scholarly journals Salt Dependent Mesoscopic Model for RNA with Multiple Strand Concentrations

2020 ◽  
Author(s):  
Izabela Ferreira ◽  
Tauanne Dias Amarante ◽  
Gerald Weber
Keyword(s):  
Hydrogen Bond ◽  
Stacking Interactions ◽  
Base Pairs ◽  
High Sodium ◽  
Melting Temperatures ◽  
Mesoscopic Models ◽  
Low Sodium ◽  
Rna Duplexes ◽  
Morse Potentials ◽  
Experimental Melting

Mesoscopic models can be used for the description of the thermodynamic properties of RNA duplexes. With the use of experimental melting temperatures, its parametrization can provide important insights into its hydrogen bonds and stacking interactions as has been done for high sodium concentrations. However, the RNA parametrization for lower salt concentrations is still missing due to the limited amount of published melting temperature data. While the Peyrard-Bishop (PB) parametrization was found to be largely independent of strand concentrations, it requires that all temperatures are provided at the same strand concentrations. Here we adapted the PB model to handle multiple strand concentrations and in this way we were able to make use of an experimental set of temperatures to model the hydrogen bond and stacking interactions at low and intermediate sodium concentrations. For the parametrizations we make a distinction between terminal and internal base pairs, and the resulting potentials were qualitatively similar as we obtained previously for DNA. The main difference from DNA parameters, was the Morse potentials at low sodium concentrations for terminal r(AU) which is stronger than d(AT), suggesting higher hydrogen bond strength.

scholarly journals Salt Dependent Mesoscopic Model for RNA with Multiple Strand Concentrations

2020 ◽  
Author(s):  
Izabela Ferreira ◽  
Tauanne Dias Amarante ◽  
Gerald Weber
Keyword(s):  
Hydrogen Bond ◽  
Stacking Interactions ◽  
Base Pairs ◽  
High Sodium ◽  
Melting Temperatures ◽  
Mesoscopic Models ◽  
Low Sodium ◽  
Rna Duplexes ◽  
Morse Potentials ◽  
Experimental Melting

Mesoscopic models can be used for the description of the thermodynamic properties of RNA duplexes. With the use of experimental melting temperatures, its parametrization can provide important insights into its hydrogen bonds and stacking interactions as has been done for high sodium concentrations. However, the RNA parametrization for lower salt concentrations is still missing due to the limited amount of published melting temperature data. While the Peyrard-Bishop (PB) parametrization was found to be largely independent of strand concentrations, it requires that all temperatures are provided at the same strand concentrations. Here we adapted the PB model to handle multiple strand concentrations and in this way we were able to make use of an experimental set of temperatures to model the hydrogen bond and stacking interactions at low and intermediate sodium concentrations. For the parametrizations we make a distinction between terminal and internal base pairs, and the resulting potentials were qualitatively similar as we obtained previously for DNA. The main difference from DNA parameters, was the Morse potentials at low sodium concentrations for terminal r(AU) which is stronger than d(AT), suggesting higher hydrogen bond strength.

scholarly journals DNA/TNA Mesoscopic Modeling of Melting Temperatures Suggest Weaker Hydrogen Bonding of CG than in DNA/RNA

2020 ◽  
Author(s):  
Maria Izabel Muniz ◽  
Hershel Lackey ◽  
Jennifer Heemstra ◽  
Gerald Weber
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Thermodynamic Properties ◽  
Stacking Interactions ◽  
Base Pairs ◽  
Melting Temperatures ◽  
Mesoscopic Modeling ◽  
Bond Strengths ◽  
Purine Pyrimidine

TNA/DNA hybrids share several similarities to RNA/DNA, such as the tendency to form A-type helices and a strong dependency of their thermodynamic properties on purine/pyrimidine ratio. However, unlike RNA/DNA, not much is known about the base-pair properties of TNA. Here, we use a mesoscopic analysis of measured melting temperatures to obtain an estimate of hydrogen bonds and stacking interactions. Our results reveal that the AT base pairs in TNA/DNA have nearly identical hydrogen bond strengths than their counterparts in RNA/DNA, but surprisingly CG turned out to be much weaker despite similar stability.

scholarly journals DNA/TNA Mesoscopic Modeling of Melting Temperatures Suggest Weaker Hydrogen Bonding of CG than in DNA/RNA

2020 ◽  
Author(s):  
Maria Izabel Muniz ◽  
Hershel Lackey ◽  
Jennifer Heemstra ◽  
Gerald Weber
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Thermodynamic Properties ◽  
Stacking Interactions ◽  
Base Pairs ◽  
Melting Temperatures ◽  
Mesoscopic Modeling ◽  
Bond Strengths ◽  
Purine Pyrimidine

TNA/DNA hybrids share several similarities to RNA/DNA, such as the tendency to form A-type helices and a strong dependency of their thermodynamic properties on purine/pyrimidine ratio. However, unlike RNA/DNA, not much is known about the base-pair properties of TNA. Here, we use a mesoscopic analysis of measured melting temperatures to obtain an estimate of hydrogen bonds and stacking interactions. Our results reveal that the AT base pairs in TNA/DNA have nearly identical hydrogen bond strengths than their counterparts in RNA/DNA, but surprisingly CG turned out to be much weaker despite similar stability.

scholarly journals Synthetic incorporation of Nile Blue into DNA using 2′-deoxyriboside substitutes: Representative comparison of (R)- and (S)-aminopropanediol as an acyclic linker

2010 ◽  
Vol 6 ◽  
Author(s):  
Daniel Lachmann ◽  
Sina Berndl ◽  
Otto S Wolfbeis ◽  
Hans-Achim Wagenknecht
Keyword(s):  
Fluorescence Quenching ◽  
Nile Blue ◽  
Stacking Interactions ◽  
Dna Duplexes ◽  
Base Pairs ◽  
Melting Temperatures ◽  
Postsynthetic Modification ◽  
Dna Models ◽  
Sensitive Tool ◽  
Opposite Chirality

The Nile Blue chromophore was incorporated into oligonucleotides using “click” chemistry for the postsynthetic modification of oligonucleotides. These were synthesized using DNA building block 3 bearing an alkyne group and reacted with the azide 4. (R)-3-amino-1,2-propanediol was applied as the linker between the phosphodiester bridges. Two sets of DNA duplexes were prepared. One set carried the chromophore in an A-T environment, the second set in a G-C environment. Both were characterized by optical spectroscopy. Sequence-dependent fluorescence quenching was applied as a sensitive tool to compare the stacking interactions with respect to the chirality of the acyclic linker attachment. The results were compared to recent results from duplexes that carried the Nile Blue label in a sequentially and structurally identical context, except for the opposite chirality of the linker ((S)-3-amino-1,2-propandiol). Only minor, negligible differences were observed. Melting temperatures, UV–vis absorption spectra together with fluorescence quenching data indicate that Nile Blue stacks perfectly between the adjacent base pairs regardless of whether it has been attached via an S- or R-configured linker. This result was supported by geometrically optimized DNA models.

scholarly journals Developing an Updated Strategy for Estimating the Free-Energy Parameters in RNA Duplexes

2021 ◽  
Vol 22 (18) ◽  
pp. 9708
Author(s):  
Wayne K. Dawson ◽  
Amiu Shino ◽  
Gota Kawai ◽  
Ella Czarina Morishita
Keyword(s):  
Genetic Algorithm ◽  
Free Energy ◽  
Gradient Descent ◽  
Base Pairs ◽  
New Model ◽  
Energy Parameters ◽  
Benchmark Data ◽  
Rna Duplexes ◽  
Turner Model ◽  
Experimental Melting

For the last 20 years, it has been common lore that the free energy of RNA duplexes formed from canonical Watson–Crick base pairs (bps) can be largely approximated with dinucleotide bp parameters and a few simple corrective constants that are duplex independent. Additionally, the standard benchmark set of duplexes used to generate the parameters were GC-rich in the shorter duplexes and AU-rich in the longer duplexes, and the length of the majority of the duplexes ranged between 6 and 8 bps. We were curious if other models would generate similar results and whether adding longer duplexes of 17 bps would affect the conclusions. We developed a gradient-descent fitting program for obtaining free-energy parameters—the changes in Gibbs free energy (ΔG), enthalpy (ΔH), and entropy (ΔS), and the melting temperature (Tm)—directly from the experimental melting curves. Using gradient descent and a genetic algorithm, the duplex melting results were combined with the standard benchmark data to obtain bp parameters. Both the standard (Turner) model and a new model that includes length-dependent terms were tested. Both models could fit the standard benchmark data; however, the new model could handle longer sequences better. We developed an updated strategy for fitting the duplex melting data.

scholarly journals Di-μ-chlorido-bis[(2,2′-bipyridine-5,5′-dicarboxylic acid-κ2N,N′)chloridocopper(II)] dimethylformamide tetrasolvate

2013 ◽  
Vol 69 (2) ◽  
pp. m73-m74 ◽  
Author(s):  
Sigurd Øien ◽  
David Stephen Wragg ◽  
Karl Petter Lillerud ◽  
Mats Tilset
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Title Compound ◽  
Cooh Group ◽  
Stacking Interactions ◽  
Coordination Geometry ◽  
Complex Molecules ◽  
Centroid Distance ◽  
Solvent Molecules ◽  
Hydrogen Bonded

In the title compound, [Cu2Cl4(C12H8N2O4)2]·4C3H7NO, which contains a chloride-bridged centrosymmetric CuIIdimer, the CuIIatom is in a distorted square-pyramidal 4 + 1 coordination geometry defined by the N atoms of the chelating 2,2′-bipyridine ligand, a terminal chloride and two bridging chloride ligands. Of the two independent dimethylformamide molecules, one is hydrogen bonded to a single –COOH group, while one links two adjacent –COOH groupsviaa strong accepted O—H...O and a weak donated C(O)—H...O hydrogen bond. Two of these last molecules and the two –COOH groups form a centrosymmetric hydrogen-bonded ring in which the CH=O and the –COOH groups by disorder adopt two alternate orientations in a 0.44:0.56 ratio. These hydrogen bonds link the CuIIcomplex molecules and the dimethylformamide solvent molecules into infinite chains along [-111]. Slipped π–π stacking interactions between two centrosymmetric pyridine rings (centroid–centroid distance = 3.63 Å) contribute to the coherence of the structure along [0-11].

Iodo-nitroarenesulfonamides: interplay of hard and soft hydrogen bonds, I...O interactions and aromatic π...π stacking interactions

2001 ◽  
Vol 58 (1) ◽  
pp. 94-108 ◽  
Author(s):  
Craig J. Kelly ◽  
Janet M. S. Skakle ◽  
James L. Wardell ◽  
Solange M. S. V. Wardell ◽  
John N. Low ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Three Dimensional ◽  
Stacking Interactions ◽  
Asymmetric Unit ◽  
Space Group ◽  
Rotation Axes ◽  
Π Stacking ◽  
Structural Database ◽  
A Chain

Molecules of N-(4′-iodophenylsulfonyl)-4-nitroaniline, 4-O2NC6H4NHSO2C6H4I-4′ (1), are linked by three-centre I...O2N interactions into chains and these chains are linked into a three-dimensional framework by C—H...O hydrogen bonds. In the isomeric N-(4′-nitrophenylsulfonyl)-4-iodoaniline, 4-IC6H4NHSO2C6H4NO2-4′ (2), the chains generated by the I...O2N interactions are again linked into a three-dimensional framework by C—H...O hydrogen bonds. Molecules of N,N-bis(3′-nitrophenylsulfonyl)-4-iodoaniline, 4-IC6H4N(SO2C6H4NO2-3′)2 (3), lie across twofold rotation axes in space group C2/c and they are linked into chains by paired I...O=S interactions: these chains are linked into sheets by a C—H...O hydrogen bond, and the sheets are linked into a three-dimensional framework by aromatic π...π stacking interactions. In N-(4′-iodophenylsulfonyl)-3-nitroaniline, 3-O2NC6H4NHSO2C6H4I-4′ (4), there are R^2_2(8) rings formed by hard N—H...O=S hydrogen bonds and R^2_2(24) rings formed by two-centre I...nitro interactions, which together generate a chain of fused rings: the combination of a C—H...O hydrogen bond and aromatic π...π stacking interactions links the chains into sheets. Molecules of N-(4′-iodophenylsulfonyl)-4-methyl-2-nitroaniline, 4-CH3-2-O2NC6H3NHSO2C6H4I-4′ (5), are linked by N—H...O=S and C—H...O(nitro) hydrogen bonds into a chain containing alternating R^2_2(8) and R^2_2(10) rings, but there are no I...O interactions of either type. There are two molecules in the asymmetric unit of N-(4′-iodophenylsulfonyl)-2-nitroaniline, 2-O2NC6H4NHSO2C6H4I-4′ (6), and the combination of an I...O=S interaction and a hard N—H...O(nitro) hydrogen bond links the two types of molecule to form a cyclic, centrosymmetric four-component aggregate. C—H...O hydrogen bonds link these four-molecule aggregates to form a molecular ladder. Comparisons are made with structures retrieved from the Cambridge Structural Database.

Increased Renal Sensitivity to Aldosterone in the Potassium-Loaded Rat

1976 ◽  
Vol 51 (s3) ◽  
pp. 315s-317s
Author(s):  
W. R. Adam ◽  
J. W. Funder
Keyword(s):  
Sodium Intake ◽  
Control Diet ◽  
High Potassium ◽  
High Sodium ◽  
Low Sodium Diet ◽  
Low Sodium ◽  
High K ◽  
And Control

1. The renal response to aldosterone (urinary sodium and potassium excretion) was determined in adrenalectomized rats previously fed either a high potassium diet or a control diet. High K+ rats showed an enhanced response to aldosterone at all doses tested. 2. This enhanced response to aldosterone required the presence of the adrenal glands during the induction period, could be suppressed by a high sodium intake, but could not be induced by a low sodium diet. 3. No difference between high K+ and control rats could be detected in renal mineralocorticoid receptors, assessed by both in vivo and in vitro binding of tritiated aldosterone. 4. The method of the induction, and the mechanism of the enhanced response, remain to be defined.

Melting of Aromatic Compounds: Molecular Dynamics Simulations

1995 ◽  
Vol 408 ◽  
Author(s):  
P. W.-C. Kung ◽  
J. T. Books ◽  
C. M. Freeman ◽  
S. M. Levine ◽  
B. Vessali ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Crystal ◽  
Constant Pressure ◽  
Molecular Crystals ◽  
Melting Transition ◽  
Melting Temperatures ◽  
Molecular Dynamics Calculations ◽  
Dynamics Simulations ◽  
Experimental Melting Point ◽  
Experimental Melting

AbstractWe have used constant pressure molecular dynamics calculations to explore the behavior at various temperatures of two molecular crystals: benzene and a brominated phenyl compound. We observed a melting transition by heating the crystals from a low temperature. In the case of benzene, we performed one heating run of about 1 ns and obtained agreement with the experimental melting point to within some 8%. We have also simulated the melting of a more complex molecular crystal that contains bromine and phenyl groups. We performed four heating runs, with different rates of heating. For total simulation times of about 100, 220, 770, and 1 I50ps, the heating runs predicted melting temperatures that differed from the experimental melting temperature by 53%, 33%, 25%, and 9% respectively.

Abstract P614: Relationship Of Sodium Intake And Stress With Bone Health In Women

Hypertension ◽  
2016 ◽  
Vol 68 (suppl_1) ◽  
Author(s):  
Allison Jasti ◽  
Deborah L Stewart ◽  
Gregory A Harshfield
Keyword(s):  
Bone Health ◽  
Salt Intake ◽  
Sodium Intake ◽  
Target Organ Damage ◽  
African American Adolescents ◽  
Ang Ii ◽  
Mineral Density ◽  
High Sodium ◽  
Low Sodium ◽  
Relationship Of

Background: The skeleton is vital to sodium homeostasis, accounting for 40% of the body’s sodium. Research indicates stress and low sodium intake are independently associated with RAAS activation. In certain populations, stress can induce salt sensitivity, increasing the risk of hypertension and target organ damage, but the association of low versus high sodium intake with bone health is controversial. Purpose: This study sought out the relationship of low sodium and stress-induced RAAS activation with bone health. The tested hypothesis was those with lowest sodium intake would have lower total bone mineral density (TBMD) and content (TBMC) associated with stress-induced increases in angiotensin ii (Ang II) and aldosterone (Aldo). Methods: We compared effect of stress on Ang II, Aldo, TBMD and TMBC in healthy Caucasian and African-American adolescents. Subjects were grouped by quartiles based on sodium intake, assessed by urinary sodium excretion. Results: Due to females, overall significant inverse associations are observed between TBMD, TBMC, Ang II and Aldo in the lowest sodium intake quartile. Post-stress, women in the lowest sodium intake quartile showed that increases in both Ang II and Aldo correspond with lower TMBC and TMBD. There was no significance between Ang II, Aldo, TMBC and TMBD in the three highest quartiles of women nor in any male quartile. Conclusion: These data suggest Ang II and Aldo may reduce TMBC and TMBD in women. Stress-induced increases in Ang II and Aldo, with low sodium intake, may further reduce TBMD and TBMC in women. Ang II inhibition and/or moderated salt intake may be an efficacious prevention or treatment against the development of osteoporosis.

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