Secondary structure in solution of two anti-HIV-1 hammerhead ribozymes as investigated by two-dimensional 1H 500 MHz NMR spectroscopy in water.
Two hammerhead chimeric RNA/DNA ribozymes (HRz) were synthesized in pure form. Both were 30 nucleotides long, and the sequences were such that they could be targeted to cleave the HIV-1 gag RNA. Named HRz-W and HRz-M, the former had its invariable core region conserved, the latter had a uridine in the invariable region replaced by a guanine. Their secodary structures were determined by 2D NOESY 1H 500 MHz NMR spectroscopy in 90% water and 10% D2(0), following the imino protons. The data show that both HRz-M and HRz-W form identical secondary structures with stem regions consisting of continuous stacks of AT and GT pairs. An energy minimized computer model of this stem region is provided. The results suggest that the loss of catalytic activity that is known to result when an invariant core residue is replaced is not related to the secondary structure of the ribozymes in the absence of substrate.
Sarma
R H
RH
Institute of Biomolecular Stereodynamics, State University of New York at Albany 12222.
Sarma
M H
MH
Rein
R
R
Shibata
M
M
Setlik
R S
RS
Ornstein
R L
RL
Kazim
A L
AL
Cairo
A
A
Tomasi
T B
TB
D001483:Base Sequence; D015497:HIV-1 / Q000187:drug effects*; D009682:Magnetic Resonance Spectroscopy / Q000379:methods*; D008969:Molecular Sequence Data; D017433:Protein Structure, Secondary; D016337:RNA, Catalytic / Q000737:chemistry* / Q000494:pharmacology; D012996:Solutions
D016337:RNA, Catalytic; D012996:Solutions