Plot of variation of enthalpy of binding (Δ<i>H^O</i>) with temperature.

<p>Plots for the binding of (A) spermine with CP DNA (▪), EC DNA (•), ML DNA (▴), (B) spermidine with CP DNA (□), EC DNA (○), ML DNA (▵), (C) putrescine with CP DNA (▪), EC DNA (•), ML DNA (▴) and (D) cadaverine with CP DNA (□), EC DNA (○), ML DNA (▵).</p

Plots of variationof thermodynamic parameters with entropy contribution.

<p>Plot of Δ<i>G^O</i> and Δ<i>H^O</i> versus <i>T</i>Δ<i>S^O</i> for the binding of (A) spermine with CP DNA (▪,•), EC DNA (▴,▾), ML DNA (♦,◂) (B) Plot of Δ<i>G^O</i> and Δ<i>H^O</i> versus <i>T</i>Δ<i>S^O</i> of spermidine with CP DNA (□,○), CT DNA (▵,▿), ML DNA (⋄,⊲), (C) Plot of Δ<i>G^O</i> and Δ<i>H^O</i> versus <i>T</i>Δ<i>S^O</i> of putrescine with CP DNA (▪,•), EC DNA (▴,▾), ML DNA (♦,◂) and (D) Plot of Δ<i>G^O</i> and Δ<i>H^O</i> versus <i>T</i>Δ<i>S^O</i> of cadaverine with CP DNA (□,○), EC DNA (▵,▿), ML DNA (⋄,⊲).</p

ITC profiles for the titration of polyamines with DNAs.

<p>Titration of spermine with (A) CP DNA (B) EC DNA (C) ML DNA and spermidine with (D) CP DNA (E) EC DNA (F) ML DNA at 293.15 K. The top panels represent the raw data for the sequential injection of polyamines into a solution of DNA and the bottom panels show the integrated heat data after correction of heat of dilution against molar ratio of DNA/[polyamine]. The data points were fitted to one site model and the solid line represent the best fit data.</p

ITC derived thermodynamic parameters for the binding of polyamines to MLDNA^a.

a<p>All the data in this table are derived from ITC experiments conducted in 20 mM [Na⁺] citrate-phosphate buffer, pH 7.0 and are average of four determinations, <i>K_a</i> and Δ<i>H</i>^o values were determined from ITC profiles fitting to Origin 7 software as described in the text. The values of Δ<i>G</i>^o and <i>T</i>Δ<i>S</i>^o were determined using the equation Δ<i>G</i>^o = −RTln<i>K_a</i>, and <i>T</i>Δ<i>S</i>^o = Δ<i>H</i>^o−Δ<i>G</i>^o. All the ITC were fit to a model of single binding sites.</p

Interaction of proflavine with the RNA polynucleotide polyriboadenylic acid–polyribouridylic acid: photophysical and calorimetric studies

The binding of proflavine, an acriflavine derivative, with the RNA polynucletodide polyadenylic acid–polyuridylic acid is investigated here to understand the structural and thermodynamic basis of the binding process. Such binding data are crucial for designing viable theraperutic agents. Spectroscopic studies clearly suggest a strong binding interaction between proflavine and polyadenylic acid–polyuridylic acid leading to efficient energy transfer between the poly AU base pairs and proflavine. The stoichiometry of proflavine polyadenylic acid–polyuridylic acid binding was independently estimated by continuous variation analysis of Job. An intercalative binding model is envisaged for the binding from hydrodynamic studies. Circular dichroism experiments revealed that the binding induced conformational changes in the RNA, and also led to induction of optical activity in the bound dye molecules. The binding affinity of the complex was deduced to be (6.57 ± 0.75) 105 M−1 at (298.15 ± 0.10) K from isothermal titration calorimetry experiment. Positive entropy and negative enthalpy changes characterized the complexation. The binding was observed to be weaker both at higher temperatures and increased [Na+]. The affinity of binding decreased with increasing [Na+]. When the Gibbs energy was parsed between polyelectrolytic and nonpolyelectropytic components, it surprisingly revealed a higher role for the non-polyelectrolytic forces. These results present new data for developing RNA targeted ligands. Communicated by Ramaswamy H. Sarma</p

Chemical structure of polyamines.

<p>Chemical structure of polyamines.</p

Displacement plots of ethidium bromide-DNA complexes by polyamines.

<p>Relative fluorescence intensity decrease of ethidium bromide (1.2 μM)-DNA(12.0 μM) complex induced by the binding of (A) spermine with CP DNA(-▪-), EC DNA (-•-), ML DNA (-▴-) and (B) spermidine with CP DNA(-▪-), EC DNA (-•-), ML DNA (-▴-) conducted in 10 mM SHE buffer pH 7.0 at 293.15 K (Inset: The values of IC₅₀ of CP, EC and ML DNA shown as a bar graph).</p

Targeting Double-Stranded RNA with Spermine, 1‑Naphthylacetyl Spermine and Spermidine: A Comparative Biophysical Investigation

RNA targeting is an evolving new approach to anticancer therapeutics that requires identification of small molecules to selectively target specific RNA structures. In this report, the interaction of biogenic polyamines spermine, spermidine and the synthetic analogue 1-naphthylacetyl spermine with three double-stranded RNA polynucleotidespoly­(I)·poly­(C), poly­(C)·poly­(G), and poly­(A)·poly­(U)has been described to understand the structural and thermodynamic basis of the binding and the comparative efficacy of the analogue over the natural polyamines. Circular dichroism spectroscopy, thermal melting experiments, and ethidium bromide displacement assay were used to characterize the interaction. Microcalorimetry studies were performed to deduce the energetics of the interaction and atomic force microscopy experiments done to gain insight into the interaction at the molecular level. The experiments demonstrated structural perturbations in the polynucleotides on binding of the polyamines. Thermal melting studies showed enhanced stabilization of RNA–polyamine complexes with increase in the total standard molar enthalpy of transition. The binding affinity was strongest for poly­(I)·poly­(C) as revealed by microcalorimetry results and varied as poly­(I)·poly­(C) > poly­(C)·poly­(G) > poly­(A)·poly­(U). The order of affinity for the polyamines was spermine >1-naphthylacetyl spermine > spermidine. Total enthalpy–entropy compensation and high standard molar heat capacity values characterized the interactions. The results of the study on the binding of polyamines to dsRNAs presented here have been compared to those reported earlier with dsDNAs. The present findings advance our knowledge on the mechanism of interaction of polyamines with RNA and may help in the search for analogues that can interfere with biogenic polyamine metabolism and function

Melting profiles of DNA and DNA polyamine complexes.

<p>Optical melting profiles (upper panels) of (A) CP DNA (□), spermine-CP DNA(▵), spermidine-CP DNA (O), (B) EC DNA (□), spermine-EC DNA(▵), spermidine-EC DNA(O), (C) ML DNA (□), spermine-ML DNA(▵), spermidine-ML DNA(O). DSC melting profiles (lower panels) of (D) CP DNA (solid lines) (E) EC DNA (solid lines), (F) ML DNA (solid lines) and respective DNA–spermine complex (- - - -) and DNA-spermidine complex (….).</p

Thermal melting data and the binding constants from melting data at saturating concentrations of polyamines with CP DNA, EC DNA and ML DNA^a.

a<p>Melting stabilization of DNA (Δ<i>T</i>_m) in the presence of saturating amounts of polyamines are average of optical melting and DSC data.</p>b<p><i>K_T</i>_m is the binding constant at the melting temperature.</p>c<p><i>K</i>_obs is the polyamine binding constant at 293.15 K determined using equations described in the text.</p