Sequence Dependence of the Stability of RNA Hairpin Molecules with Six Nucleotide Loops†

Biochemistry ◽  
2006 ◽  
Vol 45 (5) ◽  
pp. 1400-1407 ◽  
Author(s):  
Christopher J. Vecenie ◽  
Catherine V. Morrow ◽  
Allison Zyra ◽  
Martin J. Serra
Keyword(s):  
Sequence Dependence ◽  
The Stability ◽  
Rna Hairpin

The stability of RNA hairpin loops containing A-U-G: An-U-G-Um

Biopolymers ◽  
1974 ◽  
Vol 13 (11) ◽  
pp. 2367-2383 ◽  
Author(s):  
Eric Wickstrom ◽  
Ignacio Tinoco
Keyword(s):  
Hairpin Loops ◽  
Rna Hairpin Loops ◽  
The Stability ◽  
Rna Hairpin

scholarly journals Peptide display on live MS2 phage: restrictions at the RNA genome level

2001 ◽  
Vol 82 (7) ◽  
pp. 1797-1805 ◽  
Author(s):  
Dico van Meerten ◽  
Rene C. L. Olsthoorn ◽  
Jan van Duin ◽  
Raymond M. D. Verhaert
Keyword(s):  
Coat Protein ◽  
Wild Type ◽  
Hairpin Loop ◽  
Major Coat Protein ◽  
Large Loop ◽  
Genome Level ◽  
The Stability ◽  
Rna Hairpin ◽  
Peptide Display ◽  
Rna Phage

The potential of the RNA phage MS2 to accommodate extra amino acids in its major coat protein has been examined. Accordingly, a pentapeptide was encoded in the genome as an N-terminal extension. In the MS2 crystal structure, this part of the coat protein forms a loop that extends from the outer surface of the icosahedral virion. At the RNA level, the insert forms a large loop at the top of an existing hairpin. This study shows that it is possible to maintain inserts in the coat protein of live phages. However, not all inserts were genetically stable. Some suffer deletions, while others underwent adaptation by base substitutions. Whether or not an insert is stable appears to be determined by the choice of the nucleic acid sequence used to encode the extra peptide. This effect was not caused by differential translation, because coat-protein synthesis was equal in wild-type and mutants. We conclude that the stability of the insert depends on the structure of the large RNA hairpin loop, as demonstrated by the fact that a single substitution can convert an unstable loop into a stable one.

Continuum Solvent Studies of the Stability of RNA Hairpin Loops and Helices

1998 ◽  
Vol 16 (3) ◽  
pp. 671-682 ◽  
Author(s):  
Jayashree Srinivasan ◽  
Jennifer Miller ◽  
Peter A. Kollman ◽  
David A. Case
Keyword(s):  
Hairpin Loops ◽  
Rna Hairpin Loops ◽  
The Stability ◽  
Rna Hairpin

scholarly journals EFFECT OF THE ION TREATMENT ON AN RNA HAIRPIN: MOLECULAR DYNAMICS STUDY

2012 ◽  
Vol 12 (1) ◽  
pp. 1-11 ◽  
Author(s):  
Elisabeth Catherina Widjajakusuma ◽  
Alessandra Villa ◽  
Gerhard Stock
Keyword(s):  
Molecular Dynamics ◽  
Structural Difference ◽  
Md Simulations ◽  
Field Method ◽  
Ion Concentration ◽  
Reaction Field ◽  
The Stability ◽  
Ion Treatment ◽  
Rna Hairpin ◽  
Amber Force Fields

Molecular dynamics has been employed to study the effect of ion treatment on the stability of 14-nucleotide RNA hairpin of Coxsackievirus B3. Three AMBER force fields were used: AMBER94, AMBER98, and AMBER99, which showed no significant structural difference of the hairpin. Thereafter, we applied two different long-range electrostatic treatments that were reaction field and PME methods, and calculated the distribution of ions around the hairpin. Although the structural stabilities of the MD simulations using both methods were similar in 0.14 M Na+, ion environment around the hairpin was notably different. In particular, structural stabilition of the hairpin with increasing ion concentration and with ion Mg2+ cannot be accommodated by simulations using reaction field method. Furthermore, the MD simulations using PME method suggested the strong similarity in structural and dynamical properties of the hairpin with 0.14 M Na+, 0.50 M Na+, 1,03 M Na+, and 0.08 M Mg2+ concentrations. However, the simulations revealed different ion occupations of Na+ and Mg2+.

Open discussion

1982 ◽  
Vol 99 ◽  
pp. 605-613
Author(s):  
P. S. Conti
Keyword(s):  
Buenos Aires ◽  
Large Mass ◽  
List Type ◽  
Common Phenomenon ◽  
Open Discussion ◽  
The Stability ◽  
Ring Nebulae

Conti: One of the main conclusions of the Wolf-Rayet symposium in Buenos Aires was that Wolf-Rayet stars are evolutionary products of massive objects. Some questions:–Do hot helium-rich stars, that are not Wolf-Rayet stars, exist?–What about the stability of helium rich stars of large mass? We know a helium rich star of ∼40 MO. Has the stability something to do with the wind?–Ring nebulae and bubbles : this seems to be a much more common phenomenon than we thought of some years age.–What is the origin of the subtypes? This is important to find a possible matching of scenarios to subtypes.

Symmetric Multistep Methods Revisited: II. Numerical Experiments

1999 ◽  
Vol 173 ◽  
pp. 309-314 ◽  
Author(s):  
T. Fukushima
Keyword(s):  
Multistep Methods ◽  
Computational Time ◽  
Integration Time ◽  
Implicit Methods ◽  
Symmetric Methods ◽  
Celestial Bodies ◽  
The Stability ◽  
Predictor Corrector ◽  
Symmetric Multistep Methods ◽  
Integration Errors

AbstractBy using the stability condition and general formulas developed by Fukushima (1998 = Paper I) we discovered that, just as in the case of the explicit symmetric multistep methods (Quinlan and Tremaine, 1990), when integrating orbital motions of celestial bodies, the implicit symmetric multistep methods used in the predictor-corrector manner lead to integration errors in position which grow linearly with the integration time if the stepsizes adopted are sufficiently small and if the number of corrections is sufficiently large, say two or three. We confirmed also that the symmetric methods (explicit or implicit) would produce the stepsize-dependent instabilities/resonances, which was discovered by A. Toomre in 1991 and confirmed by G.D. Quinlan for some high order explicit methods. Although the implicit methods require twice or more computational time for the same stepsize than the explicit symmetric ones do, they seem to be preferable since they reduce these undesirable features significantly.

Uniformity of Magnification from Different Electron Microscopes

1967 ◽  
Vol 25 ◽  
pp. 32-33
Author(s):  
Godfrey C. Hoskins ◽  
V. Williams ◽  
V. Allison
Keyword(s):  
Diffraction Grating ◽  
The Other ◽  
Carbon Replica ◽  
Electron Microscopes ◽  
The Stability

The method demonstrated is an adaptation of a proven procedure for accurately determining the magnification of light photomicrographs. Because of the stability of modern electrical lenses, the method is shown to be directly applicable for providing precise reproducibility of magnification in various models of electron microscopes.A readily recognizable area of a carbon replica of a crossed-line diffraction grating is used as a standard. The same area of the standard was photographed in Phillips EM 200, Hitachi HU-11B2, and RCA EMU 3F electron microscopes at taps representative of the range of magnification of each. Negatives from one microscope were selected as guides and printed at convenient magnifications; then negatives from each of the other microscopes were projected to register with these prints. By deferring measurement to the print rather than comparing negatives, correspondence of magnification of the specimen in the three microscopes could be brought to within 2%.

Effect of Improved ThO2 Particle Dispersion in Nickel on High-Temperature Strength

1970 ◽  
Vol 28 ◽  
pp. 444-445
Author(s):  
E. R. Kimmel ◽  
H. L. Anthony ◽  
W. Scheithauer
Keyword(s):  
High Temperature ◽  
Metal Matrix ◽  
Oxide Particle ◽  
Oxide Phase ◽  
Dislocation Motion ◽  
Particle Dispersion ◽  
High Temperature Strength ◽  
Strengthening Effect ◽  
Oxide Particles ◽  
The Stability

The strengthening effect at high temperature produced by a dispersed oxide phase in a metal matrix is seemingly dependent on at least two major contributors: oxide particle size and spatial distribution, and stability of the worked microstructure. These two are strongly interrelated. The stability of the microstructure is produced by polygonization of the worked structure forming low angle cell boundaries which become anchored by the dispersed oxide particles. The effect of the particles on strength is therefore twofold, in that they stabilize the worked microstructure and also hinder dislocation motion during loading.

An Analysis of Dissociation of Molecules in a High Resolution Electron Microscope

1973 ◽  
Vol 31 ◽  
pp. 486-487
Author(s):  
Mihir Parikh
Keyword(s):  
Electron Microscope ◽  
High Resolution ◽  
Cross Sections ◽  
Resolving Power ◽  
Peak Intensity ◽  
Molecular Film ◽  
Resolution Electron ◽  
Dissociation Cross Section ◽  
High Resolution Electron Microscope ◽  
The Stability

It is well known that the resolution of bio-molecules in a high resolution electron microscope depends not just on the physical resolving power of the instrument, but also on the stability of these molecules under the electron beam. Experimentally, the damage to the bio-molecules is commo ly monitored by the decrease in the intensity of the diffraction pattern, or more quantitatively by the decrease in the peaks of an energy loss spectrum. In the latter case the exposure, EC, to decrease the peak intensity from IO to I’O can be related to the molecular dissociation cross-section, σD, by EC = ℓn(IO /I’O) /ℓD. Qu ntitative data on damage cross-sections are just being reported, However, the microscopist needs to know the explicit dependence of damage on: (1) the molecular properties, (2) the density and characteristics of the molecular film and that of the support film, if any, (3) the temperature of the molecular film and (4) certain characteristics of the electron microscope used

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