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T Neilson

Publications and source records attributed to T Neilson.

29 records · Page 2Linked to original sources
PubMed1980

Association of a synthetic precistronic region with 70S ribosomes is enhanced by an intact initiation triplet and a sequence complementary to the 3'-terminus of 16S rRNA.

The sequence, AGGACAUAUGp, which is identical to the precistronic region of the bacteriophage Q beta A protein was synthesized by chemical and enzymatic means. Methods for synthesizing this sequence and analogues of this sequence using RNA ligase forward and back reactions from short oligonucleotides of defined sequence, are reported, including a useful means of purifying the oligonucleotides by preparative electrophoresis, as well as removal of 32p-ATP, salts and buffers by a simple filter binding technique. E. coli 70S ribosomes bind the synthetic native precistronic region substantially better than related probes in which the 16S complementary region, AGCA, is replaced by the anticomplementary region, UCCU, or is altogether absent. In addition, an intact initiation codon, AUG, is essential for interaction of mRNA with prokaryotic ribosomes.

Base Sequence↗
PubMed1980

The effects of base sequence and dangling bases on the stability of short ribonucleic acid duplexes.

Variable temperature proton nuclear magnetic resonance spectroscopy is used to establish that both sequence and dangling bases affect stability of short RNA double helices. Tetraribonucleotides, CAUG, UGCA and AGCU form reference duplexes (Tm 25 degrees, 33 degrees, 34 degrees, respectively) which contain an equal number of G . C and A . U base pairs and which show primary sequence is important. Pentaribonucleotides GAUGA, ACAUG, UGCAA and AGCUA, form duplexes (Tm 36 degrees, 35 degrees, 46 degrees, 45 degrees, respectively) with dangling adenines. Average Tm difference from the reference is +11 degrees for two 3' or 5'-dangling adenines. Pentaribonucleotides, CAUGU and UCAUG, form duplexes (Tm both 30 degrees) with dangling uracils. Average Tm difference from the reference is +5 degrees for two 3' or 5'-dangling uracils. Fraying was detected only in duplexes from the AGCU series. Presence of a dangling adenine, in duplex, AGCUA, caused a reduction in fraying.

Base Composition↗
PubMed1979

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

Proton nuclear magnetic resonance has been used to examine the effect of both noncomplementary and G.U oppositions in the duplexes formed by the synthetic pentaribonucleotides CpApApUpG, CpApUpUpG, CpApGpUpG, and CpApCpUpG. The lack of any sigmoidal behavior in the chemical shift vs. temperature plots of the base protons in the individual pentaribonucleotides indicates that duplexes with noncomplementary base oppositions of the type: formula: (see text), (where X = A, U, G, or C) do not form. Variable temperature spectra of the mixture of CpApGpUpG and CpApUpUpG were recorded over the range of 70--10 degrees C. The chemical shift vs. temperature plot of the purine aromatic protons displayed sigmoidal curves. This demonstrated both duplex formation and the presence of a G.U. base pair. The average Tm of the duplex was found to be 23.4 +/- 2.0 degrees C. This is similar to that of the duplex formed by CpApUpG (24.0 +/- 1.0 degrees C) but less than the Tm of the following duplexes: CpApApUpG:CpApUpUpG (Tm = 28.5 +/- 2.1 degrees C), CpApGpUpG:CpApCpUpG (Tm = 38.4 +/- 0.6 degrees C) and CpApUpApUpG (Tm = 41.5 +/- 1.1 degrees C). The G.U base pair has a Tm (20.0 degrees C) significantly lower than the rest of the duplex (24 +/- 1 degree C) and is a region of local instability within the double helix. This 1H NMR study is the first to investigate both the formation and relative stability of an internal G.U. base pair neighboring regular Watson--Crick base pairs.

Base Composition↗
PubMed1977

Duplex formation of complementary oligoribonucleotides corresponding to the dihydrouridine loop neck region of several transfer ribonucleic acids.

Formation of short, double-stranded RNA helices by the complementary oligoribonucleotides GpApGpC, GpCpUpC, and ApGpCpUpC was established by the temperature-dependent changes in uv hypochromicity and circular dichroism spectra. These studies provide additional thermodynamic data on duplex formation. Duplexes (formula: see text) are especially significant as they: (1) correspond to a natural sequence, the dihydrouridine loop neck region, common to several tRNA molecules; (2) correspond to a proposed, partial recognition site for yeast phenylalanyl-tRNA ligase (EC 6.1.1.20); and (3) represent the first demonstration of a duplex with four base pairs, one of which is an A--U pair. These duplexes should serve as models for studies on tRNA-ligase interaction.

Binding Sites↗