Proton magnetic resonance studies on short duplexes. I. Helix formation by the duplex set GpApGpC:GpCpUpC

Abstract

Proton magnetic resonance bas been used to investigate the double stranded RNA helix GAGC:GCUC, whose sequence corresponds to the duplex neck region of several tRNAs, a possible aminoacyl-tRNA synthetase recognition site. The nonexchangeable base and ribose anomeric resonances of the separate tetranucleotides were characterized by linear and predominantly upfield chemical shift changes as the temperature was decreased from 65 to 15 °C. When these strands were mixed nonlinear, sigmoidal shift changes consistent with base pairing were observed. The melting temperature of the duplex was determined to be 42 ± 1 °C which was in excellent agreement with the value obtained from optical methods. This is the first 1Hmr study of a non-self-complementary duplex prepared from synthetic tetraribonucleotides.

Sequence and structure in double-stranded ribonucleic acid: (A-G-C-U)2 and (A-C-G-U)2

“…In support of the end-to-end association model, we note that the AH2 line broadens severely in our A-terminal oligomers while it was sharp in (C-A-U-G)2 and G-A-G-C:G-C-U-C (Romaniuk et al, 1978;Hughes et al, 1978) where the A residue was not at the duplex end. It could as easily reflect some difference in the stacking geometry or the dynamic behavior of the duplex, however.…”

Effects of internal nonbonded bases and a G.cntdot.U base pair on the stability of a short ribonucleic acid helix

“…One approach to this problem has been the investigation of model duplex systems by NMR spectroscopy. Both deoxyribonucleotide (Cross & Crothers, 1971;Crothers et al, 1973;Patel, 1976Patel, , 1977Patel, , 1979; Early et al, 1978) and ribonucleotide sequences (Arter et al, 1974;Borer et al, 1975;Kan et al, 1975;Hughes et al, 1978;Romaniuk et al, 1978a,b) have been studied. In sufficiently simple sequences, each nucleotide is identifiable by several resonances, and, by the nature of an NMR experiment, the helix to coil transition of each base pair in the duplex can be monitored.…”

“…We have begun a series of experiments which probe various aspects of RNA secondary structure using an assortment of short oligoribonucleotides (Hughes et al, 1978;Romaniuk et al, 1978a,b). We have reported previously on the stabilizing effect of a dangling base on a neighboring duplex (Romaniuk et al, 1978a).…”

Comparative study of ribonucleotides, deoxyribonucleotides, and hybrid oligonucleotide helixes by nuclear magnetic resonance

“…Melting of the end base pairs before the rest of the helix has been seen in several of the systems with A-U or • base pairs on the ends of the helix (Borer et al, 1975;Patel, 1975;Kallenbach et al, 1976). In helices with C-G base pairs on the ends, there seems to be no (Hughes et al, 1978) or little (Patel, 1979) differential melting of the ends of the helix before the rest of the oligonucleotide. However, most of the systems studied thus far have been self-complementary oligonucleotides [except for that of Hughes et al (1978)]; this precludes measurement of the temperature dependence of the single strands.…”