scholarly journals An RNA Triangle with Six Ribozyme Units Can Promote a Trans-Splicing Reaction through Trimerization of Unit Ribozyme Dimers

2021 ◽  
Vol 11 (6) ◽  
pp. 2583 ◽  
Author(s):  
Junya Akagi ◽  
Takahiro Yamada ◽  
Kumi Hidaka ◽  
Yoshihiko Fujita ◽  
Hirohide Saito ◽  
...  
Keyword(s):  
Rna Aptamer ◽  
Biological Functions ◽  
Reporter System ◽  
Force Microscopy ◽  
Unit Structure ◽  
Catalytic Rnas ◽  
Atomic Force ◽  
Group I ◽  
Trans Splicing ◽  
Dimeric Form

Ribozymes are catalytic RNAs that are attractive platforms for the construction of nanoscale objects with biological functions. We designed a dimeric form of the Tetrahymena group I ribozyme as a unit structure in which two ribozymes were connected in a tail-to-tail manner with a linker element. We introduced a kink-turn motif as a bent linker element of the ribozyme dimer to design a closed trimer with a triangular shape. The oligomeric states of the resulting ribozyme dimers (kUrds) were analyzed biochemically and observed directly by atomic force microscopy (AFM). Formation of kUrd oligomers also triggered trans-splicing reactions, which could be monitored with a reporter system to yield a fluorescent RNA aptamer as the trans-splicing product.

scholarly journals Direct Imaging of Human SWI/SNF-Remodeled Mono- and Polynucleosomes by Atomic Force Microscopy Employing Carbon Nanotube Tips

2001 ◽  
Vol 21 (24) ◽  
pp. 8504-8511 ◽  
Author(s):  
Gavin R. Schnitzler ◽  
Chin Li Cheung ◽  
Jason H. Hafner ◽  
Andrew J. Saurin ◽  
Robert E. Kingston ◽  
...  
Keyword(s):  
Atomic Force Microscopy ◽  
Carbon Nanotube ◽  
Rrna Gene ◽  
Weakly Bound ◽  
Force Microscopy ◽  
Atomic Force ◽  
Biochemical Assays ◽  
Chromatin Remodeling Complexes ◽  
Dimeric Form ◽  
Regulatory Sites

ABSTRACT Chromatin-remodeling complexes alter chromatin structure to facilitate, or in some cases repress, gene expression. Recent studies have suggested two potential pathways by which such regulation might occur. In the first, the remodeling complex repositions nucleosomes along DNA to open or occlude regulatory sites. In the second, the remodeling complex creates an altered dimeric form of the nucleosome that has altered accessibility to transcription factors. The extent of translational repositioning, the structure of the remodeled dimer, and the presence of dimers on remodeled polynucleosomes have been difficult to gauge by biochemical assays. To address these questions, ultrahigh-resolution carbon nanotube tip atomic force microscopy was used to examine the products of remodeling reactions carried out by the human SWI/SNF (hSWI/SNF) complex. We found that mononucleosome remodeling by hSWI/SNF resulted in a dimer of mononucleosomes in which ∼60 bp of DNA is more weakly bound than in control nucleosomes. Arrays of evenly spaced nucleosomes that were positioned by 5S rRNA gene sequences were disorganized by hSWI/SNF, and this resulted in long stretches of bare DNA, as well as clusters of nucleosomes. The formation of structurally altered nucleosomes on the array is suggested by a significant increase in the fraction of closely abutting nucleosome pairs and by a general destabilization of nucleosomes on the array. These results suggest that both the repositioning and structural alteration of nucleosomes are important aspects of hSWI/SNF action on polynucleosomes.

scholarly journals Bionic effects of nano hydroxyapatite dentifrice on demineralised surface of enamel post orthodontic debonding: in-vivo split mouth study

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Purva Verma ◽  
Srirengalakshmi Muthuswamy Pandian
Keyword(s):  
Surface Roughness ◽  
Enamel Surface ◽  
Roughness Parameters ◽  
Force Microscopy ◽  
Atomic Force ◽  
Group I ◽  
Significant Difference ◽  
Envelope Method ◽  
Group Ii

Abstract Background Orthodontic debonding procedure produces inevitable enamel surface alterations, sequelae to which are enamel demineralization, sensitivity and retention of pigments. Several agents have been employed to counterbalance the same. The purpose of this study was (1) To evaluate the hypothesis that no significant difference exists in the remineralising potential of nano hydroxyapatite (NanoHAP) dentifrice and fluoridated dentifrice after orthodontic debonding, (2) To estimate the enamel topographic parameters following use of nano HAP dentifrice, post orthodontic debonding. Methods Sixty upper first bi-cuspids (30 subjects) planned for therapeutic extraction for the orthodontic treatment were bonded with a light cured adhesive. Envelope method of randomisation was followed in this prospective in-vivo study. In each subject, one of the first premolar brackets was debonded using a debonding plier and polished following standard protocols. Envelope method of randomisation was used to determine the side of the premolar to be debonded first. Patient was advised to use fluoridated (Group I) dentifrice for the first 15 days, then the first premolar was covered with a heavy-bodied putty cap, extracted and subjected to atomic force microscopy (AFM). Contralateral first premolar was then debonded and polished using similar protocol, and patient was advised to use nano hydroxyapatite dentifrice (Group II) for next 15 days. The premolar was then extracted and analyzed for surface roughness using AFM. The remineralizing potential of dentifrices was assessed by evaluating surface roughness parameters of the two groups and were compared using a two-sample t test. Results A significant difference was found amongst Group I (Fluoridated dentifrice) and Group II (NanoHAP dentifrice) (p > 0.001***) for enamel surface roughness variables which reflect remineralising potential of dentifrices. Group II showed significantly lesser value of surface roughness characteristics. Conclusions NanoHAP dentifrice was shown, after 15 days, to be superior to fluoridated dentifrice in remineralising enamel post orthodontic debonding.

Cryogenic atomic force microscopy

1991 ◽  
Vol 49 ◽  
pp. 54-55
Author(s):  
K. A. Fisher ◽  
M. G. L. Gustafsson ◽  
M. B. Shattuck ◽  
J. Clarke
Keyword(s):  
Room Temperature ◽  
Rapid Freezing ◽  
Cryogenic Temperatures ◽  
Soft Or ◽  
Electrically Conductive ◽  
Force Microscopy ◽  
Flexible Molecules ◽  
Advantages And Disadvantages ◽  
Atomic Force ◽  
Chemical Perturbation

The atomic force microscope (AFM) is capable of imaging electrically conductive and non-conductive surfaces at atomic resolution. When used to image biological samples, however, lateral resolution is often limited to nanometer levels, due primarily to AFM tip/sample interactions. Several approaches to immobilize and stabilize soft or flexible molecules for AFM have been examined, notably, tethering coating, and freezing. Although each approach has its advantages and disadvantages, rapid freezing techniques have the special advantage of avoiding chemical perturbation, and minimizing physical disruption of the sample. Scanning with an AFM at cryogenic temperatures has the potential to image frozen biomolecules at high resolution. We have constructed a force microscope capable of operating immersed in liquid n-pentane and have tested its performance at room temperature with carbon and metal-coated samples, and at 143° K with uncoated ferritin and purple membrane (PM).

AFM study of the dynamics of α-alumina surface faceting during high-temperature processing

1995 ◽  
Vol 53 ◽  
pp. 334-335 ◽  
Author(s):  
Michael W. Bench ◽  
Jason R. Heffelfinger ◽  
C. Barry Carter
Keyword(s):  
High Temperature ◽  
Thin Foil ◽  
Sem Analysis ◽  
Conductive Coatings ◽  
Force Microscopy ◽  
Minimal Sample ◽  
Atomic Force ◽  
Formation And Evolution ◽  
High Temperature Processing ◽  
Nominal Surface

To gain a better understanding of the surface faceting that occurs in α-alumina during high temperature processing, atomic force microscopy (AFM) studies have been performed to follow the formation and evolution of the facets. AFM was chosen because it allows for analysis of topographical details down to the atomic level with minimal sample preparation. This is in contrast to SEM analysis, which typically requires the application of conductive coatings that can alter the surface between subsequent heat treatments. Similar experiments have been performed in the TEM; however, due to thin foil and hole edge effects the results may not be representative of the behavior of bulk surfaces.The AFM studies were performed on a Digital Instruments Nanoscope III using microfabricated Si3N4 cantilevers. All images were recorded in air with a nominal applied force of 10-15 nN. The alumina samples were prepared from pre-polished single crystals with (0001), , and nominal surface orientations.

Scanning tunneling microscopy and atomic force microscopy: New tools for biology

1989 ◽  
Vol 47 ◽  
pp. 778-779
Author(s):  
CE Bracker ◽  
P. K. Hansma
Keyword(s):  
Physical Property ◽  
Scanning Probe ◽  
Scanning Tunneling ◽  
Small Scale ◽  
Tunneling Microscopy ◽  
Force Microscopy ◽  
New Family ◽  
Small Probe ◽  
Atomic Force ◽  
Transmission Electron

A new family of scanning probe microscopes has emerged that is opening new horizons for investigating the fine structure of matter. The earliest and best known of these instruments is the scanning tunneling microscope (STM). First published in 1982, the STM earned the 1986 Nobel Prize in Physics for two of its inventors, G. Binnig and H. Rohrer. They shared the prize with E. Ruska for his work that had led to the development of the transmission electron microscope half a century earlier. It seems appropriate that the award embodied this particular blend of the old and the new because it demonstrated to the world a long overdue respect for the enormous contributions electron microscopy has made to the understanding of matter, and at the same time it signalled the dawn of a new age in microscopy. What we are seeing is a revolution in microscopy and a redefinition of the concept of a microscope.Several kinds of scanning probe microscopes now exist, and the number is increasing. What they share in common is a small probe that is scanned over the surface of a specimen and measures a physical property on a very small scale, at or near the surface. Scanning probes can measure temperature, magnetic fields, tunneling currents, voltage, force, and ion currents, among others.

Morphology and development of flow-pattern defect with extended nonagitated Secco etching

1994 ◽  
Vol 52 ◽  
pp. 868-869
Author(s):  
Y. Pan
Keyword(s):  
Flow Pattern ◽  
Silicon Crystal ◽  
Gate Oxide ◽  
Crystal Growth Rate ◽  
Etch Depth ◽  
Force Microscopy ◽  
Etch Pit ◽  
Float Zone ◽  
Atomic Force ◽  
Multiple Step

The D defect, which causes the degradation of gate oxide integrities (GOI), can be revealed by Secco etching as flow pattern defect (FPD) in both float zone (FZ) and Czochralski (Cz) silicon crystal or as crystal originated particles (COP) by a multiple-step SC-1 cleaning process. By decreasing the crystal growth rate or high temperature annealing, the FPD density can be reduced, while the D defectsize increased. During the etching, the FPD surface density and etch pit size (FPD #1) increased withthe etch depth, while the wedge shaped contours do not change their positions and curvatures (FIG.l).In this paper, with atomic force microscopy (AFM), a simple model for FPD morphology by non-crystallographic preferential etching, such as Secco etching, was established.One sample wafer (FPD #2) was Secco etched with surface removed by 4 μm (FIG.2). The cross section view shows the FPD has a circular saucer pit and the wedge contours are actually the side surfaces of a terrace structure with very small slopes. Note that the scale in z direction is purposely enhanced in the AFM images. The pit dimensions are listed in TABLE 1.

Surface roughness measurements of vanadium-contaminated fluidized cracking catalysts by atomic force microscopy

1996 ◽  
Vol 54 ◽  
pp. 866-867
Author(s):  
H. Kinney ◽  
M.L. Occelli ◽  
S.A.C. Gould
Keyword(s):  
Surface Roughness ◽  
Zeolite Y ◽  
Atomic Level ◽  
Microporous Structure ◽  
Contact Mode ◽  
Force Microscopy ◽  
Atomic Force ◽  
Before And After ◽  
Roughness Measurements ◽  
Cracking Catalysts

For this study we have used a contact mode atomic force microscope (AFM) to study to topography of fluidized cracking catalysts (FCC), before and after contamination with 5% vanadium. We selected the AFM because of its ability to well characterize the surface roughness of materials down to the atomic level. It is believed that the cracking in the FCCs occurs mainly on the catalysts top 10-15 μm suggesting that the surface corrugation could play a key role in the FCCs microactivity properties. To test this hypothesis, we chose vanadium as a contaminate because this metal is capable of irreversibly destroying the FCC crystallinity as well as it microporous structure. In addition, we wanted to examine the extent to which steaming affects the vanadium contaminated FCC. Using the AFM, we measured the surface roughness of FCCs, before and after contamination and after steaming.We obtained our FCC (GRZ-1) from Davison. The FCC is generated so that it contains and estimated 35% rare earth exchaged zeolite Y, 50% kaolin and 15% binder.

Development of the UHV-STM

1990 ◽  
Vol 48 (1) ◽  
pp. 322-323
Author(s):  
M. Iwatsuki ◽  
S. Kitamura ◽  
A. Mogami
Keyword(s):  
Surface Science ◽  
Real Space ◽  
Atomic Scale ◽  
Scanning Tunneling ◽  
Great Promise ◽  
Force Microscopy ◽  
Atomic Force ◽  
Stm Image ◽  
Surface Construction ◽  
Very High

Since Binnig, Rohrer and associates observed real-space topographic images of Si(111)-7×7 and invented the scanning tunneling microscope (STM),1) the STM has been accepted as a powerful surface science instrument.Recently, many application areas for the STM have been opened up, such as atomic force microscopy (AFM), magnetic force microscopy (MFM) and others. So, the STM technology holds a great promise for the future.The great advantages of the STM are its high spatial resolution in the lateral and vertical directions on the atomic scale. However, the STM has difficulty in identifying atomic images in a desired area because it uses piezoelectric (PZT) elements as a scanner.On the other hand, the demand to observe specimens under UHV condition has grown, along with the advent of the STM technology. The requirment of UHV-STM is especially very high in to study of surface construction of semiconductors and superconducting materials on the atomic scale. In order to improve the STM image quality by keeping the specimen and tip surfaces clean, we have built a new UHV-STM (JSTM-4000XV) system which is provided with other surface analysis capability.

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