After infection and a prolonged incubation period, the scrapie agent causes a degenerative disease of the central nervous system in sheep and goats. Six lines of evidence including sensitivity to proteases demonstrate that this agent contains a protein that is required for infectivity. Although the scrapie agent is irreversibly inactivated by alkali, five procedures with more specificity for modifying nucleic acids failed to cause inactivation. The agent shows heterogeneity with respect to size, apparently a result of its hydrophobicity; the smallest form may have a molecular weight of 50,000 or less. Because the novel properties of the scrapie agent distinguish it from viruses, plasmids, and viroids, a new term "prion" is proposed to denote a small proteinaceous infectious particle which is resistant to inactivation by most procedures that modify nucleic acids. Knowledge of the scrapie agent structure may have significance for understanding the causes of several degenerative diseases.

http://science.sciencemag.org/content/sci/216/4542/136.full.pdf

Novel proteinaceous infectious particles cause scrapie

IA. Cause and Effect . . . . . . . . . . . . . . 465 1.2. Prerequisites of Selforganization . . . . . . . 467 1.2.3. Evolut ion Must S ta r t f rom R andom Even ts 467 1.2.2. Ins t ruc t ion Requires In format ion . . . . 467 1.2.3. In format ion Originates or Gains Value by S e l e c t i o n . . . . . . . . . . . . . . . 469 1.2.4. Selection Occurs wi th Special Substances under Special Conditions . . . . . . . . 470

/pdf/selforganization-of-matter-and-the-evolution-of-biological-3ms9rkbxjp.pdf

Selforganization of matter and the evolution of biological macromolecules

An algorithm and a computer program have been prepared for determining RNA secondary structures within any prescribed increment of the computed global minimum free energy. The mathematical problem of determining how well defined a minimum energy folding is can now be solved. All predicted base pairs that can participate in suboptimal structures may be displayed and analyzed graphically. Representative suboptimal foldings are generated by selecting these base pairs one at a time and computing the best foldings that contain them. A distance criterion that ensures that no two structures are "too close" is used to avoid multiple generation of similar structures. Thermodynamic parameters, including free-energy increments for single-base stacking at the ends of helices and for terminal mismatched pairs in interior and hairpin loops, are incorporated into the underlying folding model of the above algorithm.

https://science.sciencemag.org/content/sci/244/4900/48.full.pdf

On finding all suboptimal foldings of an RNA molecule

To understand an RNA sequence's mechanism of action, the structure must be known. Furthermore, target RNA structure is an important consideration in the design of small interfering RNAs and antisense DNA oligonucleotides. RNA secondary structure prediction, using thermodynamics, can be used to develop hypotheses about the structure of an RNA sequence. RNAstructure is a software package for RNA secondary structure prediction and analysis. It uses thermodynamics and utilizes the most recent set of nearest neighbor parameters from the Turner group. It includes methods for secondary structure prediction (using several algorithms), prediction of base pair probabilities, bimolecular structure prediction, and prediction of a structure common to two sequences. This contribution describes new extensions to the package, including a library of C++ classes for incorporation into other programs, a user-friendly graphical user interface written in JAVA, and new Unix-style text interfaces. The original graphical user interface for Microsoft Windows is still maintained. The extensions to RNAstructure serve to make RNA secondary structure prediction user-friendly. The package is available for download from the Mathews lab homepage at http://rna.urmc.rochester.edu/RNAstructure.html
 .

/pdf/rnastructure-software-for-rna-secondary-structure-prediction-3e42o4sg6f.pdf

RNAstructure: software for RNA secondary structure prediction and analysis

Viroids are uncoated infectious RNA molecules pathogenic to certain higher plants. Four different highly purified viroids were studied. By ultracentrifugation, thermal denaturation, electron microscopy, and end group analysis the following features were established: (i) the molecular weight of cucumber pale fruit viroid from tomato is 110,000, of citrus exocortis viroid from Gynura 119,000, of citrus exocortis viroid from tomato 119,000 and of potato spindle tuber viroid from tomato 127,000. (ii) Viroids are single-stranded molecules. (iii) Virods exhibit high thermal stability, cooperativity, and self-complementarity resulting in a rod-like native structure. (iv) Viroids are covalently closed circular RNA molecules.

https://www.pnas.org/content/pnas/73/11/3852.full.pdf

Viroids are single-stranded covalently closed circular RNA molecules existing as highly base-paired rod-like structures.

Structure and structure formation of viroids.

Viroids are single-stranded circular RNA molecules of 240 to 400 nucleotides which are pathogens of certain higher plants and replicate autonomously in the host cell. Virusoids are similar to viroids in respect to size and circularity but replicate only as genomic part of a plant virus. Their structure and structural transitions have been investigated by thermo-dynamic, kinetic and hydrodynamic methods. The special features of the sequences of these RNAs, which are the basis for their secondary structures and structural flexibility, are investigated with theoretical methods. A set of thermodynamic parameters for helix growth and loop formation is selected from the literature to calculate secondary structures and structural transitions of single-stranded RNAs. Appropriate modifications of the chosen parameter set are discussed. For calculations we used either Tinoco-plots and the model of "cooperative helices" or the Zuker-program based on the exact algorithm of Nussinov et al, or both. Calculations were done for viroids and virusoids. As both are single-stranded, circular RNAs we had to modify the Zuker-program as described in the appendix. Calculations are done for different viroids, i.e. potato spindle tuber, citrus exocortis, chrysanthemum stunt, coconut cadang-cadang, and avocado sunblotch, and for two virusoids, i.e. the circular RNAs of Solanum nodiflorum mottle virus, and velvet tobacco mottle virus. For viroids the calculations confirm our earlier theoretical and experimental results about the extended native structure and the highly cooperative transition into a branched structure. Virusoids show less base pairing, branching in the native secondary structure, and only low cooperativity during denaturation. They resemble more closely the properties of random sequences with length, G:C content, and circularity as in viroids but statistical sequences. The comparison of viroids, virusoids, and circular RNA or random sequences confirms the uniqueness of viroid structure.

Conformational transitions in viroids and virusoids: comparison of results from energy minimization algorithm and from experimental data.

https://febs.onlinelibrary.wiley.com/doi/pdf/10.1016/0014-5793%2879%2980262-8

Conversion of circular viroid molecules to linear strands

Conformational transitions of the anticodon branch, the acceptor branch and the tertiary structure of yeast tRNAPhe were investigated using tRNAPhe fragments Thermodynamic and kinetic methods were employed using the optical absorbance of the fragments and the fluorescence of the Y-base Related results of partial nuclease digestions on tRNAPhe fragments are also reported



1
Hypochromicity, reaction enthalpy and rate constants of helix-coil transitions of the anti codon branch agree with the values expected from the cloverleaf model The dissociation of the branch is accompanied by a quenching of the fluorescence of the Y-base

2
In some isolated fragments the anticodon branch is more stable than in the intact tRNA The destabilization in the intact tRNA is attributed to electrostatic effects

3
The anticodon half Phe 21–57, at low concentrations and temperatures, assumes a structure which is different from a segment of the cloverleaf model A transition from this structure to the one of a segment of the cloverleaf is observed with increasing temperature At higher fragment concentrations and in the presence of Mg2+ dimers are formed

4
Bimolecular recombinations are observed between fragments Phe 1–18 and Phe 21–76 reconstituting the acceptor and dihydrouridine stems, and between Phe 1–18 and Phe 38–76 where only the base pairs of the acceptor stem are newly formed The mechanism of the recombination and the relationship of the fragment combination to the intact tRNA are discussed

5
The thermodynamic properties of the fragment Phe 1-69/70 are very similar to those of the intact tRNA It can be concluded that the tertiary structure is essentially unchanged anti that the terminal nucleotides 70–76 are not directly involved in its formation

6
The thermal denaturation process of intact tRNAPhe can now be interpreted as follows: at first the tertiary structure is converted to a cloverleaf-like structure; this process is followed by the melting of the acceptor and anticodon stems; finally the ribosylthymine and dihydrouridine stems dissociate independently

https://febs.onlinelibrary.wiley.com/doi/pdf/10.1111/j.1432-1033.1973.tb02887.x

The conformational transitions in yeast tRNAPhe as studied with tRNAPhe fragments.

A high precision differential absorption technique has been developed for the detailed experimental analysis of the complex melting behaviour of specific tRNAs. This technique allows the resolution of overlapping transitions which have been observed in a study of the interaction of Mg2+ ions with tRNAAla (yeast). On the basis of these experimental observations a strong coupling between two adjacent transitions in tRNAAla is proposed and discussed with respect to the structure of tRNAAla. The sedimentation coefficient of tRNAAla as a function of temperature up to 80° has been studied in detail. The wavelength dependences of the hyperchromicities of various transitions in tRNA and tRNA half molecules are discussed with regard to A · U and G · C pairs melting in these processes. From a comparison of the melting behaviour of tRNAAla, tRNATyr, tRNASer, and tRNAPhe in the presence and the absence of Mg2+ ions it is shown that tRNAAla is best suited for detailed studies of conformational changes in tRNA.

https://febs.onlinelibrary.wiley.com/doi/pdf/10.1111/j.1432-1033.1970.tb00978.x

The coupling of conformational transitions in alanine specific transfer ribonucleic acid from yeast studied by a modified differential absorption technique.

Detlev Riesner

Papers

Structure and structure formation of viroids.

Conformational transitions in viroids and virusoids: comparison of results from energy minimization algorithm and from experimental data.

Conversion of circular viroid molecules to linear strands

The conformational transitions in yeast tRNAPhe as studied with tRNAPhe fragments.

The coupling of conformational transitions in alanine specific transfer ribonucleic acid from yeast studied by a modified differential absorption technique.