Studies on the structure and stabilizing factor of the CUUCGG hairpin RNA using chemically synthesized oligonucleotides.
A tridecaribonucleotide, r-UGAGCUUCGGCUC, and two analogues r(UGAGC)d(UUCG)r(GCUC) and r-UGAGCUUCIGCUC, which form a hairpin structure with a four-base-paired stem and a UUCG loop, were synthesized by the solid-phase phosphoramidite method. Properties of these three oligomers and d-TGAGCTTCGGCTC, the DNA analogue, were studied by UV, CD and NMR spectroscopy. The melting temperature (Tm) data suggest that the 2'-hydroxy1 groups and the 2-amino group of guanosine in the loop (9G) stabilize the CUUCGG hairpin which is known to have an unusually high Tm. NMR studies show that this 9G takes a syn conformation and the phosphodiester backbone has a turn at 9G-10G which is a junction of the stem and loop.
Sakata
T
T
Faculty of Pharmaceutical Sciences, Osaka University, Japan.
Hiroaki
H
H
Oda
Y
Y
Tanaka
T
T
Ikehara
M
M
Uesugi
S
S
D001483:Base Sequence; D002942:Circular Dichroism; D009682:Magnetic Resonance Spectroscopy; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009843:Oligoribonucleotides / Q000138:chemical synthesis; D011131:Polyribonucleotides / Q000138:chemical synthesis; D012313:RNA / Q000235:genetics*; D013056:Spectrophotometry, Ultraviolet; D013696:Temperature
D009843:Oligoribonucleotides; D011131:Polyribonucleotides; D012313:RNA