Incorporation of a cationic aminopropyl chain in DNA hairpins: thermodynamics and hydration

We report on the physicochemical effects resulting from incorporating a 5-( 3-aminopropyl) side chain onto a 2 ' -deoxyuridine (dU) residue in a short DNA hairpin. A combination of spectroscopy, calorimetry, density and ultras ound techniques were used to investigate both the helix-coil transition of a set of hairpins with the following sequence: d(GCGACTTTTTGNCGG) [N = dU, deoxythymidine, (dT) or 5-(3-aminopropyl)-2 ' -deoxyuridine (dU*)], and the interaction of each hairpin with Mg2+. All three molecules undergo two-sta te transitions with melting temperatures (T-M) independent of strand concen tration that indicates their intramolecular hairpin formation. The unfoldin g of each hairpin takes place with similar T-M values of 64-66 degreesC and similar thermodynamic profiles. The unfavorable unfolding free energies of 6.4-6.9 kcal/mol result from the typical compensation of unfavorable entha lpies, 36-39 kcal/mol, and favorable entropies of similar to 110 cal/mol. F urthermore, the stability of each hairpin increases as the salt concentrati on increases, the T-M-dependence on salt yielded slopes of 2.3-2.9 degreesC , which correspond to counterion releases of 0.53 (dU and dT) and 0.44 (dU* ) moles of Na+ per mole of hairpin. Absolute volumetric and compressibility measurements reveal that all three hairpins have similar hydration levels. The electrostatic interaction of Mg2+ with each hairpin yielded binding af finities in the order: dU > dT > dU*, and a similar release of 2-4 electros tricted water molecules. The main result is that the incorporation of the c ationic 3-aminopropyl side chain in the major groove of the hairpin stem ne utralizes some local negative charges yielding a hairpin molecule with lowe r charge density.