Application of differential scanning calorimetry to measure the differential binding of ions, water and protons in the unfolding of DNA molecules.

BACKGROUND: The overall stability of DNA molecules globally depends on base-pair stacking, base-pairing, polyelectrolyte effect and hydration contributions. In order to understand how they carry out their biological roles, it is essential to have a complete physical description of how the folding of nucleic acids takes place, including their ion and water binding. SCOPE OF REVIEW: To investigate the role of ions, water and protons in the stability and melting behavior of DNA structures, we report here an experimental approach i.e., mainly differential scanning calorimetry (DSC), to determine linking numbers: the differential binding of ions (Δnion), water (ΔnW) and protons (ΔnH(+)) in the helix-coil transition of DNA molecules. GENERAL SIGNIFICANCE: We use DSC and temperature-dependent UV spectroscopic techniques to measure the differential binding of ions, water, and protons for the unfolding of a variety of DNA molecules: salmon testes DNA (ST-DNA), one dodecamer, one undecamer and one decamer duplexes, nine hairpin loops, and two triplexes. These methods can be applied to any conformational transition of a biomolecule. MAJOR CONCLUSIONS: We determined complete thermodynamic profiles, including all three linking numbers, for the unfolding of each molecule. The favorable folding of a DNA helix results from a favorable enthalpy-unfavorable entropy compensation. DSC thermograms and UV melts as a function of salt, osmolyte and proton concentrations yielded releases of ions and water. Therefore, the favorable folding of each DNA molecule results from the formation of base-pair stacks and uptake of both counterions and water molecules. In addition, the triplex with C(+)GC base triplets yielded an uptake of protons. Furthermore, the folding of a DNA duplex is accompanied by a lower uptake of ions and a similar uptake of four water molecules as the DNA helix gets shorter. In addition, the oligomer duplexes and hairpin thermodynamic data suggest ion and water binding depends on the DNA sequence rather than DNA composition.

Probing the Temperature Unfolding of a Variety of DNA Secondary Structures Using the Fluorescence Properties of 2-aminopurine.

The fluorescence probe 2-aminopurine (2AP) is widely used to monitor the molecular environment, including the local solvent environment, and overall dynamics of nucleic acids and nucleic acid-ligand complexes. This work reports on the temperature-induced conformational flexibility of a variety of secondary structures of nucleic acids using optical and calorimetric melting techniques, and evaluates the usefulness of fluorescence melting curves obtained from monitoring the fluorescence changes of 2AP as a function of temperature. Furthermore, the base stacking properties of 2AP are examined in these structures for a first time. Specifically, we incorporated single A → 2AP substitutions into a variety of DNA structures, such as a single strand (SS), a dodecamer duplex (Duplex), a hairpin loop (Hairpin), a G-quadruplex (G2), and an intramolecular triplex (Triplex). A combination of fluorescence, UV, and circular dichroism spectroscopies, and differential scanning calorimetric (DSC) techniques is used to investigate their temperature-induced unfolding. The melting curves of each molecule show monophasic transitions with similar TMs and van't Hoff enthalpies indicating that all transitions are two-state and that the fluorescence changes for the unstacking of 2AP follow the unfolding of the whole molecule. The DSC thermodynamic profiles of each 2AP modified molecule, relative to their unmodified control molecules, yielded folding ΔΔG°s of 1.6 kcal/mol (Duplex), 3.1 kcal/mol (Hairpin), 1.6 kcal/mol (Triplex), and -1.7 kcal/mol (G2). These ΔΔG°s are driven by unfavorable differential enthalpies (Duplex and Hairpin), favorable differential enthalpy (G2), and by a favorable differential entropy term for Triplex. These enthalpy effects are explained in terms of stacking and hydration contributions, that are associated with the local environment that 2AP is experiencing. For example, the lower ΔΔHcal value of 8.7 kcal/mol (Hairpin), relative to Duplex, is due to weaker base-pair stacks and higher hydration state of the stem of Hairpin. We conclude that the incorporation of 2AP in nucleic acids is a useful tool to monitor their temperature-induced unfolding; especially, when these sensitive fluorescent moieties are placed in the proper molecular environment of the nucleic acid.

Energetic and hydration contributions of the removal of methyl groups from thymine to form uracil in G-quadruplexes.

A combination of spectroscopic and calorimetric techniques is used to investigate the unfolding of two G-quadruplexes: d(G2U2G2UGUG2U2G2), G2-U, and d(G2T2G2TGTG2T2G2), G2. The comparisons of their thermodynamic data allow us to elucidate the role of methylation on the energetic and hydration properties accompanying their stable formation. The favorable formation of each G-quadruplex results from the characteristic enthalpy-entropy compensation, uptake of ions, and release of water molecules. The loops of G2-U and G2 contribute favorably to their formation, and the absence of methyl groups stabilizes the G-quadruplex. The unfolding of G2-U produces a larger DeltaV, indicating a difference in the hydration states of the two oligonucleotides, while the opposite signs between DeltaDeltaG with the DeltaDeltaV suggest that the differential hydration reflects structural, or hydrophobic, water is involved in the unfolding of G-quadruplexes.

Unfolding thermodynamics of intramolecular G-quadruplexes: base sequence contributions of the loops.

G-quadruplexes are a highly studied DNA motif with a potential role in a variety of cellular processes and more recently are considered novel targets for drug therapy in aging and anticancer research. In this work, we have investigated the thermodynamic contributions of the loops on the stable formation of G-quadruplexes. Specifically, we use a combination of UV, circular dichroism (CD) and fluorescence spectroscopies, and differential scanning calorimetry (DSC) to determine thermodynamic profiles, including the differential binding of ions and water, for the unfolding of the thrombin aptamer: d(GGT2GGTGTGGT2GG) that is referred to as G2. The sequences in italics, TGT and T2, are known to form loops. Other sequences examined contained base substitutions in the TGT loop (TAT, TCT, TTT, TAPT, and UUU), in the T2 loops (T4, U2), or in both loops (UGU and U2, UUU and U2). The CD spectra of all molecules show a positive band centered at 292 nm, which corresponds to the "chair" conformation. The UV and DSC melting curves of each G-quadruplex show monophasic transitions with transition temperatures (T(M)s) that remained constant with increasing strand concentration, confirming their intramolecular formation. These G-quadruplexes unfold with T(M)s in the range from 43.2 to 56.5 degrees C and endothermic enthalpies from 22.9 to 37.2 kcal/mol. Subtracting the contribution of a G-quartet stack from each experimental profile indicated that the presence of the loops stabilize each G-quadruplex by favorable enthalpy contributions, larger differential binding of K+ ions (0.1-0.6 mol K+/ mol), and a variable uptake/release of water molecules (-6 to 8 mol H2O/mol). The thermodynamic contributions for these specific base substitutions are discussed in terms of loop stacking (base-base stacking within the loops) and their hydration effects.

Thermodynamic contributions of the reactions of DNA intramolecular structures with their complementary strands.

One focus of our research is to further our understanding of the physico-chemical properties of unusual DNA structures and their interaction with complementary oligonucleotides. We have investigated three types of reactions involving the interaction of intramolecular DNA complexes with their complementary single strands of varied length. Specifically, we have used a combination of isothermal titration (ITC) and differential scanning (DSC) calorimetry and spectroscopy techniques to determine standard thermodynamic profiles for the reaction of an i-motif, G-quadruplex, and triplex with their complementary strands. The enthalpies for each reaction are measured directly in ITC titrations and compared with those obtained indirectly from Hess cycles using DSC unfolding data. All reactions investigated yielded favorable free energy contributions, indicating that each single strand is able to invade and disrupt the corresponding intramolecular DNA complex. These favorable free energy terms are enthalpy driven, which result from a compensation of exothermic contributions, due to the formation of additional base-pair stacks (or base-triplet stacks) in the duplex product (or triplex product), immobilization of electrostricted water by the base-pair and base-triplet stacks, and the removal of structural water from the reactant single strands; and endothermic contributions from the disruption of base-base stacking interactions of the reactant single strands. This investigation of nucleic acid reactions has provided new methodology, based on physico-chemical principles, to determine the molecular forces involved in the interactions between DNA nucleic acid structures. This methodology may be used in targeting reactions for the control of gene expression.

Unfolding of G-quadruplexes: energetic, and ion and water contributions of G-quartet stacking.

It has been shown that DNA oligonucleotides composed, in part, of G repeat sequences can adopt G-quadruplex structures in the presence of specific metal ions. In this work, we use a combination of spectroscopic and calorimetric techniques to determine the spectral and thermodynamic characteristics of two DNA aptamers, d(G2T2G2TGTG2T2G2), G2, and d(G3T2G3TGTG3T2G3), G3; a sequence in the promoter region of the c-MYC oncogene, d(TG4AG3TG4AG3TG4A2G2), NHE-III; and the human telomere sequence d(AG3T2AG3T2AG3T2AG3), 22GG. The circular dichroism spectra of these oligonucleotides in the presence of K+ indicate that all form G-quadruplexes with G-quartets in an antiparallel arrangement (G2), in a parallel arrangement (NHE-III and 22GG), or in a mixed parallel and antiparallel G-quartet arrangement (G3). Melting profiles show transition temperatures, TM, above 45 degrees C that are independent of strand concentration, consistent with the formation of very stable intramolecular G-quadruplexes. We used differential scanning calorimetry to obtain complete thermodynamic profiles for the unfolding of each quadruplex. Subtracting the thermodynamic folding profiles of G2 from those of G3 yielded the following thermodynamic profile for the formation of a G-quartet stack: DeltaG degrees 20 = -2.2 kcal/mol, DeltaHcal = -14.6 kcal/mol, TDeltaScal = -12.4 kcal/mol, DeltanK+ = -0.3 mol of K+/mol, and DeltanW = 13 mol of H2O/mol. Furthermore, we used this profile to estimate the thermodynamic contributions of the loops and/or extra base sequences of each oligonucleotide in the G-quadruplex state. The average free energy contributions of the latter indicate that the incorporation of loops and base overhangs stabilizes quadruplex structures. This stabilization is enthalpy-driven and is due to base-stacking contributions.

Advances in vaccines against neglected tropical diseases: enhancing physical stability of a recombinant hookworm vaccine through biophysical and formulation studies.

A bivalent recombinant vaccine for human hookworm disease is under development. One of the lead candidate antigens in the vaccine is a glutathione S-transferase cloned from the hookworm Necator americanus (Na-GST-1) which is expressed in the yeast Pichia pastoris. Based on preliminary studies demonstrating that the recombinant protein was not stable in an acetate buffer at pH 6, we undertook an extensive stability analysis of the molecule. To improve and optimize stability we complemented traditional methods employed for macromolecule and vaccine stabilization with biophysical techniques that were incorporated into a systematic process based on an eigenvector approach. Large data sets, obtained from a variety of experimental methods were used to establish a color map ("empirical phase diagram") of the physical stability of the vaccine antigen over a wide range of temperature and pH. The resulting map defined "apparent phase boundaries" that were used to develop high throughput screening assays. These assays were then employed to identify excipients that stabilized the antigen against physical degradation that could otherwise result in losses of physicochemical integrity, immunogenicity, and potency of the vaccine. Based on these evaluations, the recombinant Na-GST-1 antigen was reformulated and ultimately produced under Good Manufacturing Practices and with an acceptable stability profile.

The stability of a model substrate for topoisomerase 1-mediated DNA religation depends on the presence of mismatched base pairs.

Topoisomerase 1 (Top1) enzymes regulate DNA superhelicity by forming covalent cleavage complexes that undergo controlled rotation. Substitution of nucleoside analogs at the +1 position of the DNA duplex relative to the Top1 cleavage site inhibits DNA religation. The reduced efficiency for Top1-mediated religation contributes to the anticancer activity of widely used anticancer drugs including fluoropyrimidines and gemcitabine. In the present study, we report that mismatched base pairs at the +1 position destabilize the duplex DNA components for a model Top1 cleavage complex formation even though one duplex component does not directly include a mismatched base pair. Molecular dynamics simulations reveal G-dU and G-FdU mismatched base pairs, but not a G-T mismatched base pair, increase flexibility at the Top1 cleavage site, and affect coupling between the regions required for the religation reaction to occur. These results demonstrate that substitution of dT analogs into the +1 position of the non-scissile strand alters the stability and flexibility of DNA contributing to the reduced efficiency for Top1-mediated DNA religation. These effects are inherent in the DNA duplex and do not require formation of the Top1:DNA complex. These results provide a biophysical rationale for the inhibition of Top1-mediated DNA religation by nucleotide analog substitution.

A thermodynamic approach for the targeting of nucleic acid structures using their complementary single strands.

The main focus of our investigations is to further our understanding of the physicochemical properties of nucleic acid structures. We report on a thermodynamic approach to study the reaction of a variety of intramolecular nucleic acid structures with their respective complementary strands. Specifically, we have used a combination of isothermal titration (ITC) and differential scanning calorimetry (DSC) and spectroscopy techniques to determine standard thermodynamic profiles for the reaction of a triplex, G-quadruplex, hairpin loops, pseudoknot, and three-arm junctions with their complementary strands. Reaction enthalpies are measured directly in ITC titrations, and compared with those obtained indirectly from Hess cycles using DSC unfolding data. All reactions investigated yielded favorable free energy contributions, indicating that each single strand is able to invade and disrupt the corresponding intramolecular DNA structure. These favorable free energy terms are enthalpy-driven, resulting from a favorable compensation of exothermic contributions due to the formation of additional base-pair stacks in the duplex product, and endothermic contributions, from the disruption of base stacking contributions of the reactant single strands. The overall results provide a thermodynamic approach that can be used in the targeting of nucleic acids, especially the secondary structures formed by mRNA, with oligonucleotides for the control of gene expression.

Monitoring the temperature unfolding of G-quadruplexes by UV and circular dichroism spectroscopies and calorimetry techniques.

DNA oligonucleotides containing guanine repeat sequences can adopt G-quadruplex (GQ) structures in the presence of specific metal ions. We report on how to use a combination of spectroscopic and calorimetric techniques to determine the spectral characteristics and thermodynamic parameters for the temperature-unfolding of GQs. Specifically, we investigated the unfolding of d(G(2)T(2)G(2)TGTG(2)T(2)G(2)), G2, and d(G(3)T(2)G(3)TGTG(3)T(2)G(3)), G3 by a combination of UV and circular dichroism (CD) spectroscopies, and differential scanning calorimetry (DSC).Analysis of the UV and CD spectra of these GQs at low (100% helix) and high (100% random coil) temperatures yielded the optimal wavelengths to determine the melting curves. In addition, the CD spectra yielded the particular conformation(s) that each GQ adopted at low temperature. DSC curves yielded complete thermodynamic profiles for the unfolding of each GQ. We use these profiles to determine the thermodynamic contributions for the formation of a G-quartet stack.