scholarly journals Zn2+–DNA interactions in aqueous systems: A Raman spectroscopic study

2009 ◽  
Vol 23 (3-4) ◽  
pp. 155-163 ◽  
Author(s):  
Cristina M. Muntean ◽  
Konstantinos Nalpantidis ◽  
Ingo Feldmann ◽  
Volker Deckert
Keyword(s):  
Room Temperature ◽  
Helical Structure ◽  
Intensity Change ◽  
Dna Melting ◽  
Dna Interactions ◽  
Raman Spectroscopic ◽  
Double Helical Structure ◽  
Calf Thymus ◽  
Concentration Changes ◽  
Phosphate Groups

The influence of Zn2+ions on the structure of natural calf thymus DNA was studied by Raman spectroscopy. Measurements were done at room temperature and pH 6.2±0.1, in the presence of 10 mM Na+, and of Zn2+in a concentration range varying between 0 and 250 mM, respectively. No condensation of DNA was observed.As judging from the marker bands near 681 cm−1(dG), 729 cm−1(dA), 752 cm−1(dT), and 787 cm−1(dC, dT) altered nucleoside conformations in these residues are supposed to occur, in different intervals of Zn2+ions concentration. Changes in the conformational marker centered around 835 cm−1, upon Zn2+binding to DNA, were detected. Binding of zinc(II) ions to the charged phosphate groups of DNA, stabilizing the double helical structure, is indicated in the spectra. We have found that binding of metal ions at N3 of cytosine takes place at zinc(II) concentrations between 150–250 mM and interaction of Zn2+ions with adenine is observed in a concentration range from 10 to 250 mM. Binding of zinc(II) ions to N7 of guanine and, possibly, in a lesser extent to adenine was also observed as indicated by the Raman marker bands near 1490 and 1581 cm−1. There is no intensity change of the band at 1668 cm−1, suggesting no change in their base pairing and no change induced in the structure of water by Zn2+cations. No evidence for DNA melting was identified.

scholarly journals The Influence of Mn2+on DNA structure in the presence of Na+ions: A Raman spectroscopic study

2006 ◽  
Vol 20 (5-6) ◽  
pp. 261-268 ◽  
Author(s):  
Cristina M. Muntean ◽  
Rolf Misselwitz ◽  
Heinz Welfle
Keyword(s):  
Conformational Changes ◽  
Room Temperature ◽  
Dna Structure ◽  
Dna Melting ◽  
Physiological Concentration ◽  
Raman Spectroscopic ◽  
Calf Thymus ◽  
Dna Backbone ◽  
Na Ions ◽  
Phosphate Groups

The influence of Mn2+ions on the structure of natural calf thymus DNA was studied by Raman spectroscopy. Measurements were done at room temperature and pH 6.2±0.2, in the presence of the physiological concentration of 150 mM Na+ions, and in the presence of Mn2+concentrations that varied between 0 and 600 mM. No condensation of DNA was observed at any of the Mn2+concentrations. At 5 mM Mn2+and 150 mM Na+no significant influence of Mn2+ions on the DNA structure can be observed. Compared with our previous results obtained at 10 mM Na+ions, binding of Mn2+ions to charged phosphate groups and to DNA bases is inhibited in the presence of 150 mM Na+ions. DNA backbone conformational changes were not observed in the whole concentration range of Mn2+ions as judging from the Raman spectra. No evidence for DNA melting was identified. A high Mn2+affinity for binding to guanine N7 and possibly, in a much lesser extent, to adenine have been found.

scholarly journals Mn2+–DNA interactions in aqueous systems: A Raman spectroscopic study

2006 ◽  
Vol 20 (1) ◽  
pp. 29-35 ◽  
Author(s):  
Cristina M. Muntean ◽  
Rolf Misselwitz ◽  
Lubomir Dostál ◽  
Heinz Welfle
Keyword(s):  
Conformational Changes ◽  
Room Temperature ◽  
Critical Concentration ◽  
Dna Denaturation ◽  
Dna Interactions ◽  
Raman Spectroscopic ◽  
Calf Thymus ◽  
Cacodylate Buffer ◽  
Dna Backbone ◽  
Phosphate Groups

Interaction of natural calf thymus DNA with Mn2+ions was studied by means of Raman spectroscopy. Spectra of DNA in 10 mM Na-cacodylate buffer, pH 6.2, 10 mM NaCl and in buffer containing Mn2+ions were measured at room temperature. Mn2+concentrations varied between 0 and 0.6 M. DNA backbone conformational changes and DNA denaturation were not observed in the concentration range 0 and 0.5 M, however, DNA condensation was observed at a critical concentration of 100 mM Mn2+that prevented the measurement of Raman spectra. Binding of Mn2+to the charged phosphate groups of DNA is indicated in the spectra. A high affinity of Mn2+for guanine N7 was obvious, and binding to adenine was barely suggested.

scholarly journals Incorporation of 3-Aminobenzanthrone into 2′-Deoxyoligonucleotides and Its Impact on Duplex Stability

2011 ◽  
Vol 2011 ◽  
pp. 1-10 ◽  
Author(s):  
Mark Lukin ◽  
Tanya Zaliznyak ◽  
Francis Johnson ◽  
Carlos R. de los Santos
Keyword(s):  
Dna Adducts ◽  
Nmr Spectra ◽  
Room Temperature ◽  
Helical Structure ◽  
Environmental Pollutant ◽  
Synthetic Approach ◽  
Amino Groups ◽  
Double Helical Structure ◽  
Duplex Stability ◽  
Living Organisms

3-Nitrobenzanthrone (3NBA), an environmental pollutant and potent mutagen, causes DNA damage via the reaction of its metabolically activated form with the exocyclic amino groups of purines and the C-8 position of guanine. The present work describes a synthetic approach to the preparation of oligomeric 2′-deoxyribonucleotides containing a 2-(2′-deoxyguanosin-N2-yl)-3-aminobenzanthrone moiety, one of the major DNA adducts found in tissues of living organisms exposed to 3NBA. The NMR spectra indicate that the damaged oligodeoxyribonucleotide is capable of forming a regular double helical structure with the polyaromatic moiety assuming a single conformation at room temperature; the spectra suggest that the 3ABA moiety resides in the duplex minor groove pointing toward the 5′-end of the modified strand. Thermodynamic studies show that the dG(N2)-3ABA lesion has a stabilizing effect on the damaged duplex, a fact that correlates well with the long persistence of this damage in living organisms.

scholarly journals DNA Interaction and DNA Cleavage Studies of a New Platinum(II) Complex Containing Aliphatic and Aromatic Dinitrogen Ligands

2011 ◽  
Vol 2011 ◽  
pp. 1-10 ◽  
Author(s):  
Nahid Shahabadi ◽  
Soheila Kashanian ◽  
Maryam Mahdavi ◽  
Noorkaram Sourinejad
Keyword(s):  
Dna Cleavage ◽  
Helical Structure ◽  
Dna Interaction ◽  
Van Der Waals Interactions ◽  
Double Helical Structure ◽  
Intercalative Mode ◽  
Physico Chemical ◽  
Calf Thymus ◽  
Enthalpy And Entropy Changes ◽  
Ct Dna

A new Pt(II) complex, [Pt(DIP)(LL)](NO3)2(in which DIP is 4,7-diphenyl-1,10-phenanthroline and LL is the aliphatic dinitrogen ligand,N,N-dimethyl-trimethylenediamine), was synthesized and characterized using different physico-chemical methods. The interaction of this complex with calf thymus DNA (CT-DNA) was investigated by absorption, emission, circular dichroism (CD), and viscosity measurements. The complex binds to CT-DNA in an intercalative mode. The calculated binding constant,Kb, was  M−1. The enthalpy and entropy changes of the reaction between the complex and CT-DNA showed that the van der Waals interactions and hydrogen bonds are the main forces in the interaction with CT-DNA. In addition, CD study showed that phenanthroline ligand insert between the base pair stack of double helical structure of DNA. It is remarkable that this complex has the ability to cleave the supercoiled plasmid.

scholarly journals Degradation of nucleic acids with ozone. VI. Labilization of the double-helical structure of calf thymus deoxyribonucleic acid.

1984 ◽  
Vol 32 (9) ◽  
pp. 3636-3640 ◽  
Author(s):  
NARIKO SHINRIKI ◽  
KOZO ISHIZAKI ◽  
SHOKO SATO ◽  
KAZUNOBU MIURA ◽  
KAZUYUKI SAWADAISHI ◽  
...  
Keyword(s):  
Nucleic Acids ◽  
Deoxyribonucleic Acid ◽  
Helical Structure ◽  
Double Helical Structure ◽  
Calf Thymus

scholarly journals Base-pair resolution analysis of the effect of supercoiling on DNA flexibility and major groove recognition by triplex-forming oligonucleotides

2019 ◽  
Author(s):  
Alice L. B. Pyne ◽  
Agnes Noy ◽  
Kavit Main ◽  
Victor Velasco-Berrelleza ◽  
Michael M. Piperakis ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Base Pair ◽  
Helical Structure ◽  
Local Variation ◽  
Md Simulations ◽  
Dna Supercoiling ◽  
Dna Interactions ◽  
Force Microscopy ◽  
Double Helical Structure ◽  
Resolution Analysis

In the cell, DNA is arranged into highly-organised and topologically-constrained (supercoiled) structures. It remains unclear how this supercoiling affects the detailed double-helical structure of DNA, largely because of limitations in spatial resolution of the available biophysical tools. Here, we overcome these limitations, by a combination of atomic force microscopy (AFM) and atomistic molecular dynamics (MD) simulations, to resolve structures of negatively-supercoiled DNA minicircles at base-pair resolution. We observe that negative superhelical stress induces local variation in the canonical B-form DNA structure by introducing kinks and defects that affect global minicircle structure and flexibility. We probe how these local and global conformational changes affect DNA interactions through the binding of triplex-forming oligonucleotides to DNA minicircles. We show that the energetics of triplex formation is governed by a delicate balance between electrostatics and bonding interactions. Our results provide mechanistic insight into how DNA supercoiling can affect molecular recognition, that may have broader implications for DNA interactions with other molecular species.

scholarly journals Base-pair resolution analysis of the effect of supercoiling on DNA flexibility and major groove recognition by triplex-forming oligonucleotides

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Alice L. B. Pyne ◽  
Agnes Noy ◽  
Kavit H. S. Main ◽  
Victor Velasco-Berrelleza ◽  
Michael M. Piperakis ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Base Pair ◽  
Helical Structure ◽  
Local Variation ◽  
Md Simulations ◽  
Dna Supercoiling ◽  
Dna Interactions ◽  
Force Microscopy ◽  
Double Helical Structure ◽  
Resolution Analysis

AbstractIn the cell, DNA is arranged into highly-organised and topologically-constrained (supercoiled) structures. It remains unclear how this supercoiling affects the detailed double-helical structure of DNA, largely because of limitations in spatial resolution of the available biophysical tools. Here, we overcome these limitations, by a combination of atomic force microscopy (AFM) and atomistic molecular dynamics (MD) simulations, to resolve structures of negatively-supercoiled DNA minicircles at base-pair resolution. We observe that negative superhelical stress induces local variation in the canonical B-form DNA structure by introducing kinks and defects that affect global minicircle structure and flexibility. We probe how these local and global conformational changes affect DNA interactions through the binding of triplex-forming oligonucleotides to DNA minicircles. We show that the energetics of triplex formation is governed by a delicate balance between electrostatics and bonding interactions. Our results provide mechanistic insight into how DNA supercoiling can affect molecular recognition, that may have broader implications for DNA interactions with other molecular species.

CsOH and its Lighter Homologues – a Comparison

2014 ◽  
Vol 69 (11-12) ◽  
pp. 1229-1236
Author(s):  
Matthias Wörsching ◽  
Constantin Hoch
Keyword(s):  
Gas Phase ◽  
Room Temperature ◽  
Structure Type ◽  
Alkali Metal Hydroxide ◽  
X Ray ◽  
Raman Spectroscopic ◽  
Cesium Hydroxide ◽  
Free Ion ◽  
The One ◽  
First Time

Abstract Cesium hydroxide, CsOH, was for the first time characterised on the basis of single-crystal data. The structure is isotypic to the one of the room-temperature modification of NaOH and can be derived from the NaCl structure type thus allowing the comparison of all alkali metal hydroxide structures. Raman spectroscopic investigations show the hydroxide anion to behave almost as a free ion as in the gas phase. The X-ray investigations indicate possible H atom positions.

scholarly journals Living supramolecular polymerization of fluorinated cyclohexanes

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Oleksandr Shyshov ◽  
Shyamkumar Vadakket Haridas ◽  
Luca Pesce ◽  
Haoyuan Qi ◽  
Andrea Gardin ◽  
...  
Keyword(s):  
Dipole Moment ◽  
Self Assembly ◽  
Materials Science ◽  
Helical Structure ◽  
The Self ◽  
Supramolecular Polymers ◽  
Aliphatic Compound ◽  
Double Helical Structure ◽  
Key Driver ◽  
Supramolecular Polymerization

AbstractThe development of powerful methods for living covalent polymerization has been a key driver of progress in organic materials science. While there have been remarkable reports on living supramolecular polymerization recently, the scope of monomers is still narrow and a simple solution to the problem is elusive. Here we report a minimalistic molecular platform for living supramolecular polymerization that is based on the unique structure of all-cis 1,2,3,4,5,6-hexafluorocyclohexane, the most polar aliphatic compound reported to date. We use this large dipole moment (6.2 Debye) not only to thermodynamically drive the self-assembly of supramolecular polymers, but also to generate kinetically trapped monomeric states. Upon addition of well-defined seeds, we observed that the dormant monomers engage in a kinetically controlled supramolecular polymerization. The obtained nanofibers have an unusual double helical structure and their length can be controlled by the ratio between seeds and monomers. The successful preparation of supramolecular block copolymers demonstrates the versatility of the approach.

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