NMR study of the effect of sugar-phosphate backbone ethylation on the stability and conformation of DNA double helix

Biochemistry ◽  
1987 ◽  
Vol 26 (13) ◽  
pp. 3807-3812 ◽  
Author(s):  
Pradip Pramanik ◽  
Lou Sing Kan
Keyword(s):  
Double Helix ◽  
Sugar Phosphate ◽  
Nmr Study ◽  
Phosphate Backbone ◽  
The Stability ◽  
Dna Double Helix

DNA mimicry by proteins

2006 ◽  
Vol 34 (2) ◽  
pp. 317-319 ◽  
Author(s):  
D.T.F. Dryden ◽  
M.R. Tock
Keyword(s):  
Double Helix ◽  
Restriction Enzymes ◽  
Repair Enzymes ◽  
Phosphate Backbone ◽  
Dna Mimicry ◽  
Associated Proteins ◽  
Bonding Properties ◽  
Dna Restriction ◽  
Dna Double Helix ◽  
Dna Restriction Enzymes

It has been discovered recently, via structural and biophysical analyses, that proteins can mimic DNA structures in order to inhibit proteins that would normally bind to DNA. Mimicry of the phosphate backbone of DNA, the hydrogen-bonding properties of the nucleotide bases and the bending and twisting of the DNA double helix are all present in the mimics discovered to date. These mimics target a range of proteins and enzymes such as DNA restriction enzymes, DNA repair enzymes, DNA gyrase and nucleosomal and nucleoid-associated proteins. The unusual properties of these protein DNA mimics may provide a foundation for the design of targeted inhibitors of DNA-binding proteins.

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 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.

Viscometric Studies on the Stability of DNA-Proflavine Complex

1972 ◽  
Vol 27 (11) ◽  
pp. 1385-1387 ◽  
Author(s):  
G. C. Das ◽  
N. N. Das Gupta
Keyword(s):  
Double Helix ◽  
Thermal Stabilization ◽  
Binding Mode ◽  
Stable Configuration ◽  
P Value ◽  
Binding Modes ◽  
Specific Viscosity ◽  
Complex Variation ◽  
The Stability ◽  
Dna Double Helix

Viscometric technique has been used to estimate the relative contributions of strong and weak binding modes towards thermal stabilization of the Proflavine-DNA complex. Variation of the ratio of the specific viscosity of the dye-bound DNA to that of the DNA solution (η′sp/η sp) with different dye to DNA-phosphate ratios (D/P) shows that the saturation is attained at D/P value of about 0.2. This effect is more pronounced at lower ionic strengths. Heat-induced helix-coil transition curves at different D/P values at a fixed ionic strength of the buffer reveal a gradual shift towards higher temperature with the increase of D/P and levelling off at D/P of about 0.22. It is suggested that only the strong binding mode causes thermal stabilization of the DNA double helix and the double helix having all the possible intercalating sites saturated by the dye molecules attains the most stable configuration.

scholarly journals Understanding the Origin of Structural Diversity of DNA Double Helix

Computation ◽  
2021 ◽  
Vol 9 (9) ◽  
pp. 98
Author(s):  
Valeri Poltev ◽  
Victor M. Anisimov ◽  
Veronica Dominguez ◽  
Andrea Ruiz ◽  
Alexandra Deriabina ◽  
...  
Keyword(s):  
Double Helix ◽  
3D Structure ◽  
Structural Diversity ◽  
Local Energy ◽  
Single Chain ◽  
Sequence Dependence ◽  
Torsion Angles ◽  
Sequence Dependent ◽  
Phosphate Backbone ◽  
Dna Double Helix

Deciphering the contribution of DNA subunits to the variability of its 3D structure represents an important step toward the elucidation of DNA functions at the atomic level. In the pursuit of that goal, our previous studies revealed that the essential conformational characteristics of the most populated “canonic” BI and AI conformational families of Watson–Crick duplexes, including the sequence dependence of their 3D structure, preexist in the local energy minima of the elemental single-chain fragments, deoxydinucleoside monophosphates (dDMPs). Those computations have uncovered important sequence-dependent regularity in the superposition of neighbor bases. The present work expands our studies to new minimal fragments of DNA with Watson–Crick nucleoside pairs that differ from canonic families in the torsion angles of the sugar-phosphate backbone (SPB). To address this objective, computations have been performed on dDMPs, cdDMPs (complementary dDMPs), and minimal fragments of SPBs of respective systems by using methods of molecular and quantum mechanics. These computations reveal that the conformations of dDMPs and cdDMPs having torsion angles of SPB corresponding to the local energy minima of separate minimal units of SPB exhibit sequence-dependent characteristics representative of canonic families. In contrast, conformations of dDMP and cdDMP with SPB torsions being far from the local minima of separate SPB units exhibit more complex sequence dependence.

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.

scholarly journals Thermodynamic basis of the α-helix and DNA duplex

2021 ◽  
Author(s):  
A. I. Dragan ◽  
C. Crane-Robinson ◽  
P. L. Privalov
Keyword(s):  
Hydrogen Bonds ◽  
Double Helix ◽  
Van Der Waals ◽  
Van Der Waals Interactions ◽  
Base Pairs ◽  
The Stability ◽  
Α Helix ◽  
Dna Double Helix ◽  
Conjugate Base ◽  
Thermodynamic Basis

AbstractAnalysis of calorimetric and crystallographic information shows that the α-helix is maintained not only by the hydrogen bonds between its polar peptide groups, as originally supposed, but also by van der Waals interactions between tightly packed apolar groups in the interior of the helix. These apolar contacts are responsible for about 60% of the forces stabilizing the folded conformation of the α-helix and their exposure to water on unfolding results in the observed heat capacity increment, i.e. the temperature dependence of the melting enthalpy. The folding process is also favoured by an entropy increase resulting from the release of water from the peptide groups. A similar situation holds for the DNA double helix: calorimetry shows that the hydrogen bonding between conjugate base pairs provides a purely entropic contribution of about 40% to the Gibbs energy while the enthalpic van der Waals interactions between the tightly packed apolar parts of the base pairs provide the remaining 60%. Despite very different structures, the thermodynamic basis of α-helix and B-form duplex stability are strikingly similar. The general conclusion follows that the stability of protein folds is primarily dependent on internal atomic close contacts rather than the hydrogen bonds they contain.

Protamine-DNA interaction

1978 ◽  
Vol 36 (2) ◽  
pp. 200-201
Author(s):  
D.P. Bazett-Jones ◽  
F.P. Ottensmeyer
Keyword(s):  
Small Volume ◽  
Double Helix ◽  
Dna Interaction ◽  
Dark Field ◽  
Sperm Head ◽  
Nuclear Proteins ◽  
Field Electron Microscopy ◽  
Dark Field Electron ◽  
Dna Double Helix ◽  
Positively Charged

Dark field electron microscopy has been used for the study of the structure of individual macromolecules with a resolution to at least the 5Å level. The use of this technique has been extended to the investigation of structure of interacting molecules, particularly the interaction between DNA and fish protamine, a class of basic nuclear proteins of molecular weight 4,000 daltons.Protamine, which is synthesized during spermatogenesis, binds to chromatin, displaces the somatic histones and wraps up the DNA to fit into the small volume of the sperm head. It has been proposed that protamine, existing as an extended polypeptide, winds around the minor groove of the DNA double helix, with protamine's positively-charged arginines lining up with the negatively-charged phosphates of DNA. However, viewing protamine as an extended protein is inconsistent with the results obtained in our laboratory.

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