Hybridization of antisense oligonucleotides with alpha-sarcin loop region of Escherichia coli 23S rRNA.
Binding of complementary oligonucleotides (ONs) with alpha-sarcin loop region (2638-2682) of Escherichia coli 23S rRNA was investigated. Four of the tested pentadecanucleotides efficiently bound to target sequences with association rate and equilibrium constants approximately 10(3) M(-1)s(-1) and 10(7) M(-1), respectively. ON S5 (CGAGAGGACCGGAGU) complementary to the sequence 2658-2672 displayed the highest affinity to the target. Activation energy for binding of ON S5 was measured to be 11 kcal/mol; this value corresponds to approximately 10% of the calculated enthalpy of the local RNA structure unfolding in the presence of this oligonucleotide. The activation energy value is evidence for the heteroduplex formation to occur via strand displacement pathway; the initiation of heteroduplex formation requires disruption of 1-2 base pairs in RNA hairpin.
Petyuk
Vladislav A
VA
Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia.
Serikov
Roman N
RN
Vlassov
Valentin V
VV
Zenkova
Marina A
MA
D001483:Base Sequence; D004722:Endoribonucleases / Q000737:chemistry*; D004926:Escherichia coli / Q000235:genetics*; D005656:Fungal Proteins / Q000737:chemistry*; D007700:Kinetics; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D016376:Oligonucleotides, Antisense / Q000737:chemistry*; D012329:RNA, Bacterial / Q000737:chemistry*; D012338:RNA, Ribosomal, 23S / Q000737:chemistry*; D013816:Thermodynamics
D005656:Fungal Proteins; D016376:Oligonucleotides, Antisense; D012329:RNA, Bacterial; D012338:RNA, Ribosomal, 23S; C014801:alpha-sarcin; D004722:Endoribonucleases