A transient species of poly(A)+ RNA detected by a myosin heavy chain cDNA probe in muscle cell culture during terminal differentiation

Primary cell cultures were prepared from breast muscles of 11 day 4 hour-embryonic chicks. Cytoplasmic RNAs were isolated from the cultured cells at various time intervals from day 3 to day 8. A [P32] DNA probe complementary to messenger RNA of myosin heavy chain was used to hybridize with the RNAs after gel electrophoresis. A transient species of polyadenylated RNA with a decreased mobility in electrophoresis was detected during a period of time when contractions of syncytial fibers were first observed.     

Markov chain analysis finds a significant influence of neighboring bases on the occurrence of a base in eucaryotic nuclear DNA sequences both protein-coding and noncoding

Summary Sixty-four eucaryotic nuclear DNA sequences, half of them coding and half noncoding, have been examined as expressions of first-, second-, or third-order Markov chains. Standard statistical tests found that most of the sequences required at least second-order Markov chains for their representation, and some required chains of third order. For all 64 sequences the observed one-step second-order transition count matrices were effective in predicting the two-step transition count matrices, and 56 of 64 were effective in predicting the three-step transition count matrices. The departure from random expectation of the observed first- and second-order transition count matrices meant that a considerable sample of eucaryotic nuclear DNA sequences, both protein coding and noncoding, have significant local structure over subsequences of three to five contiguous bases, and that this structure occurs throughout the total length of the sequence. These results suggested that present DNA sequences may have arisen from the duplication, concatenation, and gradual modification of very early short sequences.     

Sulphatides and pollination in Oenothera missouriensis

Analyses of the sulphatides in the pollen and style of Oenothera missouriensis show that these membranous lipids are comparatively less important in the styles than in the pollen. Incompatible pollination is followed by a large increase in sulphatides, whereas cross-pollination also causes an increase in sulphatide but to a much lesser extent. This mobilization of sulphatides in the membrane is discussed in term of permeability.     

A prevalent persistent global nonrandomness that distinguishes coding and non-coding eucaryotic nuclear DNA sequences

Summary Coding sequences of eucaryotic nuclear DNA were characterized by an excess of short runs and a deficit of long runs of weak and of strong hydrogen bonding bases; non-coding sequences by a deficit of short runs and an excess of long runs, in the same of purines and of pyrimidines. The conservation of these attributes across DNA sequences coding for proteins of widely different function, across widely different eucaryotic species for the same protein and across related genes that diverged a long time ago and that now show large differences in base and, if coding, amino acid sequence suggested that these attributes have survival value. It was concluded that these attributes constitute probalistic constraints on th primary structure (base sequence) of both coding and non-coding DNA.     

Mutagenic role of Watson-Crick protons in alkylated DNA bases: A theoretical study

Loss of Watson-Crick protons following DNA base alkylation has been proposed as a key event which confers mutation-inducing properties on to alkylated DNA bases. In this theoretical study, the promutagenic O⁶-guanine and O⁴-thymine sites are clearly distinguished from the nonmutagenic N⁷-guanine site on the basis of calculated values of mechanistic indicators for Watson-Crick proton acidity following alkylation at these respective sites. The degree of acidity predicted for these protons for each type of alkylated base accords well with the presence or absence of mutagenicity observed experimentally in each case.     

New technique in optical resolutions

The present paper illustrates the development of an advanced technique in optical resolution. Both of the amphetamine enantiomers can be obtained by a two-step distillation in nearly quantitative yield without any loss of the resolving agent. It is proved that the second-order interactions (H-bond) are sufficient for separation of enantiomers by distillation. © 1994 Wiley-Liss, Inc.     

Assessment of a model for intron RNA secondary structure relevant to RNA self-splicing--a review

A widespread class of introns is characterized by a particular RNA secondary structure, based upon four conserved nucleotide sequences. Among such "class I" introns are found the majority of introns in fungal mitochondrial genes and the self-splicing intron of the large ribosomal RNA of several species of Tetrahymena. A model of the RNA secondary structure, which must underlie the self-splicing activity, is here evaluated in the light of data on 16 further introns. The main body or "core structure" of the intron always consists of the base-paired regions P3 to P9 with the associated single-stranded loops, with P2 present also in most cases. Two minority sub-classes of core structure occur, one of which is typical of introns in fungal ribosomal RNA. Introns in which the core structure is close to the 5' splice site all have an internal guide sequence (IGS) which can pair with exon sequences adjacent to the 5' and 3' splice sites to align them precisely, as proposed by Davies et al. [Nature 300 (1982) 719-724]. In these cases, the internal guide model allows us to predict correctly the exact location of splice sites. All other introns probably use other mechanisms of alignment. This analysis provides strong support for the RNA splicing model which we have developed.     

Secondary structure-based profiles: use of structure-conserving scoring tables in searching protein sequence databases for structural similarities

The profile method, for detecting distantly related proteins by sequence comparison, has been extended to incorporate secondary structure information from known X-ray structures. The sequence of a known structure is aligned to sequences of other members of a given folding class. From the known structure, the secondary structure (alpha-helix, beta-strand or "other") is assigned to each position of the aligned sequences. As in the standard profile method, a position-dependent scoring table, termed a profile, is calculated from the aligned sequences. However, rather than using the standard Dayhoff mutation table in calculating the profile, we use distinct amino acid mutation tables for residues in alpha-helices, beta-strands or other secondary structures to calculate the profile. In addition, we also distinguish between internal and external residues. With this new secondary structure-based profile method, we created a profile for eight-stranded, antiparallel beta barrels of the insecticyanin folding class. It is based on the sequences of retinol-binding protein, insecticyanin and beta-lactoglobulin. Scanning the sequence database with this profile, it was possible to detect the sequence of avidin. The structure of streptavidin is known, and it appears to be distantly related to the antiparallel beta barrels. Also detected is the sequence of complement component C8, which we therefore predict to be a member of this folding class.     

Binding of nickel (II) to 5′-nucleoside monophosphates and related compounds

Summary The interactions of Ni(II) cation with a representative suite of purine bases and the respective nucleosides and nucleotides have been studied by ultraviolet difference spectroscopy. Apparent association constants, K_app, were determined for each system at pH 7.0, using computer linear regression coupled with an iteration technique. The specificity of binding of Ni²⁺ for the purine nucleotides studied at pH 7.0 was 5-GMP > 5-IMP > 5-AMP; a similiar ordering was also found for the respective nucleosides and bases. In this study binding was not observed for the suite of pyramidines used, although a Ni²⁺ - cytidine complex has been observed (Fiskin and Beer, 1965). It was also found that Ni²⁺ bound more strongly to the purine 5-nucleotides than to the respective nucleosides and bases. These trends are explained in terms of metal-ligand bonds and available bonding positions on the ligands. A role for metal-ion-nucleotide types of complexes is suggested in the processes that might have given rise to the origin of life.     

The possible role of soluble salts in chemical evolution

Summary A model is proposed for a prebiotic environment in which concentration, condensation, and chemical evolution of biomolecules could have taken place. The main reactions expected of proteins, nucleic acids, lipids, and some of their precursors in this environment are examined.The model is based on our previously developed concept of a fluctuating system in which hydration and dehydration processes take place in a cyclic manner. In the present model, however, high concentrations of soluble salts, such as chlorides and sulfates, are taken into account, whereas previously a more or less salt-free system had been assumed. Thus the preponderance of surfaces of soluble salts is implied, even though sparingly soluble minerals, such as clay minerals or quartz, are also present.During the dehydration stage biomolecules tend to leave the solution and concentrate at certain microenvironments, such as in micelles and aggregates, at the liquid-gas surface and, possibly, at the emerging solid surfaces. Moreover, in these brines, and especially during the last stages of dehydration, high temperatures are attainable, which may enhance certain reactions between the organic molecules, and result in a net increase of condensation over degradation.In the dehydrated state, solid-state condensation and synthesis reactions are possible in which the surface of soluble salts may serve as a catalyst. Several reports in the literature support this hypothesis. Hydration brings about dissolution of the minerals and redistribution of the biomolecules. In such a system, evolutionary processes like those postulated by White (1980) and by Lahav and White (1980) are possible. Moreover, since several soluble salts of known geological occurrence are optically active in their crystalline state, the involvement of the model system in the selection and evolution of chiral organic compounds should also be considered. In addition, organic molecules in the above microenvironments are also expected to undergo selective interactions based on factors such as molecular pattern and chiral recognition and hydrophobicity. The proposed system emphasizes the need to develop the theoretical background and experimental methods for the study of interactions among biomolecules in the presence of high salt concentrations and solid surfaces of soluble salts, as well as interactions between the biomolecules and these surfaces.