scholarly journals Second generation silver(I)-mediated imidazole base pairs

2014 ◽  
Vol 10 ◽  
pp. 2139-2144 ◽  
Author(s):  
Susanne Hensel ◽  
Nicole Megger ◽  
Kristina Schweizer ◽  
Jens Müller
Keyword(s):  
Thermal Stability ◽  
Melting Temperature ◽  
Base Pair ◽  
Metal Ion ◽  
Second Generation ◽  
Dna Duplex ◽  
Base Pairs ◽  
Double Helices ◽  
Thermal Stability Of

The imidazole–Ag(I)–imidazole base pair is one of the best-investigated artificial metal-mediated base pairs. We show here that its stability can be further improved by formally replacing the imidazole moiety by a 2-methylimidazole or 4-methylimidazole moiety. A comparison of the thermal stability of several double helices shows that the addition of one equivalent of Ag(I) leads to a 50% larger increase in the melting temperature when a DNA duplex with methylated imidazole nucleosides is applied. This significant effect can likely be attributed to a better steric shielding of the metal ion within the metal-mediated base pair.

scholarly journals Thermal Stability Changes in Telomeric G-Quadruplex Structures Due to N6-Methyladenine Modification

Epigenomes ◽  
2021 ◽  
Vol 5 (1) ◽  
pp. 5 ◽  
Author(s):  
Ryohei Wada ◽  
Wataru Yoshida
Keyword(s):  
Thermal Stability ◽  
Base Pair ◽  
Genomic Dna ◽  
Biological Functions ◽  
Duplex Structure ◽  
Stacking Interaction ◽  
Hybrid Type ◽  
G Quadruplex ◽  
Melting Analysis ◽  
Thermal Stability Of

N6-methyladenine modification (m6dA) has recently been identified in eukaryote genomic DNA. The methylation destabilizes the duplex structure when the adenine forms a Watson–Crick base pair, whereas the methylation on a terminal unpaired adenine stabilizes the duplex structure by increasing the stacking interaction. In this study, the effects of m6dA modification on the thermal stability of four distinct telomeric G-quadruplex (G4) structures were investigated. The m6dA-modified telomeric oligonucleotide d[AGGG(TTAGGG)3] that forms a basket-type G4 in Na+, d[(TTAGGG)4TT] that forms a hybrid-type G4 in K+ (Form-2), d[AAAGGG(TTAGGG)3AA] that forms a hybrid-type G4 in K+ (Form-1), and d[GGG(TTAGGG)3T] that forms a basket-type G4 with two G-tetrads in K+ (Form-3) were analyzed. Circular dichroism melting analysis demonstrated that (1) A7- and A19-methylation destabilized the basket-type G4 structure that formed in Na+, whereas A13-methylation stabilized the structure; (2) A15-methylation stabilized the Form-2 G4 structure; (3) A15- and A21-methylations stabilized the Form-1 G4 structure; and (4) A12-methylation stabilized the Form-3 G4 structure. These results suggest that m6dA modifications may affect the thermal stability of human telomeric G4 structures in regulating the biological functions.

The thermal stability of RNA duplexes containing modified base pairs placed at internal and terminal positions of the oligoribonucleotides

2002 ◽  
Vol 97 (2-3) ◽  
pp. 233-241 ◽  
Author(s):  
Krzysztof Ziomek ◽  
Elżbieta Kierzek ◽  
Ewa Biała ◽  
Ryszard Kierzek
Keyword(s):  
Thermal Stability ◽  
Base Pairs ◽  
Rna Duplexes ◽  
Thermal Stability Of

scholarly journals The Structure and Thermal Properties of Solid Ternary Compounds Forming with Ca2+, Al3+ and Heptagluconate Ions

Molecules ◽  
2020 ◽  
Vol 25 (20) ◽  
pp. 4715
Author(s):  
Ákos Buckó ◽  
Zsolt Kása ◽  
Márton Szabados ◽  
Bence Kutus ◽  
Ottó Berkesi ◽  
...  
Keyword(s):  
Thermal Stability ◽  
Metal Ion ◽  
Icp Oes ◽  
X Ray Diffraction ◽  
Metal Compounds ◽  
X Ray ◽  
Ternary Compounds ◽  
Centrally Symmetric ◽  
Ir And Raman ◽  
Thermal Stability Of

In the present work, the structure and thermal stability of Ca–Al mixed-metal compounds, relevant in the Bayer process as intermediates, have been investigated. X-ray diffraction (XRD) measurements revealed the amorphous morphology of the compounds, which was corroborated by SEM-EDX measurements. The results of ICP-OES and UV-Vis experiments suggested the formation of three possible ternary calcium aluminum heptagluconate (Ca-Al-Hpgl) compounds, with the formulae of CaAlHpgl(OH)40, Ca2AlHpgl2(OH)50 and Ca3Al2Hpgl3(OH)90. Additional IR and Raman experiments revealed the centrally symmetric arrangement of heptagluconate around the metal ion. The increased thermal stability was demonstrated by thermal analysis of the solids and confirmed our findings.

Thermal stability of marks gold nanoparticles: A molecular dynamics simulation

2017 ◽  
Vol 31 (07) ◽  
pp. 1741001
Author(s):  
Yanlin Jia ◽  
Siqi Li ◽  
Weihong Qi ◽  
Mingpu Wang ◽  
Zhou Li ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Thermal Stability ◽  
Melting Temperature ◽  
Cohesive Energy ◽  
Au Nanoparticles ◽  
Mean Square Displacement ◽  
Dynamics Simulation ◽  
Structure Variation ◽  
Deformation Parameters ◽  
Thermal Stability Of

Molecular dynamics (MDs) simulations were used to explore the thermal stability of Au nanoparticles (NPs) with decahedral, cuboctahedral, icosahedral and Marks NPs. According to the calculated cohesive energy and melting temperature, the Marks NPs have a higher cohesive energy and melting temperature compared to these other shapes. The Lindemann index, radial distribution function, deformation parameters, mean square displacement and self-diffusivity have been used to characterize the structure variation during heating. This work may inspire researchers to prepare Marks NPs and apply them in different fields.

Additive Effects of Chlorin E6 and Metal Ion Binding on the Thermal Stability of RhodopsinIn Vitro

2009 ◽  
Vol 85 (2) ◽  
pp. 471-478 ◽  
Author(s):  
Fernanda Balem ◽  
Naveena Yanamala ◽  
Judith Klein-Seetharaman
Keyword(s):  
Thermal Stability ◽  
Metal Ion ◽  
Chlorin E6 ◽  
Ion Binding ◽  
Additive Effects ◽  
Metal Ion Binding ◽  
Thermal Stability Of

Influence of Helix Length on Cleavage Efficiency of Hammerhead Ribozymes

2005 ◽  
Vol 58 (12) ◽  
pp. 851 ◽  
Author(s):  
Philip Hendry ◽  
Maxine J. McCall ◽  
Trevor J. Lockett
Keyword(s):  
Optimal Design ◽  
Base Pair ◽  
Hammerhead Ribozymes ◽  
Base Pairs ◽  
Physiological Conditions ◽  
Rna Transcripts ◽  
Cleavage Efficiency ◽  
Double Helices

The cleavage rates of RNA substrates by trans-acting, hammerhead ribozymes are controlled by interactions between helices I and II. The interactions are affected by the relative lengths of these two double helices and by unpaired nucleotides protruding beyond helix I, either in the substrate or the ribozyme strand. Maximum cleavage rates are observed for ribozyme–substrate complexes with three or more base pairs in helix II and six or less base pairs in helix I. However, for these helix combinations, rates fall sharply with unpaired nucleotides at the end of helix I. Cleavage rates by ribozymes with one or two base pairs in helix II increase as helix I is lengthened, and are unaffected by unpaired nucleotides on the end. Since miniribozymes, with one base pair in helix II, efficiently cleave long RNA transcripts under physiological conditions, they represent the optimal design for the simple hammerheads for application in vivo.

scholarly journals Symmetry in Nucleic-Acid Double Helices

Symmetry ◽  
2020 ◽  
Vol 12 (5) ◽  
pp. 737
Author(s):  
Udo Heinemann ◽  
Yvette Roske
Keyword(s):  
Nucleic Acid ◽  
Base Pair ◽  
Rna Structure ◽  
Test Tube ◽  
Base Pairs ◽  
Dna And Rna ◽  
Left Handed ◽  
Double Helices ◽  
Rna Duplexes ◽  
The Right

In nature and in the test tube, nucleic acids occur in many different forms. Apart from single-stranded, coiled molecules, DNA and RNA prefer to form helical arrangements, in which the bases are stacked to shield their hydrophobic surfaces and expose their polar edges. Focusing on double helices, we describe the crucial role played by symmetry in shaping DNA and RNA structure. The base pairs in nucleic-acid double helices display rotational pseudo-symmetry. In the Watson–Crick base pairs found in naturally occurring DNA and RNA duplexes, the symmetry axis lies in the base-pair plane, giving rise to two different helical grooves. In contrast, anti-Watson–Crick base pairs have a dyad axis perpendicular to the base-pair plane and identical grooves. In combination with the base-pair symmetry, the syn/anti conformation of paired nucleotides determines the parallel or antiparallel strand orientation of double helices. DNA and RNA duplexes in nature are exclusively antiparallel. Watson–Crick base-paired DNA or RNA helices display either right-handed or left-handed helical (pseudo-) symmetry. Genomic DNA is usually in the right-handed B-form, and RNA double helices adopt the right-handed A-conformation. Finally, there is a higher level of helical symmetry in superhelical DNA in which B-form double strands are intertwined in a right- or left-handed sense.

Second Generation Nanostructured Metal Oxide Matrices to Increase the Thermal Stability of CO and NO2 Sensing Layers Based on Iron(II) Phthalocyanine

2007 ◽  
Vol 17 (7) ◽  
pp. 1188-1198 ◽  
Author(s):  
J. F. Fernández-Sánchez ◽  
I. Fernández ◽  
R. Steiger ◽  
R. Beer ◽  
R. Cannas ◽  
...  
Keyword(s):  
Thermal Stability ◽  
Metal Oxide ◽  
Second Generation ◽  
Thermal Stability Of ◽  
Nanostructured Metal
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