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

Ana Maria Soto, Besik I. Kankia, Prasad Dande, Barry Gold, Luis A Marky

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Abstract

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 ultrasound techniques were used to investigate both the helix-coil transition of a set of hairpins with the following sequence: d(GCGACTTTTTGNCGC) [N = dU, deoxythymidine (dT) or 5-(3-aminopropyl)-2′-deoxyuridine (dU*)], and the interaction of each hairpin with Mg2+. All three molecules undergo two-state transitions with melting temperatures (TM) independent of strand concentration that indicates their intramolecular hairpin formation. The unfolding of each hairpin takes place with similar TM values of 64-66°C and similar thermodynamic profiles. The unfavorable unfolding free energies of 6.4-6.9 kcal/mol result from the typical compensation of unfavorable enthalpies, 36-39 kcal/mol, and favorable entropies of ∼110 cal/mol. Furthermore, the stability of each hairpin increases as the salt concentration increases, the TM-dependence on salt yielded slopes of 2.3-2.9°C, 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 affinities in the order: dU > dT > dU*, and a similar release of 2-4 electrostricted water molecules. The main result is that the incorporation of the cationic 3-aminopropyl side chain in the major groove of the hairpin stem neutralizes some local negative charges yielding a hairpin molecule with lower charge density.

Original languageEnglish (US)
Pages (from-to)3638-3645
Number of pages8
JournalNucleic acids research
Volume29
Issue number17
StatePublished - Sep 1 2001

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Deoxyuridine
Thermodynamics
DNA
Thymidine
Temperature
Salts
Calorimetry
Entropy
Static Electricity
Freezing
Spectrum Analysis
Water

ASJC Scopus subject areas

  • Genetics

Cite this

Incorporation of a cationic aminopropyl chain in DNA hairpins : Thermodynamics and hydration. / Soto, Ana Maria; Kankia, Besik I.; Dande, Prasad; Gold, Barry; Marky, Luis A.

In: Nucleic acids research, Vol. 29, No. 17, 01.09.2001, p. 3638-3645.

Research output: Contribution to journalArticle

Soto, Ana Maria ; Kankia, Besik I. ; Dande, Prasad ; Gold, Barry ; Marky, Luis A. / Incorporation of a cationic aminopropyl chain in DNA hairpins : Thermodynamics and hydration. In: Nucleic acids research. 2001 ; Vol. 29, No. 17. pp. 3638-3645.
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