On the stability of peptide nucleic acid duplexes in the presence of organic solvents

Abstract

Nucleic acid double helices are stabilized by hydrogen bonding and stacking forces (a combination of hydrophobic, dispersive and electrostatic forces) of the base pairs in the helix. One would predict the hydrogen bonding contributions to increase and the stacking contributions to decrease as the water activity in the medium decreases. Study of nucleobase paired duplexes in the absence of water and ultimately in pure aprotic, non-polar organic solvents is not possible with natural phosphodiester nucleic acids due to the ionic phosphate groups and the associated cations, but could be possible with non-ionic nucleic acid analogues or mimics such as peptide nucleic acids. We now report that peptide nucleic acid (PNA) (in contrast to DNA) duplexes show almost unaffected stability in up to 70% dimethylformamide (DMF) or dioxane, and extrapolation of the data to conditions of 100% organic solvents indicates only minor (or no) destabilization of the PNA duplexes. Our data indicate that stacking forces contribute little if at all to the duplex stability under these conditions. The differences in behaviour between the PNA and the DNA duplexes are attributed to the differences in hydration and counter ion release rather than to the differences in nucleobase interaction. These results support the possibility of having stable nucleobase paired double helices in organic solvents.

Optimization of a peptide nucleic acid fluorescence in situ hybridization (PNA-FISH) method for the detection of bacteria and disclosure of a formamide effect

“…Interestingly, the application of hot formamide for the isolation of peptidoglycan is reported in the literature, which is in agreement with the proposed explanation (Fuller, 1938;Greenblatt et al, 1978;Perkins, 1965). As the preservation of cells integrity is crucial for a proper hybridization, bacteria with cell envelope damaged by FA would not benefit from its hybridization adjuvant function (Sen and Nielsen, 2007).…”

Hydrogen bonding versus stacking stabilization by modified nucleobases incorporated in PNA·DNA duplexes

“…In a previous study on the effect of the aprotic, organic solvent DMF on the stability of iso-sequential PNA·PNA, PNA·DNA and DNA·DNA duplexes, we have shown that the change in the number of bound water molecules associated upon thermal melting of PNA·PNA duplexes is the smallest [21], and that PNA duplexes (in contrast to DNA duplexes) show almost unaffected stability in 70% DMF [22]. In order to assess the contributions from stacking forces and H-bonds to the thermal stability of the duplexes of the present study, we have investigated the effect of increasing amount of DMF on the thermal stabilities of the PNA duplexes containing D base and/or bT base ( Figure 2; thermal and thermodynamic data are presented in Tables S2-S6 with representative thermal melting curves in Figures S4 and S5, and the corresponding plots in Figure S6).…”

Toward Peptide Nucleic Acid (PNA) Directed Peptide Translation Using Ester Based Aminoacyl Transfer

“…However, increasing temperature as well as pH, and the presence of organic solvents including DMSO, weaken the stability of PNA duplexes, 30 and therefore, conditions that favor chemical acyl transfer disfavor hybridization including hairpin formation. Therefore, we measured the thermal stability of PNA 3751 in the presence of DMSO in order to elucidate the importance of the "hairpin structure" for Phe-transfer.…”