title: Thermodynamics and kinetics of PNA-DNA quadruplex-forming chimeras.
abstract: PNA-DNA chimeras present the interesting properties of PNA, such as the high binding affinity to complementary single-strand (DNA or RNA), and the resistance to nuclease and protease degradation. At the same time, the limitations of an oligomer containing all PNA residues, such as low water solubility, self-aggregation, and low cellular uptake, are effectively overcome. Further, PNA-DNA chimeras possess interesting biological properties as antisense agents. We have explored the ability of PNA-DNA chimeric strands to assemble in quadruplex structures. The rate constant for association of the quadruplexes and their thermodynamic properties have been determined by CD spectroscopy and differential scanning calorimetry (DSC). Thermal denaturation experiments indicated higher thermal and thermodynamic stabilities for chimeric quadruplexes in comparison with the corresponding unmodified DNA quadruplex. Singular value decomposition analysis (SVD) suggests the presence of kinetically stable intermediate species in the quadruplex formation process. The experimental results have been discussed on the basis of molecular dynamic simulations. The ability of PNA-DNA chimeras to form stable quadruplex structures expands their potential utility as therapeutic agents.
authors.affiliation: Dipartimento di Scienze Farmaceutiche, Via Ponte Don Melillo, 84084, Fisciano (SA), Italy.
authors.forename: Luigi
authors.initials: L
authors.lastname: Petraccone
authors.forename: Bruno
authors.initials: B
authors.lastname: Pagano
authors.forename: Veronica
authors.initials: V
authors.lastname: Esposito
authors.forename: Antonio
authors.initials: A
authors.lastname: Randazzo
authors.forename: Gennaro
authors.initials: G
authors.lastname: Piccialli
authors.forename: Guido
authors.initials: G
authors.lastname: Barone
authors.forename: Carlo A
authors.initials: CA
authors.lastname: Mattia
authors.forename: Concetta
authors.initials: C
authors.lastname: Giancola
mesh_terms: D002151:Calorimetry; D002942:Circular Dichroism; D004247:DNA / Q000737:chemistry*; D054856:G-Quadruplexes; D007700:Kinetics; D008956:Models, Chemical; D009690:Nucleic Acid Conformation; D020135:Peptide Nucleic Acids / Q000737:chemistry*; D011487:Protein Conformation; D013696:Temperature; D013816:Thermodynamics
chemical_list: D020135:Peptide Nucleic Acids; D004247:DNA