scholarly journals Influence of perylenediimide–pyrene supramolecular interactions on the stability of DNA-based hybrids: Importance of electrostatic complementarity

2014 ◽  
Vol 10 ◽  
pp. 1589-1595 ◽  
Author(s):  
Christian B Winiger ◽  
Simon M Langenegger ◽  
Oleg Khorev ◽  
Robert Häner
Keyword(s):  
Double Helix ◽  
Building Blocks ◽  
Supramolecular Interactions ◽  
Stacking Interactions ◽  
Average Value ◽  
Π Stacking ◽  
Dna Strands ◽  
Polycyclic Aromatic ◽  
The Stability ◽  
Dna Double Helix

Aromatic π–π stacking interactions are ubiquitous in nature, medicinal chemistry and materials sciences. They play a crucial role in the stacking of nucleobases, thus stabilising the DNA double helix. The following paper describes a series of chimeric DNA–polycyclic aromatic hydrocarbon (PAH) hybrids. The PAH building blocks are electron-rich pyrene and electron-poor perylenediimide (PDI), and were incorporated into complementary DNA strands. The hybrids contain different numbers of pyrene–PDI interactions that were found to directly influence duplex stability. As the pyrene–PDI ratio approaches 1:1, the stability of the duplexes increases with an average value of 7.5 °C per pyrene–PDI supramolecular interaction indicating the importance of electrostatic complementarity for aromatic π–π stacking interactions.

scholarly journals Hachimoji DNA and RNA: A genetic system with eight building blocks

Science ◽  
2019 ◽  
Vol 363 (6429) ◽  
pp. 884-887 ◽  
Author(s):  
Shuichi Hoshika ◽  
Nicole A. Leal ◽  
Myong-Jung Kim ◽  
Myong-Sang Kim ◽  
Nilesh B. Karalkar ◽  
...  
Keyword(s):  
Double Helix ◽  
Building Blocks ◽  
Genetic System ◽  
Molecular Structures ◽  
Darwinian Evolution ◽  
Structural Requirements ◽  
Dna And Rna ◽  
The Stability ◽  
Dna Double Helix ◽  
Orthogonal Pairs

We report DNA- and RNA-like systems built from eight nucleotide “letters” (hence the name “hachimoji”) that form four orthogonal pairs. These synthetic systems meet the structural requirements needed to support Darwinian evolution, including a polyelectrolyte backbone, predictable thermodynamic stability, and stereoregular building blocks that fit a Schrödinger aperiodic crystal. Measured thermodynamic parameters predict the stability of hachimoji duplexes, allowing hachimoji DNA to increase the information density of natural terran DNA. Three crystal structures show that the synthetic building blocks do not perturb the aperiodic crystal seen in the DNA double helix. Hachimoji DNA was then transcribed to give hachimoji RNA in the form of a functioning fluorescent hachimoji aptamer. These results expand the scope of molecular structures that might support life, including life throughout the cosmos.

Coordination Polymers with a Bulky Perylene-Based Tetracarboxylate Ligand: Syntheses, Crystal Structures, and Luminescent Properties

2010 ◽  
Vol 63 (3) ◽  
pp. 463 ◽  
Author(s):  
Chun-Sen Liu ◽  
Min Hu ◽  
Song-Tao Ma ◽  
Qiang Zhang ◽  
Li-Ming Zhou ◽  
...  
Keyword(s):  
Coordination Polymers ◽  
Three Dimensional ◽  
Luminescent Properties ◽  
Supramolecular Interactions ◽  
Polymeric Chain ◽  
Stacking Interactions ◽  
One Dimensional ◽  
Π Stacking ◽  
Higher Dimensional ◽  
Interchain Interactions

To explore the coordination possibilities of perylene-based ligands with a larger conjugated π-system, four ZnII, MnII, and CoII coordination polymers with perylene-3,4,9,10-tetracarboxylate (ptc) and the chelating 1,10-phenanthroline (phen) ligands were synthesized and characterized: {[Zn2(ptc)(phen)2](H2O)10}∞ (1), {[Zn3(ptc)(OH)2(phen)2](H2O)3}∞ (2), {[Mn(ptc)0.5(phen)(H2O)2](H2O)1.5}∞ (3), and {[Co(ptc)0.5(phen)(H2O)2](H2O)2.5}∞ (4). Structural analysis reveals that complexes 1 and 2 both take one-dimensional polymeric chain structures with dinuclear and trinuclear units as nodes, respectively, which are further extended via the accessorial secondary interchain interactions, such as C–H···O H-bonding or aromatic π···π stacking interactions, to give rise to the relevant higher-dimensional frameworks. Compound 3 has a two-dimensional sheet structure that is further assembled to form a three-dimensional framework by interlayer π···π stacking interactions. Complex 4 is a one-dimensional ribbon-like array structure that is interlinked by the co-effects of intermolecular π···π stacking and C–H···π supramolecular interactions, resulting in a higher-dimensional framework from the different crystallographic directions. Moreover, complexes 1–4 exhibit strong solid-state luminescence emissions at room temperature, which mainly originate from intraligand π→π* transitions of ptc.

Polyamine derivatives as potential bisintercalators with antiproliferative activity

2016 ◽  
Vol 4 ◽  
pp. 9-15
Author(s):  
Marta Szumilak
Keyword(s):  
Ethidium Bromide ◽  
Antiproliferative Activity ◽  
Double Helix ◽  
Structural Features ◽  
Discovery Studio ◽  
Polycyclic Aromatic ◽  
Ic50 Values ◽  
Dna Double Helix ◽  
Polyamine Derivatives

Bisntercalators are very interesting group of compounds with potential antitumor activity. They interact reversibly with DNA double helix. These agents share common structural features such as the presence of two, planar, polycyclic aromatic or heteroaromatic systems separated by a spacer chain which must be long enough to enable double intercalation between base pairs. The unique chemical structure of these compounds provides numerous modifications within their structure resulting either in higher activity or increased selectivity toward tumor cells. Within the framework of the project, new polyamine derivatives containing dimeric phthalimide, quinoline, cinnoline and chromone moieties were obtained. Three different polyamines: 1,4-bis(3-aminopropyl)piperazine, 4,9-dioxa-1,12-dodecanediamine, 3,3’-diamino-N-methyldipropylamine were used as linkers. The biological activity of compounds was assessed in vitro in a highly aggressive melanoma cell line A375. Quinoline derivatives were found to have a higher antiproliferative activity than cinnoline ones. The lowest IC50 values, below 20 μM, were obtained for quinoline and 2H-chromene-2,4(3H)-dione derivatives. Quinoline diamides were more efficient than cinnoline ones. Polyamine diimides containing phthalimide moieties demonstrated no inhibitory activities against melanoma cells. Preliminary studies of mechanism of action have shown that obtained derivatives were capable of quenching the fluorescence of ethidium bromide-DNA complex, indicating that they bound to ds-DNA in competition with ethidium bromide for binding sites. All the compounds were also subjected to preliminary in silico ADME screening by evaluating their theoretical drug-likeness and physicochemical properties using Discovery Studio 3.0 obtained from Accelrys. Compounds meeting the required ADME and drug-likeness criteria were selected.

Symmetry-adapted digital modeling II. The double-helix B-DNA

2016 ◽  
Vol 72 (3) ◽  
pp. 312-323 ◽  
Author(s):  
A. Janner
Keyword(s):  
Dimensional Space ◽  
Double Helix ◽  
Three Dimensional ◽  
Reduction Factor ◽  
Lattice Points ◽  
Three Dimensions ◽  
Coarse Grained ◽  
Digital Modeling ◽  
Dna Strands ◽  
Dna Double Helix

The positions of phosphorus in B-DNA have the remarkable property of occurring (in axial projection) at well defined points in the three-dimensional space of a projected five-dimensional decagonal lattice, subdividing according to the golden mean ratio τ:1:τ [with τ = (1+\sqrt {5})/2] the edges of an enclosing decagon. The corresponding planar integral indicesn1,n2,n3,n4(which are lattice point coordinates) are extended to include the axial indexn5as well, defined for each P position of the double helix with respect to the single decagonal lattice ΛP(aP,cP) withaP= 2.222 Å andcP= 0.676 Å. A finer decagonal lattice Λ(a,c), witha=aP/6 andc=cP, together with a selection of lattice points for each nucleotide with a given indexed P position (so as to define a discrete set in three dimensions) permits the indexing of the atomic positions of the B-DNA d(AGTCAGTCAG) derived by M. J. P. van Dongen. This is done for both DNA strands and the single lattice Λ. Considered first is the sugar–phosphate subsystem, and then each nucleobase guanine, adenine, cytosine and thymine. One gets in this way a digital modeling of d(AGTCAGTCAG) in a one-to-one correspondence between atomic and indexed positions and a maximal deviation of about 0.6 Å (for the value of the lattice parameters given above). It is shown how to get a digital modeling of the B-DNA double helix for any given code. Finally, a short discussion indicates how this procedure can be extended to derive coarse-grained B-DNA models. An example is given with a reduction factor of about 2 in the number of atomic positions. A few remarks about the wider interest of this investigation and possible future developments conclude the paper.

scholarly journals MUTABLE R-NAVAJO ALLELES OF CYCLIC ORIGIN IN MAIZE

Genetics ◽  
1973 ◽  
Vol 73 (2) ◽  
pp. 273-296
Author(s):  
R Alexander Brink ◽  
Elizabeth Williams
Keyword(s):  
Nucleotide Sequence ◽  
Gene Action ◽  
Double Helix ◽  
Donor Site ◽  
Chromosome Breakage ◽  
Strand Breaks ◽  
Single Strand Breaks ◽  
Unstable Compound ◽  
The Stability ◽  
Dna Double Helix

ABSTRACT The generation in cyclic fashion of 26 mutable R-Navajo (mRnj) alleles in maize involved transposition of a non-specific repressor of gene action, Modulator (Mp), first away from, and then back to, the R locus represented by the R-Navajo (Rnj) all ele on chromosome 10. The mPnj alleles reconstituted in this way vaned widely, and continuously, in mutability to Rnj-that is, in transposition of Mp away from the R locus, thus derepressing the Rnj gene. They were alike, or nearly so, however, in activating Ds chromosome breakage and in increasing the stability of variegated pericarp, another unstable compound allele comprising Mp conjoined with Prr on chromosomal 1. These latter two phenomena are based primarily on loci elsewhere in the genome. It is postulated that the 26 reconstituted mRnj alleles carry a common Mp which, however, is intercalated at a different site within each allele. Nucleotide sequence in the regions adjacent to Mp is assumed to determine the frequency with which a form of micro-nondisjunction occurs whereby Mp is released from a donor site. Transposition to a new site is interpreted in terms of a chromosome model that gives effect to nicking, or single strand breaks, occurring throughout the genome as a prerequisite to unwinding, strand separation, and replication, of the DNA double helix.

scholarly journals Untersuchungen über die Bindung pflanzlicher Wuchsstoffe an verschiedene Komponenten des Chromatins in vitro. I. Bindung an DNS / Investigations Upon the Binding of Plant Growth Substances to Several Components of the Chromatin in vitro. I. Binding to DNA

1971 ◽  
Vol 26 (6) ◽  
pp. 607-612 ◽  
Author(s):  
Günter Fellenberg
Keyword(s):  
Hydrogen Bonds ◽  
Absorption Maximum ◽  
Double Helix ◽  
Specific Effect ◽  
Growth Substance ◽  
Growth Substances ◽  
Plant Growth Substances ◽  
The Stability ◽  
Dna Double Helix

At pH 9,5 the DNA absorption maximum at 190 nm was shifted to 212 nm. This absorption maximum showed a bathochrome effect in the presence of IAA, GA and KI. The amplitude of this maximum was reduced at the same time. By addition of urea (0.1 —2.0 moles/l) the bathochrome effect, induced by the growth substances, was completely reversed, whereas application of NaCl (0.1 — 2.0 moles/l) did not affect the bathochrome movement of this DNA maximum. At pH 6.0 in the presence of 0.9% NaCl this DNA maximum did not show any visible bathochrome movement in the presence of the growth substances investigated. The DNA maximum at 260 nm did not show any alteration in the presence of growth substances.The thermal denaturation of DNA-complexes with IAA and GA showed, that with increasing concentration of these growth substances, the Tm-value of the DNA was reduced. On the other hand, KI increased the Tm-point of DNA. By biphasic melting at 260 nm and 280 nm no specific effect of the investigated growth substances on the stability of the A — T or G—C pairs was detected.Tryptophan and β-NAA closely related in structure to the auxins IAA and α-NAA did not reduce the Tm-value of DNA.At pH < 7 IAA, GA and KI did not show any detectable influence on the Tm-value of DNA.The data presented show that at a pH > 7 IAA, GA and KI are obviously bound to DNA by hydrogen bonds. There is evidence that these bonds are very unstable. Nevertheless, IAA and GA can loosen part of the hydrogen bonds of DNA double helix while KI cannot. Possible consequences of these growth substance effects on DNA are discussed.

scholarly journals Piecing Together Large Polycyclic Aromatic Hydrocarbons and Fullerenes: A Combined ChemTEM Imaging and MALDI-ToF Mass Spectrometry Approach

2021 ◽  
Vol 9 ◽  
Author(s):  
R. K. E. Gover ◽  
T. W. Chamberlain ◽  
P. J. Sarre ◽  
A. N. Khlobystov
Keyword(s):  
Mass Spectrometry ◽  
Materials Science ◽  
Building Blocks ◽  
Supramolecular Interactions ◽  
Combined Approach ◽  
Top Down ◽  
Transmission Electron ◽  
Graphene Flakes ◽  
Polycyclic Aromatic ◽  
Large Polycyclic Aromatic Hydrocarbons

Motivated by their importance in chemistry, physics, astronomy and materials science, we investigate routes to the formation of large polycyclic aromatic hydrocarbon (PAH) molecules and the fullerene C60 from specific smaller PAH building blocks. The behaviour of selected PAH molecules under electron (using transmission electron microscopy, TEM) and laser irradiation is examined, where four specific PAHs—anthracene, pyrene, perylene and coronene—are assembling into larger structures and fullerenes. This contrasts with earlier TEM studies in which large graphene flakes were shown to transform into fullerenes via a top-down route. A new combined approach is presented in which spectrometric and microscopic experimental techniques exploit the stabilisation of adsorbed molecules through supramolecular interactions with a graphene substrate and enable the molecules to be characterised and irradiated sequentially. Thereby allowing initiation of transformation and characterisation of the resultant species by both mass spectrometry and direct-space imaging. We investigate the types of large PAH molecule that can form from smaller PAHs, and discuss the potential of a “bottom-up” followed by “top-down” mechanism for forming C60.

Stereoscopic Visualization of Spermidine-DNA Torus Structure Prepared by the Freeze-Fracture, Deep-Etch Technique

1981 ◽  
Vol 39 ◽  
pp. 438-439
Author(s):  
George C. Ruben ◽  
Kenneth A. Marx ◽  
Thomas C. Reynolds
Keyword(s):  
Double Helix ◽  
Freeze Fracture ◽  
Etching Technique ◽  
Calf Thymus ◽  
Quick Freezing ◽  
Metal Levels ◽  
Dna Strands ◽  
Dna Double Helix ◽  
Stereoscopic Visualization ◽  
Condensed Dna

Freeze-fracture TEM has been used to visualize spermidine-DNA complexes╌a model system for bacteriophage DNA packaging. We have observed the toroidal shape and bacteriophage size (770Å) of spermidine-condensed DNA particles prepared by quick freezing of DNA-spermidine solutions followed by a freeze-fracture, deep-etching technique. Single direction shadowing with low Pt-C metal levels (9Å thick) has allowed us to demonstrate that the freeze-fracture technique is capable of revealing the organization of separate double helical DNA strands on the torus surface. The spermidine-DNA toruses exhibited surface Pt-C decoration consistent with the DNA double helix being circumferentially wrapped to form the torus. In addition, we have demonstrated that a hydrated sample shows the same toroidal shapes that have been previously demonstrated by Chattoraj et. al, in a dehydrated preparation.We performed freeze-fracture TEM studies of spermidine condensed (0.2 mM) Calf Thymus DNA (5 μg/ml) complexes in 1 mM NaCl, 10 mM Tris pH 7.0. Samples were freeze-fractured and etched for 13 min at -97°C.

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