The DNA fragment d(CpGpCpGpCpG) crystallises as a left-handed double helical molecule with Watson-Crick base pairs and an antiparallel organisation of the sugar phosphate chains. The helix has two nucleotides in the asymmetric unit and contains twelve base pairs per turn. It differs significantly from right-handed B-DNA.

Molecular structure of a left-handed double helical DNA fragment at atomic resolution

We present a comprehensive software package, 3DNA, for the analysis, reconstruction and visualization of three-dimensional nucleic acid structures. Starting from a coordinate file in Protein Data Bank (PDB) format, 3DNA can handle antiparallel and parallel double helices, single-stranded structures, triplexes, quadruplexes and other complex tertiary folding motifs found in both DNA and RNA structures. The analysis routines identify and categorize all base interactions and classify the double helical character of appropriate base pair steps. The program makes use of a recently recommended reference frame for the description of nucleic acid base pair geometry and a rigorous matrix-based scheme to calculate local conformational parameters and rebuild the structure from these parameters. The rebuilding routines produce rectangular block representations of nucleic acids as well as full atomic models with the sugar-phosphate backbone and publication quality 'standardized' base stacking diagrams. Utilities are provided to locate the base pairs and helical regions in a structure and to reorient structures for effective visualization. Regular helical models based on X-ray diffraction measurements of various repeating sequences can also be generated within the program.

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3DNA: a software package for the analysis, rebuilding and visualization of three‐dimensional nucleic acid structures

Here we review studies that provided important information about conformational properties of DNA using circular dichroic (CD) spectroscopy. The conformational properties include the B-family of structures, A-form, Z-form, guanine quadruplexes, cytosine quadruplexes, triplexes and other less characterized structures. CD spectroscopy is extremely sensitive and relatively inexpensive. This fast and simple method can be used at low- as well as high-DNA concentrations and with short- as well as long-DNA molecules. The samples can easily be titrated with various agents to cause conformational isomerizations of DNA. The course of detected CD spectral changes makes possible to distinguish between gradual changes within a single DNA conformation and cooperative isomerizations between discrete structural states. It enables measuring kinetics of the appearance of particular conformers and determination of their thermodynamic parameters. In careful hands, CD spectroscopy is a valuable tool for mapping conformational properties of particular DNA molecules. Due to its numerous advantages, CD spectroscopy significantly participated in all basic conformational findings on DNA.

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Circular dichroism and conformational polymorphism of DNA

2.2.1. Polyisocyanates 6117 2.2.2. Polysilanes 6118 2.2.3. Polyacetylenes 6120 2.3. Foldamer-Based Helical Polymers 6124 2.3.1. Click Polymerization 6126 2.3.2. Ring-Closing Reaction 6126 2.4. Other Types of Helical Polymers 6127 2.4.1. π-Conjugated Helical Polymers 6127 2.4.2. Metallosupramolecular Helical Polymers 6128 2.5. Induced Helical Polymers 6130 2.5.1. Induced Helical Polyacetylenes 6130 2.5.2. Other Induced Helical Polymers and Oligomers 6132

Helical polymers: synthesis, structures, and functions

The CHARMM27 all-atom force field for nucleic acids represents a highly optimized model for investigations of nucleic acids via empirical force field calculations. The force field satisfactorily treats the A, B, and Z forms of DNA as well as RNA, and it also useful for nucleosides and nucleotides. In addition, it is compatible with the CHARMM force fields for proteins and lipids, allowing for simulation studies of heterogeneous systems. © 2001 John Wiley & Sons, Inc. Biopolymers (Nucleic Acid Sci) 56: 257–265, 2001

Development and current status of the CHARMM force field for nucleic acids

Salt-induced co-operative conformational change of a synthetic DNA: Equilibrium and kinetic studies with poly(dG-dC)☆

A salt-induced cooperative conformational transition of a synthetic DNA, poly(dG-dC), is reversed by addition of ethidium bromide. Binding of the dye at high salt concentrations is highly cooperative. Circular dichroism spectra of the complex and the kinetic data support a model for this cooperative binding that is formally equivalent to the “allosteric” one proposed for oligomeric proteins by Monod et al. Thus, double-helical DNA of at least one defined sequence can undergo a cooperative conformational change in solution, with simple salts and drug molecules as antagonistic effectors. Such transitions may be involved in regulatory phenomena operating directly at the level of nucleic acid structure.

https://www.pnas.org/content/pnas/69/12/3805.full.pdf

Ethidium Bromide as a Cooperative Effector of a DNA Structure

In globular proteins, the complicated steric arrangement of the polypeptide chain is determined by several interdependent cooperative interactions. These macromolecules are capable of reacting to changes in the environmental conditions such as temperature and pressure or the concentration of a wide range of compounds by changing their conformation and hence their biological and chemical properties. They are thus suitable for regulation processes or information storage in solution with a wide range of time constants. Environmental effects of this kind can be followed and explained in part at the molecular level by investigation of the time-dependent reversible unfolding of a number of proteins that can be described to a good approximation by a strongly cooperative “all-or-none” transition between two states.

Cooperative conformational changes in globular proteins.

In globularen Proteinen ist die komplizierte raumliche Anordnung der Polypeptidkette durch mehrere voneinander abhangige, kooperative Wechselwirkungen bestimmt. Auf Anderungen der Umwelt wie Temperatur und Druck sowie Konzentration verschiedenster Verbindungen konnen diese Makromolekule durch Anderung ihrer Konformation und damit ihrer biologischen und chemischen Eigenschaften reagieren. Sie sind dadurch fur Regelvorgange oder Informationsspeicherung in Losung mit sehr unterschiedlichen Zeitkonstanten geeignet. Am zeitlichen Verhalten bei der reversiblen Entfaltung einiger Proteine, die gut durch eine stark kooperative „Alles-oder-Nichts”-Umwandlung zwischen zwei Zustanden beschrieben werden kann, lassen sich solche Einflusse der Umwelt verfolgen und zum Teil auf molekularer Ebene erklaren.

Fritz M. Pohl

Papers

Salt-induced co-operative conformational change of a synthetic DNA: Equilibrium and kinetic studies with poly(dG-dC)☆

Ethidium Bromide as a Cooperative Effector of a DNA Structure

Cooperative conformational changes in globular proteins.

Kooperative Konformationsänderungen von globulären Proteinen