Origins of fine structure in DNA melting curves.

With the help of the one-dimensional random Potts-like model, we study the origins of fine structures observed on differential melting profiles of double-stranded DNA. We theoretically assess the effects of sequence arrangement on DNA melting curves through the comparison of results for random, correlated, and block sequences. Our results re-confirm the smearing out of the fine structure with the increase in chain length for all types of sequence arrangements and suggest that the fine structure is a finite-size effect.

DNA-based assay for calorimetric determination of protein concentrations in pure or mixed solutions.

It was recently reported that values of the transition heat capacities, as measured by differential scanning calorimetry, for two globular proteins and a short DNA hairpin in NaCl buffer are essentially equivalent, at equal concentrations (mg/mL). To validate the broad applicability of this phenomenon, additional evidence for this equivalence is presented that reveals it does not depend on DNA sequence, buffer salt, or transition temperature (Tm). Based on the equivalence of transition heat capacities, a calorimetric method was devised to determine protein concentrations in pure and complex solutions.

Calorimetric analysis using DNA thermal stability to determine protein concentration.

It was recently reported for two globular proteins and a short DNA hairpin in NaCl buffer that values of the transition heat capacities, and , for equal concentrations (mg/mL) of DNA and proteins, are essentially equivalent (differ by less than 1%). Additional evidence for this equivalence is presented that reveals this phenomenon does not depend on DNA sequence, buffer salt, or T. Sequences of two DNA hairpins were designed to confer a near 20°C difference in their T's.

Equivalence of the transition heat capacities of proteins and DNA.

It has been reported for many globular proteins that the native heat capacity at 25 °C, per gram, is the same. This has been interpreted to indicate that heat capacity is a fundamental property of native proteins that provides important information on molecular structure and stability. Heat capacities for both proteins and DNA has been suggested to be related to universal effects of hydration/solvation on native structures.

Ligand binding constants for human serum albumin evaluated by ratiometric analysis of DSC thermograms.

This paper describes an expanded application of our recently reported method (Eskew et al., Analytical Biochemistry 621,1 2021) utilizing thermogram signals for thermal denaturation measured by differential scanning calorimetry. Characteristic signals were used to quantitatively evaluate ligand binding constants for human serum albumin.

Ligand binding to natural and modified human serum albumin.

This paper reports evaluation of ligand binding constants for unmodified or biotinylated HSA (HSA) for two well-known HSA binding ligands, naproxen and bromocresol green. Results demonstrate differential scanning calorimetry (DSC) is a reliable quantitative method for straight-forward and rapid evaluation of ligand binding constants for HSA and modified derivatives. DSC measured the thermodynamic stability of free and ligand-bound HSA and HSA at pH = 6.

Competition for hydrogen-bond formation in the helix-coil transition and protein folding.

The problem of the helix-coil transition of biopolymers in explicit solvents, such as water, with the ability for hydrogen bonding with a solvent is addressed analytically using a suitably modified version of the Generalized Model of Polypeptide Chains. Besides the regular helix-coil transition, an additional coil-helix or reentrant transition is also found at lower temperatures. The reentrant transition arises due to competition between polymer-polymer and polymer-water hydrogen bonds.

Statistical analysis of plasma thermograms measured by differential scanning calorimetry.

Melting curves of human plasma measured by differential scanning calorimetry (DSC), known as thermograms, have the potential to markedly impact diagnosis of human diseases. A general statistical methodology is developed to analyze and classify DSC thermograms to analyze and classify thermograms. Analysis of an acquired thermogram involves comparison with a database of empirical reference thermograms from clinically characterized diseases.

The paradox of multiplex DNA melting on a surface.

Under equilibrium conditions, there are two regimes of target capture on a surface--target limited and probe limited. In the probe limited regime, the melting curve from multiplex target dissociation from the surface exhibits a single transition due to a reverse displacement mechanism of the low affinity species. The melting curve cannot be used in analytical methods to resolve heteroduplexes; only with the simplex system can proper thermodynamics be obtained.

Microscopic formulation of the Zimm-Bragg model for the helix-coil transition.

A microscopic spin model is proposed for the phenomenological Zimm-Bragg model for the helix-coil transition in biopolymers. This model is shown to provide the same thermophysical properties of the original Zimm-Bragg model and it allows a very convenient framework to compute statistical quantities. Physical origins of this spin model are made transparent by an exact mapping into a one-dimensional Ising model with an external field.

Intersegment interactions and helix-coil transition within the generalized model of polypeptide chains approach.

The generalized model of polypeptide chains is extended to describe the helix-coil transition in a system comprised of two chains interacting side-by-side. The Hamiltonian of the model takes into account four possible types of interactions between repeated units of the two chains, i.e.

Influence of buffer species on the thermodynamics of short DNA duplex melting: sodium phosphate versus sodium cacodylate.

Thermodynamic parameters of the melting transitions of 53 short duplex DNAs were experimentally evaluated by differential scanning calorimetry melting curve analysis. Solvents for the DNA solutions contained approximately 1 M Na+ and either 10 mM cacodylate or phosphate buffer. Thermodynamic parameters obtained in the two solvent environments were compared and quantitatively assessed.

Conformational equilibria of bulged sites in duplex DNA studied by EPR spectroscopy.

Conformational flexibility in nucleic acids provides a basis for complex structures, binding, and signaling. One-base bulges directly neighboring single-base mismatches in nucleic acids can be present in a minimum of two distinct conformations, complicating the examination of the thermodynamics by calorimetry or UV-monitored melting techniques. To provide additional information about such structures, we demonstrate how electron paramagnetic resonance (EPR) active spin-labeled base analogues, base-specifically incorporated into the DNA, are monitors of the superposition of different bulge-mismatch conformations.

Origins of the "nucleation" free energy in the hybridization thermodynamics of short duplex DNA.

Thermodynamic parameters deltaH(cal), deltaS(cal), and deltaG(cal) of the melting transitions for 19 short DNA/DNA duplexes ranging in length from 6 to 35 base pairs were systematically evaluated by differential scanning calorimetry melting experiments carried out at four salt concentrations from 85 mM to 1.0 M [Na+]. As expected, thermodynamic stabilities of the DNA duplexes increased with length and increasing [Na+].

Cellulose/DNA hybrid nanomaterials.

Cellulose nanocrystals (CNXLs) have drawn attention from researchers for their remarkable reinforcing abilities and excellent mechanical properties. CNXLs typically have high aspect ratios of around 20-50 (length/width), low density of around 1.6 g/cc, high stiffness (135 to 155 GPa), and strength (estimated at 7500 MPa).

Electrical detection of the temperature induced melting transition of a DNA hairpin covalently attached to gold interdigitated microelectrodes.

The temperature induced melting transition of a self-complementary DNA strand covalently attached at the 5' end to the surface of a gold interdigitated microelectrode (GIME) was monitored in a novel, label-free, manner. The structural state of the hairpin was assessed by measuring four different electronic properties of the GIME (capacitance, impedance, dissipation factor and phase angle) as a function of temperature from 25 degrees C to 80 degrees C. Consistent changes in all four electronic properties of the GIME were observed over this temperature range, and attributed to the transition of the attached single-stranded DNA (ssDNA) from an intramolecular, folded hairpin structure to a melted ssDNA.

Two scale generalized model of polypeptide chains.

The generalized model of polypeptide chains (GMPC) is expanded to simultaneously consider two types of interactions occurring over different scales. This new two scale GMPC is applied in several specific cases to examine: The combined influence of stacking or antistacking and hydrogen bonding, or spatial restrictions on the length of helical segments, on the cooperativity and temperature interval of the helix-coil transition of duplex DNA. For the cases of stacking or antistacking in combination with hydrogen bonding the model reduces to the basic uniscale model with a redefined scaling parameter Delta.

DNA multiplex hybridization on microarrays and thermodynamic stability in solution: a direct comparison.

Hybridization intensities of 30 distinct short duplex DNAs measured on spotted microarrays, were directly compared with thermodynamic stabilities measured in solution. DNA sequences were designed to promote formation of perfect match, or hybrid duplexes containing tandem mismatches. Thermodynamic parameters DeltaH degrees , DeltaS degrees and DeltaG degrees of melting transitions in solution were evaluated directly using differential scanning calorimetry.

Stacking heterogeneity: a model for the sequence dependent melting cooperativity of duplex DNA.

A microscopic Potts-like one-dimensional model with many particle interactions [referred as the generalized model of polypeptide chains (GMPCs)] is developed to investigate cooperativity of DNA sequence dependent melting. For modeling sequence, regular homogeneous sequences were arranged in heterogeneous blocks of various lengths. Within the framework of the GMPC the authors show that the inclusion of stacking interaction heterogeneity relative to homogeneous hydrogen bond interactions leads to an unexpected and quite remarkable increase in melting cooperativity for small blocks.

Multiplex SNP discrimination.

Multiplex hybridization reactions of perfectly matched duplexes and duplexes containing a single basepair mismatch (SNPs) were investigated on DNA microarrays. Effects of duplex length, G-C percentage, and relative position of the SNP on duplex hybridization and SNP resolution were determined. Our theoretical model of multiplex hybridization accurately predicts observed results and implicates target concentration as a critical variable in multiplex SNP detection.

Statistical thermodynamics and kinetics of DNA multiplex hybridization reactions.

A general analytical description of the equilibrium and reaction kinetics of DNA multiplex hybridization has been developed. In this approach, multiplex hybridization is considered to be a competitive multichannel reaction process: a system wherein many species can react both specifically and nonspecifically with one another. General equations are presented that can consider equilibrium and kinetic models of multiplex hybridization systems comprised, in principle, of any number of targets and probes.

Studies of DNA dumbbells VIII. Melting analysis of DNA dumbbells with dinucleotide repeat stem sequences.

Melting curves and circular dichroism spectra were measured for a number of DNA dumbbell and linear molecules containing dinucleotide repeat sequences of different lengths. To study effects of different sequences on the melting and spectroscopic properties, six DNA dumbbells whose stems contain the central sequences (AA)(10), (AC)(10), (AG)(10), (AT)(10), (GC)(10), and (GG)(10) were prepared. These represent the minimal set of 10 possible dinucleotide repeats.

The helix-coil transition in heterogeneous double stranded DNA: microcanonical method.

A microscopic Potts-like one-dimensional model with many-particle interactions is developed to construct a statistical mechanical description of the melting of heterogeneous sequence duplex DNA. For this model, referred as the generalized model of polypeptide chains (GMPC), a closed-form expression for the free energy is derived. The characteristic equation of the model enables estimates on the melting temperature and transition interval, consistent with results obtained from more classical approaches.