Showing papers on "Nucleic acid secondary structure published in 1981"

Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information

Abstract: This paper presents a new computer method for folding an RNA molecule that finds a conformation of minimum free energy using published values of stacking and destabilizing energies. It is based on a dynamic programming algorithm from applied mathematics, and is much more efficient, faster, and can fold larger molecules than procedures which have appeared up to now in the biological literature. Its power is demonstrated in the folding of a 459 nucleotide immunoglobulin gamma 1 heavy chain messenger RNA fragment. We go beyond the basic method to show how to incorporate additional information into the algorithm. This includes data on chemical reactivity and enzyme susceptibility. We illustrate this with the folding of two large fragments from the 16S ribosomal RNA of Escherichia coli.

Base pairing of RNA I with its complementary sequence in the primer precursor inhibits ColE1 replication

Abstract: Four single base pair mutations in the region that codes for RNA I create new incompatibility groups while preserving the mechanism of control of initiation of DNA replication in a ColE1-type plasmid. Sequence analysis of these base substitutions points to the primary importance of the central loop of the cloverleaf structure of RNA I in this control mechanism.

Secondary structure formation during RNA synthesis.

Abstract: We observed the secondary structures that formed in an RNA molecule during its synthesis. Some of the secondary structures seen in nascent chains were observed to form, then to dissociate in favor of an alternative structure, and then to reform, as chain growth continued. The results show that secondary structures in an RNA molecule are in a state of dynamic equilibrium, and that the extension of a sequence by chain growth, or the reduction of a sequence by processing, may result in significant changes in the secondary structures that are present.

Ribonucleic acid synthesis termination protein rho function: effects of conditions that destabilize ribonucleic acid secondary structure.

Abstract: The dependence fo rate of adenosine 5'-triphosphate (ATP) hydrolysis catalyzed by ribonucleic acid (RNA) synthesis termination protein rho from Escherichia coli with T7 RNA as cofactor is used to probe the nature of the interaction between rho and RNA. In general, reaction conditions that destabilize the secondary structure of the RNA enhance its cofactor activity. This is indicated by the effects of MgCl2 concentration, spermidine, temperature, dimethyl sulfoxide, and pretreatment of the RNA with formaldehyde. These results suggest that a functional interaction between rho and RNA depends either on the presence of a sufficiently large single-stranded region in the RNA or on the ability of rho to unwind double helices in the RNA. It is also shown that changes in reaction conditions that increase RNA secondary structure and decrease the rho protein adenosine triphosphate phosphohydrolase (rhoATPase) activity with isolated T7 RNA also decrease the stringency of rho action in RNA synthesis termination. On the other hand, monovalent salts decrease rhoATPase activity with isolated T7 RNA and binding of rho to T7 RNA independently of the MgCl2 concentration and thus the relative stability of the RNA secondary structure.

DNA sequence of the transfer RNA region of bacteriophage T4: implications for transfer RNA synthesis.

Abstract: Sequences encoding eight tRNAs and two stable RNAs of bacteriophage T4 are grouped together on the T4 genome in two clusters, separated by approximately 500 base pairs. The DNA sequence of part of this region was determined. Within each cluster coding sequences are separated by only one or a few base pairs. These findings imply that the RNAs may be processed from a single multimeric transcript, with initial endonucleolytic cleavages generating the previously characterized monomeric and dimeric precursors.

Determination of base pairing in yeast 5S and 5.8S RNA by infrared spectroscopy

Abstract: Infrared Spectroscopy was used to determine the numbers of base pairs for yeast 5S RNA and 5.8S RNA. The spectra were recorded at 20 degrees C and 50 degrees C, where tertiary interactions are assumed to be of less importance. It may be concluded that the structure of both RNAs is highly ordered and that there are large contributions of tertiary interactions. The results are compared with data derived from structural models that were proposed in the literature as well as with data previously published for prokaryotic 5S RNAs.

The nucleotide sequence of phenylalanine tRNA and 5S RNA from Rhodospirillum rubrum.

Abstract: The complete nucleotide sequence of tRNAPhe and 5S RNA from the photosynthetic bacterium Rhodospirillum rubrum has been elucidated. A combination of in vitro and in vivo labelling techniques was used. The tRNAPhe sequence is 76 nucleotides long, 7 of which are modified. The primary structure is typically prokaryotic and is most similar to the tRNAPhe of Escherichia coli and Anacystis nidulans (14 differences of 76 positions). The 5S ribosomal RNA sequence is 120 nucleotides long and again typical of other prokaryotic 5S RNAs. The invariable GAAC sequence is found starting at position 45. When aligned with other prokaryotic 5S RNA sequences, a surprising amount of nucleotide substitution is noted in the prokaryotic loop region of the R. rubrum 5S RNA. However, nucleotide complementarity is maintained reinforcing the hypothesis that this loop is an important aspect of prokaryotic 5S RNA secondary structure. The 5S and tRNAPhe are the first complete RNA sequences available from the photosynthetic bacteria.

Theoretical evidence for the significance of certain types of DNA secondary structure in the genomes of phi X174, G4, fd, SV40 and the plasmid pBR322.

Abstract: The significance of certain types of DNA secondary structure was assessed on a purely theoretical basis by analyzing their distribution over the entire genomes of bacteriophages phi X174, G4, fd, the eucaryotic virus SV40 and the E. coli plasmid pBR322. A computer program was designed to search the translated and non-translated (intercistronic) regions of these genomes for the potential of forming perfect hairpins (perfectly base paired stems: no G-T pairing; no interruptions) with small loops. The number of found occurrences was then compared to the statistically expected number. The results reveal a significant excess in each genome of perfect hairpins with stem length greater than 7 and end loops less than or equal to 20 over that expected given their nucleotide composition. For stem length of 5 to 7 the same observation holds true for the intercistronic regions, but for translated regions the number of such structures is below expectation. This suggests an evolutionary selection for these structures.

Conservation and divergence in single-stranded phage dna secondary structure: relations to origins of dna replication

Abstract: Using the same partial denaturing conditions employed for φX174 DNA (1), the secondary structure of G4 DNA was analyzed by electron microscopy. Both φX and G4 viral DNAs were folded into similar characteristic three-lobed structures, an observation consistent with their similar genetic maps and nucleotide sequences. The locations of stem and loop structures comprising the three lobes were mapped relative to the ends of Pst I-, Eco RI-, and Sst II-cleaved G4 replicative form DNA. It was found that the secondary structure surrounding the origin of viral strand replication was conserved in φX and G4 DNAs. Since φX and G4 have similar modes of viral strand replication, this conservation is consistent with our previous suggestion that secondary structure specifically folds viral DNA to promote its circularization. Two major differences between the secondary structures of φX and G4 DNAs, involving the smallest of the three lobes, were located in the region of the G4 origin of complementary strand replication. These structural changes can be correlated with the different modes of complementary strand replication utilized by φX and G4.