title: Energetic contributions for the formation of TAT/TAT, TAT/CGC(+), and CGC(+)/CGC(+) base triplet stacks.
abstract: We used a combination of spectroscopic and calorimetric techniques to determine complete thermodynamic profiles accompanying the folding of a set of triple helices and control duplexes. Specifically, we studied the sequences: d(A(7)C(5)T(7)C(5)T(7)), d(A(6)C(5)T(6)C(5)T(6)), d(A(6)C(5)T(6)), d(AGAGAGAC(5)TCTCTCTC(5)TCTCTCT), d(AGAGAC(5)TCTCTC(5)TCTCT), d(AGAGAC(5)TCTCTC(2)), d(AAGGAC(5)TCCTTC(5)TTCCT), d(AGGAAC(5)TTCCTC(5)TCCTT), and d(GAAAGC(5)CTTTCC(5)CTTTC). Circular dichroism spectroscopy indicated that all triplexes and duplexes are in the "B" conformation. DSC melting experiments revealed that the formation of triplexes is accompanied by a favorable free energy change, which arises from the compensation of a large and favorable enthalpic contribution with an unfavorable entropic contribution. Comparison of the thermodynamic profiles of these triplexes yielded enthalpic contributions of -24 kcal/mol, -23 kcal/mol, and -22 kcal/mol for the formation of TAT/TAT, TAT/CGC(+), and CGC(+)/CGC(+) base triplet stacks, respectively. UV melts as a function of sodium concentration show sodium ions stabilize the triplexes that contain only TAT triplets but destabilize the triplexes that contain CGC(+) triplets. UV melts as a function of pH indicate that the protonation of the third strand and loop cytosines stabilizes the triplexes that contain CGC(+) and TAT triplets, respectively. Our overall results suggest that the triplex to duplex transition of triplexes that contain CGC(+) triplets is accompanied by a release of protons and an uptake of sodium, while their duplex to random coil transition is accompanied by a release of sodium ions. A consequence of this opposite sodium dependence is that their coupled transitions are nearly independent of sodium concentration but are dependent on the experimental pH.
authors.affiliation: Department of Pharmaceutical Sciences, Eppley Institute for Cancer Research, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, Nebraska 68198-6025, USA.
authors.forename: Ana Maria
authors.initials: AM
authors.lastname: Soto
authors.forename: Jacqueline
authors.initials: J
authors.lastname: Loo
authors.forename: Luis A
authors.initials: LA
authors.lastname: Marky
mesh_terms: D002152:Calorimetry, Differential Scanning; D002942:Circular Dichroism; D006863:Hydrogen-Ion Concentration; D009690:Nucleic Acid Conformation; D009841:Oligonucleotides / Q000737:chemistry*; D012996:Solutions; D013056:Spectrophotometry, Ultraviolet; D013816:Thermodynamics
chemical_list: D009841:Oligonucleotides; D012996:Solutions