Peptide Nucleic Acids Containing Cationic/Amino-Alkyl Modified Bases Promote Enhanced Hybridization Kinetics and Thermodynamics with Single-Strand DNA.

Peptide nucleic acids (PNAs) are antisense molecules with excellent polynucleotide hybridization properties; they are resistant to nuclease degradation but often have poor cell permeability leading to moderate cellular activity and limited clinical results. The addition of cationic substitutions (positive charges) to PNA molecules greatly increases cell permeability. In this report, we describe the synthesis and polynucleotide hybridization properties of a novel cationic/amino-alkyl nucleotide base-modified PNA (OPNA). This study was designed to quantitate the effect the cationic/amino-alkyl nucleotide base modification had on the kinetic and thermodynamic properties of OPNA-DNA hybridization using surface plasmon resonance and UV thermal melt studies. Kinetic studies reveal a favorable 10-30 fold increase in affinity for a single cationic modification on the base of an adenine, cytosine, or guanidine OPNA sequence compared to the nonmodified PNA strand. The increase in affinity is correlated directly with a favorable decrease in the dissociation rate constant and increase in the association rate constant. Introducing additional amino-alkyl base modifications further favors a decrease in the dissociation rate (3-10-fold per amino-alkyl). The thermodynamics driving the OPNA hybridization is promoted by an additional favorable -80 kJ/mol enthalpy of binding for a single amino-alkyl modification compared to the PNA strand. This increase in enthalpy is consistent with an ion-ion interaction with the DNA strand. These kinetic and thermodynamic hybridization studies reveal for the first time that this type of cationic/amino-alkyl base-modified PNA has favorable hybridization properties suitable for development as an antisense oligomer.

Conformationally Locked Tolans, ß-Sheet Structures, and Photophysical Properties.

Conformationally locked tetrasubstituted tolans were synthesized by introducing a tether on the tolan. To demonstrate the utilities of these motifs, a ß-hairpin structure (15) was synthesized, and its additional stabilizing effects were evaluated. Moreover, the photophysical properties of cyclic tolans and their ß-sheet structure were investigated. The fluorescence quantum yield of cyclic tolan 12 is >1000 times stronger than its congener 1 in CH3CN.

A calix[2]phenol[2]pyrrole and a fused pyrrolidine-containing derivative.

The hybrid calix[2]phenol[2]pyrrole 4 and the fused pyrrolidine-containing macrocycle 9 were synthesized from two different isomeric starting materials, namely dimethyl 2-hydroxyisophthalate and 5-hydroxyisophthalate, respectively. The fused species 9 is devoid of obvious substrate binding properties. In contrast, the heterocalix system 4 displays the fluoride-induced conformational changes characteristic of the parent system.