Polymer-supported RNA synthesis and its application to test the nearest-neighbor model for duplex stability

Biochemistry ◽  
1986 ◽  
Vol 25 (24) ◽  
pp. 7840-7846 ◽  
Author(s):  
Ryszard Kierzek ◽  
Marvin H. Caruthers ◽  
Carl E. Longfellow ◽  
David Swinton ◽  
Douglas H. Turner ◽  
...  
Keyword(s):  
Rna Synthesis ◽  
Nearest Neighbor ◽  
Duplex Stability ◽  
Polymer Supported

2′-Bispyrene-Modified 2′-O-Methyl RNA Probes as Useful Tools for the Detection of RNA: Synthesis, Fluorescent Properties, and Duplex Stability

ChemBioChem ◽  
2014 ◽  
Vol 15 (13) ◽  
pp. 1939-1946 ◽  
Author(s):  
Olga A. Krasheninina ◽  
Darya S. Novopashina ◽  
Alexander A. Lomzov ◽  
Alya G. Venyaminova
Keyword(s):  
Rna Synthesis ◽  
Fluorescent Properties ◽  
Rna Probes ◽  
Duplex Stability

scholarly journals Nearest-neighbor parameters for predicting DNA duplex stability in diverse molecular crowding conditions

2020 ◽  
Vol 117 (25) ◽  
pp. 14194-14201 ◽  
Author(s):  
Saptarshi Ghosh ◽  
Shuntaro Takahashi ◽  
Tatsuya Ohyama ◽  
Tamaki Endoh ◽  
Hisae Tateishi-Karimata ◽  
...  
Keyword(s):  
Nearest Neighbor ◽  
Average Molecular Weight ◽  
Molecular Crowding ◽  
Dna Duplexes ◽  
Dna Duplex ◽  
Intracellular Environment ◽  
Duplex Stability ◽  
Key Factor ◽  
The Stability ◽  
Duplex Formation

The intracellular environment is crowded and heterogeneous. Although the thermodynamic stability of nucleic acid duplexes is predictable in dilute solutions, methods of predicting such stability under specific intracellular conditions are not yet available. We recently showed that the nearest-neighbor model for self-complementary DNA is valid under molecular crowding condition of 40% polyethylene glycol with an average molecular weight of 200 (PEG 200) in 100 mM NaCl. Here, we determined nearest-neighbor parameters for DNA duplex formation under the same crowding condition to predict the thermodynamics of DNA duplexes in the intracellular environment. Preferential hydration of the nucleotides was found to be the key factor for nearest-neighbor parameters in the crowding condition. The determined parameters were shown to predict the thermodynamic parameters (∆H°, ∆S°, and ∆G°37) and melting temperatures (Tm) of the DNA duplexes in the crowding condition with significant accuracy. Moreover, we proposed a general method for predicting the stability of short DNA duplexes in different cosolutes based on the relationship between duplex stability and the water activity of the cosolute solution. The method described herein would be valuable for investigating biological processes that occur under specific intracellular crowded conditions and for the application of DNA-based biotechnologies in crowded environments.

scholarly journals Improved nearest-neighbor parameters for the stability of RNA/DNA hybrids under a physiological condition

2020 ◽  
Vol 48 (21) ◽  
pp. 12042-12054 ◽  
Author(s):  
Dipanwita Banerjee ◽  
Hisae Tateishi-Karimata ◽  
Tatsuya Ohyama ◽  
Saptarshi Ghosh ◽  
Tamaki Endoh ◽  
...  
Keyword(s):  
Thermodynamic Parameters ◽  
Target Gene ◽  
Nearest Neighbor ◽  
Physiological Condition ◽  
Specific Binding ◽  
Published Data ◽  
Nearest Neighbour ◽  
Nacl Solution ◽  
Duplex Stability ◽  
The Stability

Abstract The stability of Watson–Crick paired RNA/DNA hybrids is important for designing optimal oligonucleotides for ASO (Antisense Oligonucleotide) and CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)–Cas9 techniques. Previous nearest-neighbour (NN) parameters for predicting hybrid stability in a 1 M NaCl solution, however, may not be applicable for predicting stability at salt concentrations closer to physiological condition (e.g. ∼100 mM Na+ or K+ in the presence or absence of Mg2+). Herein, we report measured thermodynamic parameters of 38 RNA/DNA hybrids at 100 mM NaCl and derive new NN parameters to predict duplex stability. Predicted ΔG°37 and Tm values based on the established NN parameters agreed well with the measured values with 2.9% and 1.1°C deviations, respectively. The new results can also be used to make precise predictions for duplexes formed in 100 mM KCl or 100 mM NaCl in the presence of 1 mM Mg2+, which can mimic an intracellular and extracellular salt condition, respectively. Comparisons of the predicted thermodynamic parameters with published data using ASO and CRISPR–Cas9 may allow designing shorter oligonucleotides for these techniques that will diminish the probability of non-specific binding and also improve the efficiency of target gene regulation.

Improved Nearest-Neighbor Parameters for Predicting DNA Duplex Stability†

Biochemistry ◽  
1996 ◽  
Vol 35 (11) ◽  
pp. 3555-3562 ◽  
Author(s):  
John SantaLucia, ◽  
Hatim T. Allawi ◽  
P. Ananda Seneviratne
Keyword(s):  
Nearest Neighbor ◽  
Dna Duplex ◽  
Duplex Stability

Observation of Superlattice Dislocations on Cube Planes in Ni3Al

1973 ◽  
Vol 31 ◽  
pp. 174-175 ◽  
Author(s):  
J. M. Oblak ◽  
W. H. Rand
Keyword(s):  
Nearest Neighbor ◽  
Antiphase Boundary ◽  
Nearest Neighbors ◽  
High Energy ◽  
Cross Slip ◽  
Octahedral Plane ◽  
Trapping Mechanism ◽  
Slip Traces

The energy of an a/2 <110> shear antiphase. boundary in the Ll2 expected to be at a minimum on {100} cube planes because here strue ture is there is no violation of nearest-neighbor order. The latter however does involve the disruption of second nearest neighbors. It has been suggested that cross slip of paired a/2 <110> dislocations from octahedral onto cube planes is an important dislocation trapping mechanism in Ni3Al; furthermore, slip traces consistent with cube slip are observed above 920°K.Due to the high energy of the {111} antiphase boundary (> 200 mJ/m2), paired a/2 <110> dislocations are tightly constricted on the octahedral plane and cannot be individually resolved.

Effect of Some Metabolic Inhibitors on Vinblastine-Induced Ribosomal-Granular Material Complexes

1971 ◽  
Vol 29 ◽  
pp. 548-549
Author(s):  
Awtar Krishan ◽  
Dora Hsu
Keyword(s):  
Granular Material ◽  
Rna Synthesis ◽  
Culture Medium ◽  
Actinomycin D ◽  
Metabolic Inhibitors ◽  
Protein And Rna Synthesis ◽  
Apparent Reduction ◽  
Plant Alkaloids ◽  
In Cells

Cells exposed to antitumor plant alkaloids, vinblastine and vincristine sulfate have large proteinacious crystals and complexes of ribosomes, helical polyribosomes and electron-dense granular material (ribosomal complexes) in their cytoplasm, Binding of H3-colchicine by the in vivo crystals shows that they contain microtubular proteins. Association of ribosomal complexes with the crystals suggests that these structures may be interrelated.In the present study cultured human leukemic lymphoblasts (CCRF-CEM), were incubated with protein and RNA-synthesis inhibitors, p. fluorophenylalanine, puromycin, cycloheximide or actinomycin-D before the addition of crystal-inducing doses of vinblastine to the culture medium. None of these compounds could completely prevent the formation of the ribosomal complexes or the crystals. However, in cells pre-incubated with puromycin, cycloheximide, or actinomycin-D, a reduction in the number and size of the ribosomal complexes was seen. Large helical polyribosomes were absent in the ribosomal complexes of cells treated with puromycin, while in cells exposed to cycloheximide, there was an apparent reduction in the number of ribosomes associated with the ribosomal complexes (Fig. 2).

Application of Lattice Imaging Techniques to Amorphous Films

1975 ◽  
Vol 33 ◽  
pp. 8-9
Author(s):  
S. R. Herd ◽  
P. Chaudhari
Keyword(s):  
Nearest Neighbor ◽  
Random Network ◽  
Imaging Techniques ◽  
Network Models ◽  
Accurate Method ◽  
Direct Transmission ◽  
Lattice Imaging ◽  
Transmission Electron ◽  
Lattice Planes ◽  
Nearest Neighbor Distances

Electron diffraction and direct transmission have been used extensively to study the local atomic arrangement in amorphous solids and in particular Ge. Nearest neighbor distances had been calculated from E.D. profiles and the results have been interpreted in terms of the microcrystalline or the random network models. Direct transmission electron microscopy appears the most direct and accurate method to resolve this issue since the spacial resolution of the better instruments are of the order of 3Å. In particular the tilted beam interference method is used regularly to show fringes corresponding to 1.5 to 3Å lattice planes in crystals as resolution tests.

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