TY - JOUR
T1 - Interactions of hairpin oligo-2′-O-methylribonucleotides containing methylphosphonate linkages with HIV TAR RNA
AU - Hamma, Tomoko
AU - Miller, Paul S.
PY - 2003/2
Y1 - 2003/2
N2 - Methylphosphonate-modified oligo-2′-O-methylribonucleotides 15-20 nucleotides (nt) in length were prepared whose sequences are complementary to the 5′ and 3′ sides of the upper hairpin of HIV trans-acting response element (TAR) RNA. These anti-TAR oligonucleotides (ODNs) form stable hairpins whose melting temperatures (Tm) range from 55°C to 80°C. Despite their rather high thermal stabilities, the hairpin oligo-2′-O-methylribonucleotides formed very stable complexes with TAR RNA, with dissociation constants in the nanomolar concentration range at 37°C. The affinities of the hairpin oligomers for TAR RNA were influenced by the positions of the methylphosphonate linkages. The binding affinity was reduced approximately 17-fold by the presence of two methylphosphonate linkages in the TAR loop complementary region (TLCR) of the oligomer, whereas methylphosphonate linkages outside this region increased binding affinity approximately 3-fold. The configurations of the methylphosphonate linkages in the TLCR also affected binding affinity, with the RpRp isomer showing significantly higher binding than the SpSp isomer. In addition to serving as probes of the interactions between the oligomer and TAR RNA, the presence of the methylphosphonate linkages in combination with the hairpin structure increases the resistance of these oligomers to degradation by exonucleases found in mammalian serum. The combination of high binding affinity and nuclease resistance of the hairpin ODNs containing methylphosphonate linkages suggests their potential utility as antisense compounds.
AB - Methylphosphonate-modified oligo-2′-O-methylribonucleotides 15-20 nucleotides (nt) in length were prepared whose sequences are complementary to the 5′ and 3′ sides of the upper hairpin of HIV trans-acting response element (TAR) RNA. These anti-TAR oligonucleotides (ODNs) form stable hairpins whose melting temperatures (Tm) range from 55°C to 80°C. Despite their rather high thermal stabilities, the hairpin oligo-2′-O-methylribonucleotides formed very stable complexes with TAR RNA, with dissociation constants in the nanomolar concentration range at 37°C. The affinities of the hairpin oligomers for TAR RNA were influenced by the positions of the methylphosphonate linkages. The binding affinity was reduced approximately 17-fold by the presence of two methylphosphonate linkages in the TAR loop complementary region (TLCR) of the oligomer, whereas methylphosphonate linkages outside this region increased binding affinity approximately 3-fold. The configurations of the methylphosphonate linkages in the TLCR also affected binding affinity, with the RpRp isomer showing significantly higher binding than the SpSp isomer. In addition to serving as probes of the interactions between the oligomer and TAR RNA, the presence of the methylphosphonate linkages in combination with the hairpin structure increases the resistance of these oligomers to degradation by exonucleases found in mammalian serum. The combination of high binding affinity and nuclease resistance of the hairpin ODNs containing methylphosphonate linkages suggests their potential utility as antisense compounds.
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U2 - 10.1089/108729003764097313
DO - 10.1089/108729003764097313
M3 - Article
C2 - 12691533
AN - SCOPUS:24144452762
SN - 1087-2906
VL - 13
SP - 19
EP - 30
JO - Antisense and Nucleic Acid Drug Development
JF - Antisense and Nucleic Acid Drug Development
IS - 1
ER -