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.

DNA: Not Merely the Secret of Life

2010 ◽  
Author(s):  
Nadrian C. Seeman
Keyword(s):  
Double Helix ◽  
Genetic Material ◽  
Helical Structure ◽  
Prominent Feature ◽  
Base Pairing ◽  
Double Helical Structure ◽  
Reciprocal Exchange ◽  
Sequence Selection ◽  
Living Organisms ◽  
Dna Double Helix

DNA is well-known as the genetic material of living organisms. Its most prominent feature is that it contains information that enables it to replicate itself. This information is contained in the well-known Watson-Crick base pairing interactions, adenine with thymine and guanine with cytosine. The double helical structure that results from this complementarity has become a cultural icon of our era. To produce species more diverse than the DNA double helix, we use the notion of reciprocal exchange, which leads to branched molecules. The topologies of these species are readily programmed through sequence selection; in many cases, it is also possible to program their structures. Branched species can be connected to one another using the same interactions that genetic engineers use to produce their constructs, cohesion by molecules tailed in complementary single-stranded overhangs, known as ‘sticky ends.’ Such sticky-ended cohesion is used to produce N-connected objects and lattices [1]. This notion is shown in the drawing, which shows cohesion between sticky-ended branched species.

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.

Axially Chiral Bis(α-amino Acid)s and Their Deamino Analogues. Synthesis and Configurational Assignment

1998 ◽  
Vol 63 (2) ◽  
pp. 211-221 ◽  
Author(s):  
Miloš Tichý ◽  
Luděk Ridvan ◽  
Miloš Buděšínský ◽  
Jiří Závada ◽  
Jaroslav Podlaha ◽  
...  
Keyword(s):  
Amino Acid ◽  
Nmr Spectra ◽  
Building Blocks ◽  
X Ray Diffraction ◽  
Amino Groups ◽  
X Ray ◽  
Configurational Assignment ◽  
Symmetry Properties ◽  
Axially Chiral ◽  
Polymeric Structures

The axially chiral bis(α-amino acid)s cis-2 and trans-2 as possible building blocks for polymeric structures of novel type of helicity were prepared. Their configuration has been determined by NMR spectroscopy and, in the case of the trans-isomer, confirmed by single-crystal X-ray diffraction. Analogous pair of stereoisomeric diacids cis-3 and trans-3, devoid of the amino groups, was also prepared and their configuration assigned. The observed differences in the NMR spectra of cis- and trans-isomers of 2 and 3 are discussed from the viewpoint of their different symmetry properties.

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.

scholarly journals Accurate Representation of B-DNA Double Helical Structure with Implicit Solvent and Counterions

2002 ◽  
Vol 83 (1) ◽  
pp. 382-406 ◽  
Author(s):  
Lihua Wang ◽  
Brian E. Hingerty ◽  
A.R. Srinivasan ◽  
Wilma K. Olson ◽  
Suse Broyde
Keyword(s):  
Helical Structure ◽  
Implicit Solvent ◽  
Accurate Representation ◽  
Double Helical Structure

Thiol-mediated etching of gold nanorods as a neoteric strategy for room-temperature and multicolor detection of nitrite and nitrate

2021 ◽  
Author(s):  
Marzieh Sepahvand ◽  
Forough Ghasemi ◽  
Hossein Mirseyed Hosseini
Keyword(s):  
Human Health ◽  
Gold Nanorods ◽  
Room Temperature ◽  
Scientific Communities ◽  
Negative Impacts ◽  
Living Organisms

The excessive presence of nitrite and nitrate in the environmental matrixes has raised concerns among the scientific communities due to their negative impacts on human health and living organisms. Considering...

scholarly journals Influence of molecular structure on helicoidal structure and NMR spectra of chiral liquid crystalline esters

2017 ◽  
Vol 66 (2) ◽  
pp. 25-35
Author(s):  
Anna Drzewicz ◽  
Marzena Tykarska ◽  
Mateusz Szala ◽  
Magdalena Żurowska
Keyword(s):  
Molecular Structure ◽  
Nmr Spectra ◽  
Liquid Crystalline ◽  
Room Temperature ◽  
Alkyl Chain ◽  
Light Reflection ◽  
13C Nmr Spectra ◽  
1H And 13C Nmr ◽  
Antiferroelectric Phase ◽  
Helicoidal Structure

Three-ring chiral liquid crystalline compounds, forming antiferroelectric phase, differing in the structure of alkyl chain and in the substitution of benzene ring by fluorine atoms were studied. The measurements of helical pitch, based on the selective light reflection phenomenon, were performed as well as 1H and 13C NMR spectra at room temperature were registered. The influence of molecular structure as well as the type of helicoidal structure on the chemical shift of signals coming from chiral center was observed. Keywords: liquid crystals, helicoidal structure, nuclear magnetic resonance, antiferroelectric phase

scholarly journals Atran-analoge Verbindungen des Typs / Atrane Analogous Compounds of the Type

1984 ◽  
Vol 39 (3) ◽  
pp. 341-351 ◽  
Author(s):  
Joseph Grobe ◽  
Gerald Henkel ◽  
Bernt Krebs ◽  
Nikolaos Voulgarakis
Keyword(s):  
Structure Analysis ◽  
Nmr Spectra ◽  
Room Temperature ◽  
Trigonal Bipyramid ◽  
Angular Distortion ◽  
Type I ◽  
Tetrahedral Coordination ◽  
Cage Compounds ◽  
X Ray ◽  
H Nmr

Heterocyclic cage compounds of type I (compounds 8-10) have been prepared by condensation reactions of 1,2,2-trifunctional disilanes Me(R)XSiSiMeX2 (R = Me, Ph, OEt; X = NMe2, OEt) with triethanolamine using the “Dilution Principle”. The starting compounds are obtained by Si-Me cleavage of Si2Me6 with acetylchloride/AlCl3 followed by either aminolysis with HNMe2 or alcoholysis with EtOH. 1H NMR spectra indicate N→Si(1) intraction with the more acidic Si atom in 8 and 9. This result is proved by the X-ray structure analysis of 8 (monoclinic, P21/c; a = 7,088(2), b = 15,070(4), c = 12,701(4) Å, β = 104,96(2) at -130 °C, Z = 4); the Si(1)···N distance is found to be 2,768 Å , connected with a significant angular distortion of the tetrahedral coordination around Si(1) towards a trigonal bipyramid. In compound 10, too, N→Si(1) coordination is observed at room temperature in spite of almost equal acidity for both Si atoms. This can be explained by the preference of 5- over 6-membered chelating ring systems. At higher temperatures the 1H NMR spectra show a fluctuation of the N-donor between the two Si centres.

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