Studies of DNA dumbbells. VI. Analysis of optical melting curves of dumbbells with a sixteen-base pair duplex stem and end-loops of variable size and sequence

Tandem GA residues on opposite sides of the loop in molecular beacon-like DNA hairpins compact the loop and increase hairpin stability

The free solution electrophoretic mobilities and thermal stabilities of hairpins formed by two complementary 26-nucleotide oligomers have been measured by capillary electrophoresis. The oligomers are predicted to form molecular beacon-like hairpins with 5 bp stems and 16 nucleotides in the loop. One hairpin, called hairpin2 (hp2), migrates with a relatively fast free solution mobility and exhibits melting temperatures that are reasonably well predicted by the popular structure-prediction program Mfold. Its complement, called hairpin1 (hp1), migrates with a slower free solution mobility and forms a stable hairpin only in solutions containing ≥200 mM Na(+). The melting temperatures observed for hp1 are ~18 °C lower than those observed for hp2 and ~20 °C lower than those predicted by Mfold. The greater thermal stability of hp2 is due to the presence of tandem GA residues on opposite sides of the loop. If the corresponding TC residues in the hp1 loop are replaced by tandem GA residues, the melting temperatures of the modified hairpin are close to those observed for hp2. Eliminating the tandem GA residues in the hp2 loop significantly decreases the thermal stability of hp2. If the loops are replaced by a loop of 16 thymine residues, the free solution mobilities and thermal stabilities of the T-loop hairpin are equal to those observed for hp1. Hence, the loop of hp1 appears to be relatively unstructured, with few base-base stacking interactions. Interactions between tandem GA residues on opposite sides of the hp2 loop appear to compact the loop and increase hairpin stability.

The effects of hairpin loops on ligand-DNA interactions

Hairpin nucleic acids are frequently used in physical studies due to their greater thermal stability compared to their equivalent duplex structures. They are also good models for more complex loop-containing structures such as quadruplexes, i-motifs, cruciforms, and molecular beacons. Although a connecting loop can increase stability, there is little information on how the loop influences the interactions of small molecules with attached base-paired nucleic acid regions. In this study, the effects of different hairpin loops on the interactions of A/T specific DNA minor groove binding agents with a common stem sequence have been investigated by spectroscopic and surface plasmon resonance (SPR) biosensor methods. The results indicate that the hairpin loop has little influence on the specific site interactions on the stem but significantly affects nonspecific binding. The use of a non-nucleotide loop (with a reduced negative charge) not only enhances the thermal stability of the hairpin but also reduces the nonspecific binding at the loop without compromising the primary binding affinity on the stem.

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. Numerical solutions to these systems for both equilibrium and kinetic behaviors are provided. Practical examples demonstrate clear differences between results obtained from more common simplex methods, in which individual hybridization reactions are considered to occur in isolation; and multiplex hybridization, where desired and competitive cross-hybrid reactions between all possible pairs of strands are considered. In addition, sensitivities of the hybridization process of the perfect match duplex, to temperature, target concentration, and existence of sequence homology with other strands, are examined. This general approach also considers explicit sequence-dependent interactions between targets and probes involved in the reactions. Sequence-dependent stabilities of all perfect match and mismatch duplex complexes are explicitly considered and effects of relative stability of cross-hybrid complexes are also explored. Results reveal several interdependent factors that strongly influence DNA multiplex hybridization behavior. These include: relative concentrations of all probes and targets; relative thermodynamic stability of all perfect match and mismatch complexes; sensitivity to temperature, particularly for mismatches; and amount of sequence homology shared by the probe and target strands in the multiplex mix.

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. To study effects of dinucleotide repeat length, dumbbells with the central sequences (AG)(n), n = 5 and 20, were prepared. Control molecules, dumbbells with a random central sequence, (RN)(n), n = 5, 10, and 20, were also prepared. The central sequence of each dumbbell was flanked on both sides by the same 12 base pairs and T(4) end-loops. Melting curves were measured by optical absorbance and differential scanning calorimetry in solvents containing 25, 55, 85, and 115 mM Na(+). CD spectra were collected from 20 to 45 degrees C and [Na(+)] from 25 to 115 mM. The spectral database did not reveal any apparent temperature dependence in the pretransition region. Analysis of the melting thermodynamics evaluated as a function of Na(+) provided a means for quantitatively estimating the counterion release with melting for the different sequences. Results show a very definite sequence dependence, indicating the salt-dependent properties of duplex DNA are also sequence dependent. Linear DNA molecules containing the (AG)(n) and (RN)(n), sequences, n = 5, 10, 20, and 30, were also prepared and studied. The linear DNA molecules had the exact sequences of the dumbbell stems. That is, the central repeat sequence in each linear duplex was flanked on both sides by the same 12-bp sequence. Melting and CD studies were also performed on the linear DNA molecules. Comparison of results obtained for the same sequences in dumbbell and linear molecular environments reveals several interesting features of the interplay between sequence-dependent structural variability, sequence length, and the unconstrained (linear) or constrained (dumbbell) molecular environments.

Structural flexibility of a DNA hairpin located in the long terminal repeat of the Drosophila 1731 retrotransposon

The structure of the DNA binding site of the Nuclear single-stranded Binding Factor (NssBF), located in the long terminal repeat of the Drosophila 1731 retrotransposon, was investigated by melting temperature experiments, chemical probing and fluorescence measurements using a macrocyclic bis-acridine. The most probable structure of this element, named Bc, mainly involves two hairpins in equilibrium at pH 6.0 at low concentration. The hairpins differ in their apical loop size; 4 and 8 nt. The structural flexibility of Bc probably derives from the three consecutive CATA repeats complementary to the GTAT nucleotides of the palindrome. In contrast, the Bc complementary strand adopts a single hairpin. Since Bc is implicated in repression of transcription via binding of two specific factors, its structural flexibility could be associated with this process.