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.

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

2021 ◽  
Vol 49 (18) ◽  
pp. 10796-10799
Author(s):  
Dipanwita Banerjee ◽  
Hisae Tateishi-Karimata ◽  
Tatsuya Ohyama ◽  
Saptarshi Ghosh ◽  
Tamaki Endoh ◽  
...  
Keyword(s):  
Nearest Neighbor ◽  
Physiological Condition ◽  
The 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 SYNTHESIS OF NEW SUBSTITUTED PROCAINE HYDROCHLORIDE COMPOUNDS AND THEIR USE IN SPECTROPHOTOMETRIC DETERMINATION OF TETRACYCLINE HYDROCHLORIDE THROUGH DIAZOTIZATION-COUPLING REACTIONS

2021 ◽  
Vol 18 (39) ◽  
pp. 14-32
Author(s):  
Hind Sadiq Al-WARD ◽  
Mouayed Qassssim AL-ABACHI ◽  
Mohammed Rifaat AHMED
Keyword(s):  
Stability Constant ◽  
Thermodynamic Parameters ◽  
Coupling Reaction ◽  
Water Soluble ◽  
Procaine Hydrochloride ◽  
Effect Of Temperature ◽  
Basic Medium ◽  
Fast Method ◽  
The Stability

Background: Tetracycline is one of the most important antibiotics. It is used to treat many different bacterial infections. It is often used in treating severe acne, or sexually transmitted diseases such as syphilis, gonorrhea, or chlamydia. In some cases, tetracycline is used when penicillin or another antibiotic cannot be used to treat serious infections such as the ones caused by Bacillus anthracis, Listeria, Clostridium, Actinomyces. Aim: synthesized a new novel reagent used to determine TCH spectrophotometrically by using diazonium and coupling reaction. Methods: Four new substituted procaine derivatives were prepared by simple organic methods using aniline derivatives. A spectrophotometric approach was established for the micro-determination of TCH. The stoichiometry was investigated using mole ratio and continuous variation methods, and the stability constant was also estimated. The ΔG, ΔH, and ΔS were determined as thermodynamic parameters for evaluating the effect of temperature on the reaction. Results: Substituted procaine derivatives were prepared, and o-hydroxy procaine seems to be the best reagent used to determine TCH by diazotization and coupling reaction. The result was a yellow water-soluble dye with a maximum absorbance of 380 nm. The reaction conditions were studied and optimized. Beers law was obeyed over a concentration range (2.5–50) μg.mL-1 for TCH. The molar absorptivity was (14.4669.103) L.mol-1.cm-1, and the detection limit was (0.5052) μg.mL-1. The stoichiometry of the formed product was found 1:1 (o-hydroxyprocaine: TCH). The stability constant indicated that the product formed was stable, and the thermodynamic parameters showed that the diazonium salt reaction was preferred to occur at a low temperature. Conclusions: a simple, accurate, and fast method was developed to determine TCH in pure form and pharmaceuticals by coupling the TCH with a newly synthesized procaine derivative reagent (o-hydroxy procaine) in a basic medium.

Role of Antibiotic Lock Therapy for the Treatment of Catheter-Related Bloodstream Infections

2009 ◽  
Vol 32 (9) ◽  
pp. 678-688 ◽  
Author(s):  
Jose L Del Pozo
Keyword(s):  
Antimicrobial Agents ◽  
Therapeutic Option ◽  
Bloodstream Infections ◽  
Resistance Pattern ◽  
Published Data ◽  
Sufficient Power ◽  
Lock Therapy ◽  
Antibiotic Lock ◽  
The Stability ◽  
Systemic Antibiotics

Catheter-related bloodstream infections are often difficult to treat because they are caused by organisms that embed themselves in a bio film layer on the catheter surface, resulting in an increased resistance to antimicrobial agents. Systemic antibiotics are usually administered but, although generally effective in eliminating circulating bacteria, they frequently fail to sterilize the line, leaving the patient at a continuing risk of complications or recurrence. A successful approach to managing these infections requires making an appropriate decision regarding whether the catheter should be removed or retained using antibiotic lock therapy; and choosing the type and duration of antimicrobial therapy based on the type of organism and its resistance pattern. Studies that have evaluated antibiotic lock therapy have varied in the types of antibiotics and concentrations used, the addition of heparin to the solutions, and dwell times in the catheter lumen. Guidelines from the Infectious Diseases Society of America include use of antibiotic lock therapy as a therapeutic option for intraluminal infections when the device is not removed and, although not routine, as prophylaxis for catheter-related infection in select patient populations. However, there are no published guidelines on the concentration of heparin or antibiotics that should be used, and minimal published data on the stability of heparin combinations with antibiotics. It is to be hoped that antibiotic locks will be subject to randomized controlled trials of sufficient power to confirm or refute their use.

Factors Affecting Choice of Working Stresses for High-Temperature Service

1933 ◽  
Vol 1 (3) ◽  
pp. 99-102
Author(s):  
P. G. McVetty
Keyword(s):  
High Temperature ◽  
Published Data ◽  
Creep Tests ◽  
Fundamental Study ◽  
Factors Affecting ◽  
Creep Characteristics ◽  
The Stability ◽  
Safe Working

Abstract This paper discusses the various methods which have been proposed to determine safe working stresses for high-temperature service. The question of the stability of alloys during the test and in subsequent service is considered, with particular emphasis upon probable changes in creep characteristics during long exposure to stress and temperature. It is shown that published data in general do not admit of extrapolation, and that attempts to estimate total creep in service from such data are not usually satisfactory. The author stresses the need for more fundamental study of the laws governing creep rather than creep tests of many different materials.

scholarly journals Potentiometric and spectrophotometric studies of the complexation of Schiff-base hydrazones containing the pyrimidine moiety

2003 ◽  
Vol 68 (10) ◽  
pp. 729-749 ◽  
Author(s):  
H.S. Seleem ◽  
B.A. El-Shetary ◽  
S.M.E. Khalil ◽  
M. Shebl
Keyword(s):  
Schiff Base ◽  
Ionic Strength ◽  
Thermodynamic Parameters ◽  
Stability Constants ◽  
Elemental Analysis ◽  
Mass Spectra ◽  
Dissociation Constants ◽  
The Stability ◽  
Pyrimidine Moiety ◽  
Metal Ligand

Three Schiff-base hydrazones (ONN ? donors) were prepared by condensation of 2-amino-4-hydrazino-6-methylpyrimidine with 2-hydroxyacetophenone 2-methoxybenzaldehyde and diacetyl to yield 2-OHAHP, 2-OMeBHPand DHP respectively. The structures of these ligands were elucidated by elemental analysis, UV, IR, 1H-NMR and mass spectra. The metal?ligand stability constants of Mn2+, Fe3+,Co2+,Ni2+,Cu2+, Zn2+,Cd2+,UO22+ and Th4+ chelates were determined potentiometrically in two different media (75%(v/v) dioxane?water and ethanol?water) at 283, 293, 303 and 313 K at an ionic strength of 0.05 M (KNO3). The thermodynamic parameters of the 1:1 and 1:2 complexes were evaluated and are discussed. The dissociation constants of 2-OHAHP, 2-OMeBHP and DHPligands and the stability constants of Co2+, Ni2 and Cu2+ with 2-OHAHP were determined spectrophotometrically in 75 % (v/v) dioxane?water.

Setting Attribute Weights for Nearest Neighbor Learning Algorithms Using C4.5

1997 ◽  
Vol 11 (03) ◽  
pp. 405-415 ◽  
Author(s):  
Charles X. Ling ◽  
John J. Parry ◽  
Handong Wang
Keyword(s):  
Machine Learning ◽  
Decision Trees ◽  
Distance Function ◽  
Nearest Neighbor ◽  
Learning Algorithms ◽  
Simple Approach ◽  
Nearest Neighbour ◽  
Attribute Weights ◽  
New Methods

Nearest Neighbour (NN) learning algorithms utilize a distance function to determine the classification of testing examples. The attribute weights in the distance function should be set appropriately. We study situations where a simple approach of setting attribute weights using decision trees does not work well, and design three improvements. We test these new methods thoroughly using artificially generated datasets and datasets from the machine learning repository.

Atomic Interchange Potentials Calculation of Ni-Al-Cr Alloy Based on Microscopic Phase Field Method

2013 ◽  
Vol 747-748 ◽  
pp. 739-746
Author(s):  
Wei Ping Dong ◽  
Zhang Jing ◽  
Zheng Chen
Keyword(s):  
Field Theory ◽  
Phase Field ◽  
Nearest Neighbor ◽  
Field Method ◽  
Phase Field Method ◽  
Precipitation Process ◽  
Atomic Interaction ◽  
Long Range Order ◽  
Nearest Neighbour ◽  
Good Agreement

The effects of increasing atomic interchange potentials to the precipitation process and microstructure of Ni-Al-Cr alloy have been simulated based on the microscopic phase field theory. The first nearest neighbour atomic interchange potentials of Ni-Al-Cr alloys for L12 and D022 phase was calculated out according to the formula which were referenced on the relation equation between atomic interchange potentials and long range order parameters by Khachaturyan. The results indicated that Ni-Al (WNi-Al) and Ni-Cr (WNi-Cr) s first nearest neighbor atomic interaction potentials will increase linearly while the temperatures rose. Moreover WNi-Al increased but WNi-Cr decreased roughly linearly if Al atoms concentration rose, and conversely inversed. In addition, these atomic interchange potentials changing with temperature and concentration were in good agreement with earlier study.

Stability and Hopf Bifurcation of Nearest-Neighbor Coupled Neural Networks With Delays

2020 ◽  
Vol 15 (11) ◽  
Author(s):  
Lu Wang ◽  
Min Xiao ◽  
Shuai Zhou ◽  
Yurong Song ◽  
Jinde Cao
Keyword(s):  
Neural Networks ◽  
Hopf Bifurcation ◽  
Nearest Neighbor ◽  
Multiple Delays ◽  
Dimensional System ◽  
Practical Applications ◽  
Coupled Neural Networks ◽  
The Stability ◽  
Related Characteristic ◽  
Theoretical Analyses

Abstract In this paper, a high-dimensional system of nearest-neighbor coupled neural networks with multiple delays is proposed. Nowadays, most present researches about neural networks have studied the connection between adjacent nodes. However, in practical applications, neural networks are extremely complicated. This paper further considers that there are still connection relationships between nonadjacent nodes, which reflect the intrinsic characteristics of neural networks more accurately because of the complexity of its topology. The influences of multiple delays on the local stability and Hopf bifurcation of the system are explored by selecting the sum of delays as bifurcation parameter and discussing the related characteristic equations. It is found that the dynamic behaviors of the system depend on the critical value of bifurcation. In addition, the conditions that ensure the stability of the system and the criteria of Hopf bifurcation are given. Finally, the correctness of the theoretical analyses is verified by numerical simulation.

scholarly journals Laws and Trends of the Evolution of Traditional Villages in Plane Pattern

2020 ◽  
Vol 12 (7) ◽  
pp. 3005
Author(s):  
Xi Yang ◽  
Ke Song ◽  
Fuan Pu
Keyword(s):  
Spatial Data ◽  
Nearest Neighbor ◽  
Morphological Evolution ◽  
Temporal Analysis ◽  
Mean Value ◽  
Significant Shift ◽  
Spatial Processes ◽  
Common Mean ◽  
Multi Temporal ◽  
The Stability

This study collected and analyzed dynamic spatial data of eight traditional villages scattered in different regions of China. A multi-temporal analysis of morphological metrics of spatial patterns and a regression analysis of the morphological evolution were used to analyze and contrast the historical spatial processes of different villages. These were then compared using patch texture and rural macro-morphology perspectives. This led to an assessment of the general laws and trends associated with rural spatial processes. (1) There has been a significant shift in the stability of rural spatial development since the founding of the People’s Republic of China (PRC). (2) Most small and medium-sized villages have maintained a relatively stable spatial texture, while large villages have changed significantly. (3) The mean and variance of the patch area, and the Euclidean nearest-neighbor distance, are correlated in some cases. (4) The mode of rural expansion may be relevant to limitations in the total area of growth. (5) The fractal dimension of the rural macro-morphology may follow a morphological order of oscillation around the equilibrium level. (6) The common mean value of the projected area of rural building patches is expected to be 100 m2.

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