DNA architecture: from G to Z

Abstract

G-quadruplexes and Z-DNA are two important non-B forms of DNA architecture. Results on novel structural elements, folding and unfolding kinetics, and interactions with small molecules and proteins have been reported recently for these forms. These results will enhance our understanding of the biology of these structures and provide a platform for drug design.

Hybridization of short complementary PNAs to G‐quadruplex forming oligonucleotides: An electrospray mass spectrometry study

“…Oligonucleotides were dissolved in 10 or 150 mM NH 4 OAc, pH = 7.0 buffer at a final concentration of 3 µM. Oligonucleotides were annealed by boiling for 15 min, fast cooling to 5…”

“…4-/5-ESI-MS shows that all the three intramolecular putative quadruplex sequences (PQSs) do indeed form G-quadruplexes in both 10 mM and 150 mM NH 4 OAc, and no higher-order stoichiometries were detected. ESI-MS spectra were collected tuning Q-TOF for higher sensitivity, allowing higher ion density into the TOF, and as a result the resolution is < 8000.…”

“…However the separation between ammonium adducts (17/z) is clearly visible, can be used to confirm the charge state. For example, the spectrum of TG4T4-intra in 150 mM NH 4 OAc shown in Figure 1 analyzer. Previous studies have shown that the gas-phase stability of the complex with the inner ammonium decreases as the charge state increases, 56 and when the loop constraints increase.…”

“…[1][2][3][4] G-rich sequences with the potential to form quadruplex structures are common in genomic DNA, and these have been identified in several biologically important regions, such as the telomeric ends of eukaryotic chromosomes, [5][6][7] gene promoters, [8][9][10][11][12] or mammalian immunoglobulin heavy chain switch regions. 13,14 Furthermore GROs constitute the scaffold of several aptamers that have the ability to selectively bind to biologically relevant proteins and small molecules.…”

“…[26][27][28][29][30] In this context, we have investigated the interaction between several QFOs, each containing one or more TGGGGT motif, and the short complementary [ac 4 a]-PNA. QFOs can adopt a variety of folds differing mainly by the number of the DNA strands involved and the relative orientation of the strands into the resulting G-quadruplexes (parallel or antiparallel orientation).…”