Thiazole Containing PNA Mimic Regulates c-MYC Gene Expression through DNA G-Quadruplex

Peptide nucleic acids (PNAs), besides hybridizing to complementary DNA and RNAs, bind and stabilize DNA secondary structures. Herein, we illustrate the design and synthesis of PNA-like scaffolds by incorporating five-membered thiazole rings as modified bases instead of nucleobases and their subsequent effects on gene regulation by biophysical and in vitro assays. A thiazole-modified PNA trimer selectively recognizes c-MYC G-quadruplex (G4) DNA over other G4s and duplex DNA. It displays a high stabilization potential for the c-MYC G4 DNA and shows remarkable fluorescence enhancement with the c-MYC G4. It is flexible enough to bind at 5' and 3' ends as well as in the groove region of c-MYC G4. Furthermore, the PNA trimer easily permeates the cellular membrane and suppresses c-MYC mRNA expression in HeLa cells by targeting the promoter G4. This study illuminates modified PNAs as flexible molecular tools for selective targeting of noncanonical nucleic acids and modulating gene function.

The Importance of Phosphates for DNA G-Quadruplex Formation: Evaluation of Zwitterionic G-Rich Oligodeoxynucleotides

A quaternary ammonium butylsulfonyl phosphoramidate group (N+) was designed to replace all the phosphates in a G-rich oligodeoxynucleotide d(TG₄ T), resulting in a formally charge-neutral zwitterionic N+TG₄ T sequence. We evaluated the effects of N+phosphate modifications on the structural, thermodynamic and kinetic properties of the parallel G-quadruplexes (G4) formed by TG₄ T and compared them to the properties of the recently published phosphoryl guanidine d(TG₄ T) (PG-TG₄ T). Using size-exclusion chromatography, we established that, unlike PG-TG₄ T, which exists as a mixture of complexes of different molecularity in solution, N+TG₄ T forms an individual tetramolecular complex. In contrast to PG modifications that destabilized G4s, the presence of N+ modifications increased thermal stability relative to unmodified [d(TG₄ T)]₄ . The initial stage of assembly of N+TG₄ T proceeded faster in the presence of Na⁺ than K⁺ ions and, similarly to PG-TG₄ T, was independent of the salt concentration. However, after complex formation exceeded 75 %, N+TG₄ T in solution with Na⁺ showed slower association than with K⁺ . N+TG₄ T could also form G4s in solution with Li⁺ ions at a very low strand concentration (10 μM); something that has never been reported for the native d(TG₄ T). Charge-neutral PG-G4s can invade preformed native G4s, whereas no invasion was observed between N+and native G4s, possibly due to the increased thermal stability of [N+TG₄ T]₄ . The N+ modification makes d(TG₄ T) fully resistant to enzymatic digestion, which could be useful for intracellular application of N+-modified DNA or RNA.

Neutral and Negatively Charged Phosphate Modifications Altering Thermal Stability, Kinetics of Formation and Monovalent Ion Dependence of DNA G-Quadruplexes

The effect of phosphate group modifications on formation and properties of G-quadruplexes (G4s) has not been investigated in detail. Here, we evaluated the structural, thermodynamic and kinetic properties of the parallel G-quadruplexes formed by oligodeoxynucleotides d(G₄ T), d(TG₄ T) and d(TG₅ T), in which all phosphates were replaced with N-methanesulfonyl (mesyl) phosphoramidate or phosphoryl guanidine groups resulting in either negatively charged or neutral DNA sequences, respectively. We established that all modified sequences were able to form G-quadruplexes of parallel topology; however, the presence of modifications led to a decrease in thermal stability relative to unmodified G4s. In contrast to negatively charged G4s, assembly of neutral G4 DNA species was faster in the presence of sodium ions than potassium ions, and was independent of the salt concentration used. Formation of mixed G4s composed of both native and neutral G-rich strands has been detected using native gel electrophoresis, size-exclusion chromatography and ESI-MS. In summary, our results indicate that the phosphate modifications studied are compatible with G-quadruplex formation, which could be used for the design of biologically active compounds.

Conjugation of peptide nucleic acid with a pyrrole/imidazole polyamide to specifically recognize and cleave DNA

Cut loose: A pseudocomplementary peptide nucleic acid was tethered to a pyrrole/imidazole hairpin polyamide, and was used to selectively target a specific DNA sequence. Binding even occurs under high salt conditions. Furthermore, the conjugate facilitated sequence-specific scission of long dsDNA. This simple approach promises to resolve the technical difficulties in targeting DNA sequences with PNA.