Short RNA mimetics
View Patent ↗The present invention provides synthetic oligonucleotides that mimic the function of short RNAs such as, for example, microRNAs or short interfering RNAs. In particular, the synthetic oligonucleotides comprise a duplex region comprising an unpaired bulge in one of the strands.
1. A synthetic oligonucleotide comprising a duplex region comprising a first strand whose sequence has at least about 90% sequence identity with a specific short RNA and a second strand whose sequence has at least about 60% complementarity to the first strand, wherein the duplex region comprises a bulge of one to four unpaired nucleotides in the second strand, the bulge being located between the third nucleotide and the fourth nucleotide from the 3′ end of the duplexed region of the second strand.
2. The synthetic oligonucleotide of claim 1 , wherein the specific short RNA is a microRNA; the first strand comprises ribonucleotides; the second strand comprises ribonucleotides and has a 3′ overhang of two deoxyribonucleotides; the second strand comprises a 5′ amino group; the duplex region is from about 18 base pairs to about 30 base pairs in length; the bulge comprises one or two unpaired nucleotides; and the bulge is located between the third nucleotide and the fourth nucleotide from the 3′ end of the duplexed region of the second strand.
3. A kit for mimicking the function of a specific short RNA, the kit comprising at least one oligonucleotide, wherein each oligonucleotide comprises a first strand whose sequence has at least about 90% sequence identity with the specific short RNA and a second strand whose sequence has at least about 60% complementarity to the first strand; the second strand comprising an insertion of one to four nucleotides near its 3′ end such that upon base pairing between the first strand and the second strand to form a duplex region there is a bulge of unpaired nucleotides in the second strand, wherein the bulge is located between the third nucleotide and the fourth nucleotide from the 3′ end of the duplexed region of the second strand.
4. A method for preparing an oligonucleotide that mimics the function of a specific short RNA, the method comprising:
a) providing a first strand whose sequence has at least about 90% sequence identity with a specific short RNA;
b) providing a second strand whose sequence has at least about 60% complementarity to the first strand, the second strand comprising an insertion of one to four nucleotides near its 3′ end; and
c) allowing the first strand to base pair with the second strand to form a duplex region, wherein the second strand has a bulge of unpaired nucleotides located between the third nucleotide and the fourth nucleotide from the 3′ end of the duplexed region of the second strand.