Charge dependent behavior of PNA/DNA/PNA triplexes in the gas phase

Abstract

Intact noncovalent complexes were studied in the gas phase using negative ion nano-ESI mass spectrometry. Among various noncovalent systems studied in the gas phase, the interaction of DNA strands with peptide nucleic acids (PNAs) presents a strong interest as biologically relevant systems. PNAs originally described by Nielsen are used as DNA mimics as possible medical agents by imprisoning DNA single strands into stable noncovalent complexes. Two types of PNAs were investigated in the PNA/DNA multiplex: the original Nielsen's PNA and a modified backbone PNA by the introduction of syn- and anti-(aminoethyl)thiazolidine rings. We first investigated the stoichiometry of PNA/DNA multiplexes formed in solution and observed them in the gas phase via qualitative kinetics of complementary strand associations. It resulted in observing PNA2/DNA triplexes (ts) as the multiply deprotonated species, most stable in both the solution and gas phase. Second, charge-dependant decompositions of these species were undertaken under low-energy collision conditions. It appears that covalent bond cleavages (base releasing or skeleton cleavage) occur from lower ts charge states rather than ts unzipping, which takes place from higher charge states. This behavior can be explained by considering the presence of zwitterions depending on the charge state. They result in strong salt-bridge interactions between the positively charged PNA side chain and the negatively charged DNA backbone. We propose a general model to clearly display the involved patterns in the noncovalent triplex decompositions. Third, the relative stability of three PNA2/DNA complexes was scrutinized in the gas phase by acquiring the breakdown curves of their ts(6-) form, corresponding to the ts unzipping. The chemical structures of the studied PNAs were chosen in order to evidence the possible influence of backbone stereochemistry on the rigidity of PNA2/DNA complexes. It provided significantly different stabilities via V(m) measurements. The relative gas-phase stability order obtained was compared to that found in solution by Chassaing et al., and shows qualitative agreement.

The role of phosphorylated residues in peptide-peptide noncovalent complexes formation

“…One explanation for this observation is that as the protonation of the complex increases, the triple resonance stabilization3 of the arginine residues’ guanidinium group decreases and the deprotonation state of the phosphate group in the phosphorylated amino acid residue decreases, thus weakening the electrostatic bond, and requiring less energy for the dissociation of the NCX. A similar pattern of NCX dissociation due to charge state has been observed for DNA duplexes13, PNA/DNA/PNA triplexes14, and complexes of DNA and penta-L-arginine15 in negative ion mode. In these studies, an increase in the charge state of the complex weakened the noncovalent interaction holding the complex together.…”

“…In these studies, an increase in the charge state of the complex weakened the noncovalent interaction holding the complex together. It was inferred from theses results, that as the charge increased coulombic repulsions increased13–15 and the number of zwitterions decreased14. Another interesting result in Table 1 is the strength of the electrostatic interaction between VLRRRRKRVN and AAApYAAA in the [NCX+2H] 2+ ion.…”

Charge state effect on the zwitterion influence on stability of non‐covalent interaction of single‐stranded DNA with peptides

“…The purpose of this study is to identify the structural elements that drive the interaction. Our group previously reported the detection of non‐covalent complexes between highly acidity oligonucleotides and highly basic PNA molecules using ESI mass spectrometry and assumed the existence of the zwitterion (ZW) 30. We aim at establishing the role played by the ZW on DNA–peptide complex stabilisation.…”

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

“…After the evaporation of the charged droplets, analytes in the form of desolvated ions are transferred into the mass spectrometer. Furthermore, if the evaporation and transfer steps are conducted in soft conditions, intact noncovalently bound DNA structures like duplexes, 43,44 quadruplexes, 39,[44][45][46][47][48] and PNA•DNA assemblies [49][50][51][52] can be preserved from the solution and detected in the mass spectrometer. Three review articles [53][54][55] describing various application of mass spectrometry for the study of nucleic acid non-covalent complexes by ESI-MS can be consulted for more references.…”