The Interaction of a Gemini Surfactant with a DNA Quadruplex.

DNA secondary structures are stabilized by mono- and divalent cations. To examine the stability of the DNA quadruplex formed from (TTAGGG), its interaction with a dicationic Gemini surfactant in standard phosphate buffer was investigated. The Gemini surfactant begins to form micelles in buffer at a (critical micelle concentration) of 1.

Structural Characteristics, Electronic Properties, and Coupling Behavior of 12-4-12, 12-3-12, 12-2-12 Cationic Surfactants: A First-Principles Computational Investigation and Experimental Raman Spectroscopy.

In this study, we present a comprehensive first-principles computational investigation focused on the structural characteristics, electronic properties, and coupling integrations of three cationic Gemini surfactants: 12-4-12, 12-3-12, and 12-2-12 ((CH(CH))(CH)-N-(CH)-N(CH(CH))(CH), where = 2, 3, or 4). By employing Density Functional Theory (DFT) computations, we aimed to gain insights into the fundamental aspects of these surfactant molecules, and the intermolecular interactions among these surfactant molecules. We examined different conformers of each surfactant, including parallel, wing, and bent conformers, and compared their relative stability and properties.

Linking Temperature, Cation Concentration and Water Activity for the B to Z Conformational Transition in DNA.

High concentrations of Na⁺ or [Co(NH₃)₆] can induce the B to Z conformational transition in alternating (dC-dG) oligo and polynucleotides. The use of short DNA oligomers (dC-dG)₄ and (dm⁵C-dG)₄ as models can allow a thermodynamic characterization of the transition. Both form right handed double helical structures (B-DNA) in standard phosphate buffer with 115 mM Na⁺ at 25 °C.

Stability of the Na Form of the Human Telomeric G-Quadruplex: Role of Adenines in Stabilizing G-Quadruplex Structure.

G-quadruplexes are higher order DNA structures that play significant roles in gene transcription and telomeric maintenance. The formation and stability of the G-quadruplex structures are under thermodynamic control and may be of biological significance for regulatory function of cellular processes. Here, we report the structural influence and energetic contributions of the adenine bases in the loop sequences that flank G-repeats in human telomeric DNA sequence.

Linking pH, Temperature, and K Concentration for DNA i-Motif Formation.

The conformation a particular DNA segment assumes depends upon its sequence context and the environment under which it is prepared. To complement our findings with G-rich sequences related to the human telomere, we have been investigating the pH induced transition from single strand to i-motif for sequences related to the human telomere C-rich strand. We have carried out titrations of (CCCTAA) from pH 7.

Loop Sequence Context Influences the Formation and Stability of the i-Motif for DNA Oligomers of Sequence (CCCXXX)4, where X = A and/or T, under Slightly Acidic Conditions.

The structure and stability of DNA is highly dependent upon the sequence context of the bases (A, G, C, and T) and the environment under which the DNA is prepared (e.g., buffer, temperature, pH, ionic strength).

The human telomere sequence, (TTAGGG)4, in the absence and presence of cosolutes: a spectroscopic investigation.

Historically, biophysical studies of nucleic acids have been carried out under near ideal conditions, i.e., low buffer concentration (e.

Thermodynamics of forming a parallel DNA crossover.

The process of genetic recombination involves the formation of branched four-stranded DNA structures known as Holliday junctions. The Holliday junction is known to have an antiparallel orientation of its helices, i.e.

Biophysical characterization of the human telomeric (TTAGGG)4 repeat in a potassium solution.

Quadruplex structures arise from four coplanar G bases arranged in a Hoogsteen base pairing motif to create a central pore that can coordinate cations. The termini of eukaryotic chromosomes contain structures, known as telomeres, which are capable of forming quadruplex structures. Quadruplexes have been implicated in a variety of disease states, including cancer.

Enthalpy of the B-to-Z conformational transition of a DNA oligonucleotide determined by isothermal titration calorimetry.

The influence of high concentrations of Na(+) or [Co(NH(3))(6)](3+) on the conformation of two related DNA oligomers was investigated by circular dichroism spectropolarimetry (CD), isothermal titration calorimetry (ITC), and differential scanning calorimetry (DSC). As revealed by CD, DNA oligomers, (dC-dG)(4) and (dm(5)C-dG)(4), both form right-handed double helical structures (B-DNA) in standard phosphate buffer with 115 mM Na(+) at 25 degrees C. However, at 2.

Characterization of the secondary structure and stability of an RNA aptamer that binds vascular endothelial growth factor.

Thermal denaturation studies and spectroscopic studies were employed to investigate the secondary structure and stability of an RNA-PEG conjugate commercially called Macugen. The RNA aptamer is conjugated to a pegylated moiety, and the majority of its 2'-hydroxyl groups are methylated or otherwise modified. UV optical melting studies and differential scanning calorimetry (DSC) were carried out under different conditions to evaluate the effects of Na+ and oligomer concentrations on the stability of the secondary structure of the RNA oligomer.

The influence of sequence context and length on the kinetics of DNA duplex formation from complementary hairpins possessing (CNG) repeats.

The formation of unusual structures during DNA replication has been invoked for gene expansion in genomes possessing triplet repeat sequences, CNG, where N = A, C, G, or T. In particular, it has been suggested that the daughter strand of the leading strand partially dissociates from the parent strand and forms a hairpin. The equilibrium between the fully duplexed parent:daugter species and the parent:hairpin species is dependent upon their relative stabilities and the rates of reannealing of the daughter strand back to the parent.

Influence of sequence context and length on the structure and stability of triplet repeat DNA oligomers.

Genetic expansion diseases have been linked to the properties of triplet repeat DNA sequences during replication. The most common triplet repeats associated with such diseases are CAG, CCG, CGG, and CTG. It has been suggested that gene expansion occurs as a result of hairpin formation of long stretches of these sequences on the leading daughter strand synthesized during DNA replication [Gellibolian, R.