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D Riesner

Publications and source records attributed to D Riesner.

At least 91 records · Page 5Linked to original sources
PubMed1981

Binding of tRNA to Escherichia coli ribosomes as measured by velocity sedimentation.

We followed the binding of initiator and elongator tRNA to 70-S ribosomes and its subunits by velocity sedimentation in the analytical ultracentrifuge. This technique shows the advantage over the previously used methods (adsorption of the complexes to nitrocellulose filters or fluorescence titrations) in that no kinetic effects obscure the equilibrium data and that none of the components has to be chemically modified. The concentrations of the macromolecular compounds are kept constant and the binding equilibria are shifted by varying the Mg2+ concentration in a range which is accessible to experimental analysis. Free 30-S ribosomes bind no tRNA, whereas one tRNA molecule is bound to 50-S ribosomal subunits. In the presence of the cognate codon one tRNA can be associated with the small subunit. Free, programmed, or misprogrammed 70-S ribosomes bind exactly two elongator tRNAs. Only the initiator tRNA does discriminate significantly between the two ribosomal sites when bound to a ribosome . A-U-G complex.

Binding Sites↗
PubMed1980

Helix-coil transitions in double-stranded viral RNA. Fine resolution melting and ionic strength dependence.

Helix-coil transitions of double-stranded RNA from reovirus and infectious bursal disease virus were measured optically in aqueous medium of different ionic strengths. In RNA from reovirus four transitions and in RNA from infectious bursal disease virus two transitions were resolved and evaluated quantitatively. The ionic strength dependence of their midpoint temperatures dTm/dlog[Na+] were 13.5 +/- 0.3 degrees C for reovirus RNA and 14.9 +/-0.7 degrees C for infectious bursal disease virus RNA. The midpoint temperatures extrapolated to 1 M ionic strength were 102.9, 104.3, 105.6, and 108.8 +/- 0.3 degrees C for reovirus RNA, and 108.8 +/- 1.8 and 109.6 +/- 1.0 degrees C for infectious bursal disease virus RNA. The G + C content of the regions in reovirus RNA melting in the different transitions were determined from the spectrum of the hypochromicity. The quantitative interpretation of the data is carried out on the basis of the ion condensation theory. It is estimated for double-stranded RNA of 100% G + C, that dTm/dlog[na+] = 8.4 degrees C. The two-dimensional dependence Tm = Tm (ionic strength, G + C content) is given. The ionic strength dependence in different double-stranded RNAs is correlated to the spacing of the phosphate backbone, secondary structure, and tertiary structure.

Animals↗
PubMed1979

Fine structure melting of viroids as studied by kinetic methods.

The conformational transitions of five viroid species were studied by melting analysis and by fast and slow temperature jump techniques. Experiments with the fast temperature jump technique had to be carried out in 10 mM Na-cacodylate, 0.1 M NaCl, 4 M urea, 1 mM EDTA, pH 6.8. In addition to the highly cooperative main transition (Tm between 46.5 and 49 degrees C for different viroid species [1]) all viroids show at higher temperatures an intermediate transition (Tm approximately equal to 57 degrees C) and a high temperature transition (Tm approximately equal to 68 degrees C). The maximum amplitudes of these transitions amount only to about 1% of that of the main transition. The main transition represents a net dissociation of 78 to 94 base pairs depending on the viroid species. The intermediate transition corresponds to the dissociation of two hairpins with 5-10 base pairs each, and 10-20 nucleotides in the loops. The high temperature transition corresponds to a hairpin of 9 G:C pairs and 1 A:U pair and more than 40 bases in the loop. It is shown that these stable hairpins are not part of the native structure but are newly formed during the main transition. Their formation is responsible for the extraordinary cooperativity observed in the main transition. Hairpins can be correlated to defined sequences of PSTV. Based on these studies, on the sequence of PSTV [2], and on a theoretical treatment [3] a detailed description of the whole mechanism of PSTV denaturation is given.

Base Sequence↗
PubMed1979

Evidence from ultraviolet absorbance measurements for a codon-induced conformational change in lysine tRNA from Escherichia coli.

From experiments with equilibrium dialysis it was concluded earlier that formation of the codon-anticodon complex triggers a conformational change in the tertiary structure of tRNAPhe from Escherichia coli. A similar conformational transition is demonstrated here in the poly(A)/tRNALys system. C-G-A or C-G-A-A was used as a probe for the conformational transition in tRNA. These probes bound to tRNAPhe and tRNALys more strongly in the presence of the corresponding codons than in the absence. In order to verify these data by an independent method, the decrease in absorbance at 300 nm that occurs on formation of the codon-anticodon complex in tRNALys (which contains 2-thio-5-methylaminomethyluridine, s2mam5U) was used. The binding constants for formation of A3 . tRNALys (Ka = 2.4 . 10(4) M-1) and A4 . tRNALys (Ka = 2.5 . 10(5) M-1) are very close to those obtained by equilibrium dialysis. In the presence of C-G-A the apparent binding constant of A3 to tRNA was raised 10-fold to 2.5 . 10(-5) M-1. It was calculated that the constant for the binding of C-G-A to the binary complex A3 . tRNALys is approximately 2 . 10(4) M-1, whereas binding to the free tRNA is lower than 10(3) M-1. Under appropriate conditions binding of A3 to tRNALys can be induced directly by the addition of C-G-A. These data demonstrate that codon-anticodon complex formation induces a conformational change in the tRNA that as a consequence allows the binding of a trinucleoside diphosphate, presumably to the T-psi-G region.

Anticodon↗
PubMed1978

Calorimetric studies on viroids.

Thermodynamic studies on highly purified viroid preparations were carried out with the help of a very sensitive adiabatic microcalorimeter. Parallel to the change of UV-absorption at 260 nm as a function of temperature, the additional heat capacity of the dilute viroid solution rises sharply within the melting interval, reaches a maximum at T = Tm and declines to a baseline again when the temperature is increased further. From the peak area the molar transition enthalpy can be calculated. The transition enthalpies of citrus exocortis viroid and cucumber pale fruit viroid are 4200 kJ/mol and 3930 kJ/mol, respectively. The calorimetric results are compared to the results obtained from melting studies using UV-absorption.

Calorimetry, Differential Scanning↗
PubMed1978

Common structural features of different viroids: serial arrangement of double helical sections and internal loops.

The thermodynamic parameters of five different highly purified viroid "species" were determined by applying UV-absorption melting analysis and temperature jump methods. Their thermal denaturation proved to be a highly cooperative process with midpoint-temperatures (Tm) between 48.5 and 51 degrees C in 0.01 M sodium cacodylate, 1 mM EDTA, pH 6.8. The values of the apparent reaction enthalpies of the different viroid species range between 3,140 and 3,770 kJ/mol. Although the cooperativity is as high as found in homogeneous RNA double helices the Tm-value of viroid melting is more than 30 degrees C lower than in the homogeneous RNA. In order to explain this deviation, melting curves were simulated for different models of the secondary structure of viroids using literature values of the thermodynamic parameters of nucleic acids. Our calculations show that the following refinement of our earlier model is in complete accordance with the experimental data: In their native conformation viroids exist as an extended rodlike structure characterized by a series of double helical sections and internal loops. In the different viroid species 250-300 nucleotides out of total 350 nucleotides are needed to interprete the thermodynamic behaviour.

Mathematics↗
PubMed1977

Conformation of viroids.

Viroids are uncoated infectious RNA molecules (MW 107 000-127 000) known as pathogens of certain higher plants. Thermodynamic and kinetic studies were carried out on highly purified viroid preparations by applying UV-absorption melting analysis and temperature jump methods. The thermal denaturation of viroids is characterized by high thermal stability, high cooperativity and a high degree of base pairing. Two relaxation processes could be resolved; a process in the sec range could be evaluated as an independent all-or-none-transition with the following properties: reaction enthalpy= 550 kcal/mol, activation enthalpy of the dissociation = 470 kcal/mol; G : C content = 72 %. These data indicate the existence of an uninterrupted double helix of 52 base pairs. A process in the msec range involves 15 - 25 base pairs which are most probably distributed over several short double helical stretches. A tentative model for the secondary structure of viroids isproposed and the possible functional implications of their physicochemical properties are discussed.

Chemical Phenomena↗
PubMed1977

Rabbit liver tRNA1Val:II. unusual secondary structure of T psi C stem and loop due to a U54:A60 base pair.

In contrast to all other known tRNAs, mammalian tRNA1Val contains two adenosines A59 and A60, opposite to U54 and psi 55 in the U psi CG sequence of the T psi C loop, which could form unusual A:U (or A: psi pairs in addition to the five "normal" G:C pairs. In order to measure the number of G:C and A:U (A: psi) pairs in the T psi C stem, we prepared the 30 nucleotide long 3'-terminal fragment of this tRNA by "m7G-cleavage". From differentiated melting curves and temperature jump experiments it was concluded that the T psi C stem in this fragment is in fact extended by an additional A60:U54 pair. A dimer of this fragment with 14 base pairs was characterized by gel electrophoresis and by the same physical methods. An additional A:U pair in the tRNA1Val fragment does not necessarily mean that this is also true for intact tRNA. However, we showed that U54 is far less available for enzymatic methylation in mammalian tRNA1Val compared to tRNA from T-E. coli. This clear difference in U54 reactivity, together with the identification of an extra A60:U54 pair in the U psi CG containing fragment suggests the presence of a 6 base pair T psi C stem and a 5 nucleotide T psi C loop in this tRNA.

Adenine Nucleotides↗
PubMed1977

Mechanism of tRNA-synthetase recognition: role of terminal A.

The function of the terminal A of tRNA Phe (yeast) with respect to complex formation with the cognate aminoacyl-tRNA synthetase has been studied using equilibrium and fast kinetic techniques. Removal of the terminal A influences the equilibrium parameters of the tRNA-synthetase interaction only slightly, the mechanism of complex formation, however, is changed significantly. The binding mechanism of unmodified tRNAPhe comprises a recombination step and a consecutive conformational change. In contrast, the reaction between tRNAPheCC and the cognate synthetase is characterized by a simple one step mechanism. It is concluded that the terminal A is responsible for the occurrence of the conformational change of the tRNA-synthetase complex. The conformational change is interpreted as a proper alignment of the terminal A of the tRNA to the active site of the synthetase.

Adenine↗
PubMed1976

Thermal unfolding of yeast glycine transfer RNA.

In the present investigations the molecular unfolding of yeast tRNA(Gly) has been studied by a combination of nuclear magnetic resonance spectroscopy, melting techniques, and relaxation kinetics. From these studies the following pathway of unfolding was found. In a coupled melting transition the tertiary, the DHU, and the anticodon structure are disrupted. This is followed by the melting of the acceptor arm, while the T psi C arm, which only contains G-C pairs, melts out last. Interestingly, during the first melting transition a new structure not belonging to the original cloverleaf structure is formed. The thermodynamic and kinetic parameters of the melting transitions were determined and are discussed in relation to earlier work. The present nuclear magnetic resonance (NMR) experiments as well as earlier studies show that the ring current calculations based on the cloverleaf structure provide a good first-order interpretation of the NMR spectra of tRNA.

Base Sequence↗
PubMed1976

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

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.

Centrifugation↗
PubMed1976

Distinct steps in the specific binding of tRNA to aminoacyl-tRNA synthetase. Temperature-jump studies on the serine-specific system from yeast and the tyrosine-specific system from Escherichia coli.

The kinetics of the interaction of tRNASer and seryl-tRNA synthetase from yeast as well as of tRNATyr and tyrosyl-tRNA synthetase from Escherichia coli have been investigated by temperature-jump experiments. It could be shown that complex formation proceeds in two distinct steps. This was demonstrated for both the first and the second binding site. The two-step mechanism was deduced from the characteristic concentration dependence of the relaxation times. Seryl-tRNA synthetase recombines with the first tRNA to form an intermediate complex (kI12, kI21), which is transformed in a fast reaction to the final 1:1 complex (kI23, kI32). At pH 7.2 with 0.1 M KCl the rate constants are: kI12 = 2.7 X 10(8) M-1 S-1; kI23, kI32). At pH 7.2 with 0.1 M KCl the rate constants are: kI12 = 2.7 x 10(8) M-1 S-1; kI21 = 220 S-1; kI23 = 760 S-1; kI32 = 330 S-1. The 1:1 complex can bind a second tRNA. At pH 7.2 without added salt the rate constants are: KII2 = 0.9 X 10(8) M-1 S-1; kII21 = 270 S-1; kII23 = 120 S-1; kII32 = 1250 S-1. The tyrosine-specific system behaves very similarly to the serine-specific system. Data are given for pH 7.2 (pH 6.0) for the binding of the second tRNA: kII12 = 1 X 10(8) (2.5 X 10(8)) M-1 S-1; kII21 = 470 (170) S-1; kII23 = 150 (530) S-1; kII32 = 1540 (720) S-1. The kinetic results are discussed in terms of their relevance to the recognition process and their relation to the anticooperative binding behaviour of tRNA to synthetase.

Amino Acyl-tRNA Synthetases↗
PubMed1976

Mechanism of discrimination between cognate and non-cognate tRNAs by phenylalanyl-tRNA synthetase from yeast.

The interaction between phenylalanyl-tRNA synthetase from yeast and Escherichia coli and tRNAPhe (yeast), tRNASer (yeast), tRNA1Val (E. coli) has been investigated by ultracentrifugation analysis, fluorescence titrations and fast kinetic techniques. The fluorescence of the Y-base of tRNAPhe and the intrinsic fluorescence of the synthetases have been used as optical indicators. 1. Specific complexes between phenylalanyl-tRNA synthetase and tRNAPhe from yeast are formed in a two-step mechanism: a nearly diffusion-controlled recombination is followed by a fast conformational transition. Binding constants, rate constants and changes in the quantum yield of the Y-base fluorescence upon binding are given under a variety of conditions with respect to pH, added salt, concentration of Mg2+ ions and temperature. 2. Heterologous complexes between phenylalanyl-tRNA synthetase (E. coli) and tRNAPhe (yeast) are formed in a similar two-step mechanism as the specific complexes; the conformational transition, however, is slower by a factor 4-5. 3. Formation of non-specific complexes between phenylalanyl-tRNA synthetase (yeast) and tRNATyr (E. coli) proceeds in a one-step mechanism. Phenylalanyl-tRNA synthetase (yeast) binds either two molecules of tRNAPhe (yeast) or only one molecule of tRNATyr (E. coli); tRNA1Val (E. coli) or tRNASer (yeast) are also bound in a 1:1 stoichiometry. Binding constants for complexes of phenylalanyl-tRNA synthetase (yeast) and tRNATyr (E. coli) are determined under a variety of conditions. In contrast to specific complex formation, non-specific binding is disfavoured by the presence of Mg2+ ions, and is not affected by pH and the presence of pyrophosphate. The difference in the stabilities of specific and non-specific complexes can be varied by a factor of 2--100 depending on the ionic conditions. Discrimination of cognate and non-cognate tRNA by phenylalanyl-tRNA synthetase (yeast) is discussed in terms of the binding mechanism, the topology of the binding sites, the nature of interacting forces and the relation between specificity and ionic conditions.

Amino Acyl-tRNA Synthetases↗