scholarly journals Ensemble simulations: folding, unfolding and misfolding of a high-efficiency frameshifting RNA pseudoknot

2017 ◽  
pp. gkx012 ◽  
Author(s):  
Khai K. Q. Nguyen ◽  
Yessica K. Gomez ◽  
Mona Bakhom ◽  
Amethyst Radcliffe ◽  
Phuc La ◽  
...  
2021 ◽  
Vol 120 (3) ◽  
pp. 314a
Author(s):  
Nguyet Nguyen ◽  
Vinh Ngo ◽  
Jessica Moore ◽  
Eric J. Sorin

1993 ◽  
Vol 13 (11) ◽  
pp. 6931-6940 ◽  
Author(s):  
P Somogyi ◽  
A J Jenner ◽  
I Brierley ◽  
S C Inglis

The genomic RNA of the coronavirus infectious bronchitis virus contains an efficient ribosomal frameshift signal which comprises a heptanucleotide slippery sequence followed by an RNA pseudoknot structure. The presence of the pseudoknot is essential for high-efficiency frameshifting, and it has been suggested that its function may be to slow or stall the ribosome in the vicinity of the slippery sequence. To test this possibility, we have studied translational elongation in vitro on mRNAs engineered to contain a well-defined pseudoknot-forming sequence. Insertion of the pseudoknot at a specific location within the influenza virus PB1 mRNA resulted in the production of a new translational intermediate corresponding to the size expected for ribosomal arrest at the pseudoknot. The appearance of this protein was transient, indicating that it was a true paused intermediate rather than a dead-end product, and mutational analysis confirmed that its appearance was dependent on the presence of a pseudoknot structure within the mRNA. These observations raise the possibility that a pause is required for the frameshift process. The extent of pausing at the pseudoknot was compared with that observed at a sequence designed to form a simple stem-loop structure with the same base pairs as the pseudoknot. This structure proved to be a less effective barrier to the elongating ribosome than the pseudoknot and in addition was unable to direct efficient ribosomal frameshifting, as would be expected if pausing plays an important role in frameshifting. However, the stem-loop was still able to induce significant pausing, and so this effect alone may be insufficient to account for the contribution of the pseudoknot to frameshifting.


1993 ◽  
Vol 13 (11) ◽  
pp. 6931-6940 ◽  
Author(s):  
P Somogyi ◽  
A J Jenner ◽  
I Brierley ◽  
S C Inglis

The genomic RNA of the coronavirus infectious bronchitis virus contains an efficient ribosomal frameshift signal which comprises a heptanucleotide slippery sequence followed by an RNA pseudoknot structure. The presence of the pseudoknot is essential for high-efficiency frameshifting, and it has been suggested that its function may be to slow or stall the ribosome in the vicinity of the slippery sequence. To test this possibility, we have studied translational elongation in vitro on mRNAs engineered to contain a well-defined pseudoknot-forming sequence. Insertion of the pseudoknot at a specific location within the influenza virus PB1 mRNA resulted in the production of a new translational intermediate corresponding to the size expected for ribosomal arrest at the pseudoknot. The appearance of this protein was transient, indicating that it was a true paused intermediate rather than a dead-end product, and mutational analysis confirmed that its appearance was dependent on the presence of a pseudoknot structure within the mRNA. These observations raise the possibility that a pause is required for the frameshift process. The extent of pausing at the pseudoknot was compared with that observed at a sequence designed to form a simple stem-loop structure with the same base pairs as the pseudoknot. This structure proved to be a less effective barrier to the elongating ribosome than the pseudoknot and in addition was unable to direct efficient ribosomal frameshifting, as would be expected if pausing plays an important role in frameshifting. However, the stem-loop was still able to induce significant pausing, and so this effect alone may be insufficient to account for the contribution of the pseudoknot to frameshifting.


1988 ◽  
Vol 102 ◽  
pp. 41
Author(s):  
E. Silver ◽  
C. Hailey ◽  
S. Labov ◽  
N. Madden ◽  
D. Landis ◽  
...  

The merits of microcalorimetry below 1°K for high resolution spectroscopy has become widely recognized on theoretical grounds. By combining the high efficiency, broadband spectral sensitivity of traditional photoelectric detectors with the high resolution capabilities characteristic of dispersive spectrometers, the microcalorimeter could potentially revolutionize spectroscopic measurements of astrophysical and laboratory plasmas. In actuality, however, the performance of prototype instruments has fallen short of theoretical predictions and practical detectors are still unavailable for use as laboratory and space-based instruments. These issues are currently being addressed by the new collaborative initiative between LLNL, LBL, U.C.I., U.C.B., and U.C.D.. Microcalorimeters of various types are being developed and tested at temperatures of 1.4, 0.3, and 0.1°K. These include monolithic devices made from NTD Germanium and composite configurations using sapphire substrates with temperature sensors fabricated from NTD Germanium, evaporative films of Germanium-Gold alloy, or material with superconducting transition edges. A new approache to low noise pulse counting electronics has been developed that allows the ultimate speed of the device to be determined solely by the detector thermal response and geometry. Our laboratory studies of the thermal and resistive properties of these and other candidate materials should enable us to characterize the pulse shape and subsequently predict the ultimate performance. We are building a compact adiabatic demagnetization refrigerator for conveniently reaching 0.1°K in the laboratory and for use in future satellite-borne missions. A description of this instrument together with results from our most recent experiments will be presented.


Author(s):  
J. M. Cowley ◽  
R. Glaisher ◽  
J. A. Lin ◽  
H.-J. Ou

Some of the most important applications of STEM depend on the variety of imaging and diffraction made possible by the versatility of the detector system and the serial nature, of the image acquisition. A special detector system, previously described, has been added to our STEM instrument to allow us to take full advantage of this versatility. In this, the diffraction pattern in the detector plane may be formed on either of two phosphor screens, one with P47 (very fast) phosphor and the other with P20 (high efficiency) phosphor. The light from the phosphor is conveyed through a fiber-optic rod to an image intensifier and TV system and may be photographed, recorded on videotape, or stored digitally on a frame store. The P47 screen has a hole through it to allow electrons to enter a Gatan EELS spectrometer. Recently a modified SEM detector has been added so that high resolution (10Å) imaging with secondary electrons may be used in conjunction with other modes.


Author(s):  
K.M. Hones ◽  
P. Sheldon ◽  
B.G. Yacobi ◽  
A. Mason

There is increasing interest in growing epitaxial GaAs on Si substrates. Such a device structure would allow low-cost substrates to be used for high-efficiency cascade- junction solar cells. However, high-defect densities may result from the large lattice mismatch (∼4%) between the GaAs epilayer and the silicon substrate. These defects can act as nonradiative recombination centers that can degrade the optical and electrical properties of the epitaxially grown GaAs. For this reason, it is important to optimize epilayer growth conditions in order to minimize resulting dislocation densities. The purpose of this paper is to provide an indication of the quality of the epitaxially grown GaAs layers by using transmission electron microscopy (TEM) to examine dislocation type and density as a function of various growth conditions. In this study an intermediate Ge layer was used to avoid nucleation difficulties observed for GaAs growth directly on Si substrates. GaAs/Ge epilayers were grown by molecular beam epitaxy (MBE) on Si substrates in a manner similar to that described previously.


Author(s):  
P. G. Kotula ◽  
D. D. Erickson ◽  
C. B. Carter

High-resolution field-emission-gun scanning electron microscopy (FESEM) has recently emerged as an extremely powerful method for characterizing the micro- or nanostructure of materials. The development of high efficiency backscattered-electron detectors has increased the resolution attainable with backscattered-electrons to almost that attainable with secondary-electrons. This increased resolution allows backscattered-electron imaging to be utilized to study materials once possible only by TEM. In addition to providing quantitative information, such as critical dimensions, SEM is more statistically representative. That is, the amount of material that can be sampled with SEM for a given measurement is many orders of magnitude greater than that with TEM.In the present work, a Hitachi S-900 FESEM (operating at 5kV) equipped with a high-resolution backscattered electron detector, has been used to study the α-Fe2O3 enhanced or seeded solid-state phase transformations of sol-gel alumina and solid-state reactions in the NiO/α-Al2O3 system. In both cases, a thin-film cross-section approach has been developed to facilitate the investigation. Specifically, the FESEM allows transformed- or reaction-layer thicknesses along interfaces that are millimeters in length to be measured with a resolution of better than 10nm.


Author(s):  
Yaru Li ◽  
Yu-Quan Zhu ◽  
Weili Xin ◽  
Song Hong ◽  
Xiaoying Zhao ◽  
...  

Rationally designing low-content and high-efficiency noble metal nanodots offers opportunities to enhance electrocatalytic performances for water splitting. However, the preparation of highly dispersed nanodots electrocatalysts remains a challenge. Herein, we...


1919 ◽  
Vol 88 (2282supp) ◽  
pp. 204-205
Author(s):  
Frank E. D. Acland
Keyword(s):  

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