3WJ) domain, the 3WJ domain comprising a 3WJa sequence comprising a first RNA polynucleotide, a 3WJb sequence comprising a second RNA polynucleotide, and a 3WJc sequence comprising a third RNA polynucleotide, wherein a first branch of the 3WJ domain is formed from a 5′ portion of the 3WJa sequence and a 3′ portion of the 3WJc sequence and comprises a first helical region, a second branch of the 3WJ domain is formed from a 3′ portion of the 3WJa sequence and a 5′ portion of the 3WJb sequence and comprises a second helical region, and a third branch of the 3WJ domain is formed from a 3′ portion of the 3WJb sequence and a 5′ portion of the 3WJc sequence and comprises a third helical region, wherein each of said helical regions comprises a plurality of RNA nucleotide pairs that form canonical Watson-Crick bonds, and wherein (i) the 3WJa sequence is absent an unpaired nucleotide positioned between the first helical region and the second helical region, and one unpaired nucleotide is positioned in the 3WJa sequence in the second branch, and (ii) two adjacent unpaired nucleotides are positioned in the 3WJb sequence between the second helical region and the third helical region.
An RNA junction scaffold, comprising:
- a three-way junction (3WJ) domain, the 3WJ domain comprising a 3WJa sequence comprising a first RNA polynucleotide, a 3WJb sequence comprising a second RNA polynucleotide, and a 3WJc sequence comprising a third RNA polynucleotide, wherein a first branch of the 3WJ domain is formed from a 5′ portion of the 3WJa sequence and a 3′ portion of the 3WJc sequence and comprises a first helical region, a second branch of the 3WJ domain is formed from a 3′ portion of the 3WJa sequence and a 5′ portion of the 3WJb sequence and comprises a second helical region, and a third branch of the 3WJ domain is formed from a 3′ portion of the 3WJb sequence and a 5′ portion of the 3WJc sequence and comprises a third helical region, wherein each of said helical regions comprises a plurality of RNA nucleotide pairs that form canonical Watson-Crick bonds, and wherein the 3WJa sequence is absent an unpaired nucleotide positioned between the first helical region and the second helical region, and is absent at least one of (1) an unpaired nucleotide in a position corresponding to an unpaired guanine nucleotide in position 31 of a wild type SF5 pRNA, and (2) an unpaired nucleotide in a position corresponding to an unpaired guanine nucleotide in position 69 of said wild type SF5 pRNA.
An RNA junction scaffold, comprising:
- a three-way junction (3WJ) domain, the 3WJ domain comprising a 3WJa sequence comprising a first RNA polynucleotide, a 3WJb sequence comprising a second RNA polynucleotide, and a 3WJc sequence comprising a third RNA polynucleotide, wherein a first branch of the 3WJ domain is formed from a 5′ portion of the 3WJa sequence and a 3′ portion of the 3WJc sequence and comprises a first helical region, a second branch of the 3WJ domain is formed from a 3′ portion of the 3WJa sequence and a 5′ portion of the 3WJb sequence and comprises a second helical region, and a third branch of the 3WJ domain is formed from a 3′ portion of the 3WJb sequence and a 5′ portion of the 3WJc sequence and comprises a third helical region, wherein each of said helical regions comprises a plurality of RNA nucleotide pairs that form canonical Watson-Crick bonds, and wherein the 3WJa sequence is absent an unpaired nucleotide in a position between the first helical region and the second helical region corresponding to an unpaired uridine nucleotide in position 29 of a wild type phi29 pRNA positioned, and is absent two unpaired nucleotides in positions corresponding to two unpaired uridine nucleotides in positions 72 and 73 of said wild type phi29 pRNA.
An RNA junction scaffold, comprising:
- a three-way junction (3WJ) domain, the 3WJ domain comprising a 3WJa sequence comprising a first RNA polynucleotide, a 3WJb sequence comprising a second RNA polynucleotide, and a 3WJc sequence comprising a third RNA polynucleotide, wherein a first branch of the 3WJ domain is formed from a 5′ portion of the 3WJa sequence and a 3′ portion of the 3WJc sequence and comprises a first helical region, a second branch of the 3WJ domain is formed from a 3′ portion of the 3WJa sequence and a 5′ portion of the 3WJb sequence and comprises a second helical region, and a third branch of the 3WJ domain is formed from a 3′ portion of the 3WJb sequence and a 5′ portion of the 3WJc sequence and comprises a third helical region, wherein each of said helical regions comprises a plurality of RNA nucleotide pairs that form canonical Watson-Crick bonds, and wherein (i) the 3WJa sequence comprises a single unpaired nucleotide positioned between the first helical region and the second helical region, and an unpaired nucleotide positioned in the 3WJa sequence in the second branch downstream of the unpaired nucleotide positioned between the first helical region and the second helical region, and (ii) a single unpaired nucleotide positioned in the 3WJc sequence between the first helical region and the third helical region.
An RNA junction scaffold, comprising:
- a three-way junction (3WJ) domain, the 3WJ domain comprising a 3WJa sequence comprising a first RNA polynucleotide, a 3WJb sequence comprising a second RNA polynucleotide, and a 3WJc sequence comprising a third RNA polynucleotide, wherein a first branch of the 3WJ domain is formed from a 5′ portion of the 3WJa sequence and a 3′ portion of the 3WJc sequence and comprises a first helical region, a second branch of the 3WJ domain is formed from a 3′ portion of the 3WJa sequence and a 5′ portion of the 3WJb sequence and comprises a second helical region, and a third branch of the 3WJ domain is formed from a 3′ portion of the 3WJb sequence and a 5′ portion of the 3WJc sequence and comprises a third helical region, wherein each of said helical regions comprises a plurality of RNA nucleotide pairs that form canonical Watson-Crick bonds, and wherein (i) zero or one unpaired nucleotide is positioned in the 3WJa sequence between the first helical region and the second helical region, and/or one or two unpaired nucleotides are positioned in the 3WJa sequence in the second branch, and (ii) one unpaired or two adjacent unpaired nucleotides are positioned in the 3WJc sequence between the first helical region and the third helical region, and/or one unpaired or two adjacent unpaired nucleotides are positioned in the 3WJb sequence between the second helical region and the third helical region.
Dependencies are inferred from the claim text.