Formation of a PNA₂−DNA₂ Hybrid Quadruplex

Abstract

DNA guanine (G) quadruplexes are stabilized by an interesting variation of the hydrogen-bonding schemes encountered in nucleic acid duplexes and triplexes. In an attempt to use this mode of molecular recognition, we target a dimeric G-quadruplex formed by the Oxytricha nova telomeric sequence d(G(4)T(4)G(4)) with a peptide nucleic acid (PNA) probe having a homologous rather than complementary sequence. UV-vis and CD spectroscopy reveal that a stable hybrid possessing G-quartets is formed between the PNA and DNA. The four-stranded character of the hybrid and the relative orientation of the strands is determined by fluorescence resonance energy transfer (FRET) experiments. FRET results indicate that (i) the two PNA strands are parallel to each other, (ii) the two DNA strands are parallel to each other, and (iii) the 5'-termini of the DNA strands align with the N-termini of the PNA strands. The resulting PNA(2)-DNA(2) quadruplex shows a preference of Na(+) over Li(+) and displays thermodynamic behavior consistent with alternating PNA and DNA strands in the hybrid. The formation of this novel supramolecular structure demonstrates a new high-affinity DNA recognition mechanism and expands the scope of molecular recognition by PNA.

Noncovalent binding and fluorogenic response of cyanine dyes to DNA homoquadruplex and PNA-DNA heteroquadruplex structures

“…An alternative strategy relies on sequence-based recognition, where complementary C-rich oligonucleotides bind via Watson-Crick base pairing to form heteroduplexes [7][8][9][10] or homologous G-rich oligonucleotides bind via Hoogsteen-based G-tetrad formation to yield heteroquadruplexes. [11][12][13][14][15] Peptide nucleic acid (PNA) probes can bind to G-quadruplexes by either of these mechanisms, leading to stable hybrid structures.…”

G-Quadruplex Formation Between G-Rich PNA and Homologous Sequences in Oligonucleotides and Supercoiled Plasmid DNA

“…An earlier study by Datta and coworkers found that G 4 T 4 G 4 PNA and DNA oligonucleotides formed parallel Gquadruplexes with 1:1 DNA:PNA stoichiometry [20]. They also observed a drastic difference in CD spectra of their DNA and PNA complexes obtained by annealing at different temperatures.…”

“…Under similar conditions without thermal annealing, Datta et al observed very similar CD spectra, which they interpreted to indicate the presence of antiparallel quadruplexes. At the same time, they demonstrated that fully equilibrated quadruplexes contained 2 PNA and 2 DNA molecules in a parallel orientation [20]. Therefore, DNA-PNA quadruplex complexes may not be limited to those with 1:1 stoichiometry, but can consist of different proportions of DNA and PNA strands with different strand orientation.…”

Combining G‐Quadruplex Targeting Motifs on a Single Peptide Nucleic Acid Scaffold: A Hybrid (3+1) PNA–DNA Bimolecular Quadruplex

“…1 H and 13 C NMR spectra were recorded on a Bruker Avance DRX 400 spectrometer at 400 and 100.6 MHz, respectively. Chemical shifts are reported as δ values (ppm) with reference to the residual solvent peaks.…”