A study of noncovalent complexes involving single-stranded DNA and polybasic compounds using nanospray mass spectrometry

Abstract

Noncovalent complexes involving a single-stranded DNA oligonucleotide and a polybasic compound (spermine, penta-L-lysine, penta-L-arginine, or polydisperse poly-L-lysine) were detected by nanospray-MS. Several control experiments tended to show that these complexes preexisted in solution and that the interactions were initially ionic ones between oligonucleotide phosphates and protonated basic sites of the polybasic compound. Collision-induced dissociation (CID) experiments carried out with these complexes allowed us to identify some differences in the nature of the interactions between the solution and the gas phase, arising from possible proton transfers. Different dissociation pathways were observed according to the nature of the polybasic compound and to the initial charge state of the complex. The complex involving spermine dissociated by cleavage of noncovalent bonds leading to the separation of the two components, whereas the one involving penta-L-arginine underwent fragmentations of covalent bonds. Both behaviors were independent of the initial charge state of the complex. On the other hand, the dissociation pathway of the complex involving penta-L-lysine has been shown to be clearly charge state dependent. Noncovalent dissociation (separation of the two components) driven by coulomb repulsion occurred for the higher charged complexes, whereas fragmentation of covalent bonds was the main pathway of the lower charged complexes. In the latter case, differences in CID behavior were observed for different lengths of poly-L-lysine. (J Am Soc Mass Spectrom 2007, 18, 346 -358)

Noncovalent complexes between DNA and basic polypeptides or polyamines by MALDI-TOF

“…However, speed and ease of use of MALDI-TOF MS support its use for this kind of study. In a previous ESI-MS report [7], it has been shown that Coulomb repulsions could have an influence on the stability of the multiply charged complexes. The production of singly charged species might be another important advantage of MALDI over the electrospray technique.…”

“…ESI-MS is generally recognized as the method of choice for the study of noncovalent complexes [6]. However, to our knowledge, this technique has not been used to survey complexes between DNA and polybasic compound until a recent report from our group [7]. Nevertheless, several works by ESI-MS focused on related systems in which two peptides formed a noncovalent complex by ionic bonds [8 -11].…”

Excursions in polynuclear platinum DNA binding

“…Many of these interactions are facilitated through arginine–phosphate recognition. Indeed the arginine moiety mediates many biological noncovalent events, including protein/metal, protein/protein, protein/peptide, and protein/oligonucleotide interactions 76–78. Phosphorylation and dephosphorylation of amino acid residues in serine, threonine and tyrosine govern numerous biochemical and physiological processes 79.…”

Mass spectrometry of protein-ligand complexes: Enhanced gas-phase stability of ribonuclease-nucleotide complexes

“…Two dissociation pathways were observed for the complex: disruption of the electrostatic interactions between the Arg residues and the phosphate groups, and separation of the peptides with concurrent dissociation of the C-O side-chain covalent bond and transfer of HPO 3 from either pT or pSi to the basic peptide. Terrier et al recently reported a study of noncovalent complexes involving single-stranded DNA and polybasic compounds, including poly-lysine and penta-arginine [51]. For some of the complexes, MS/MS of the DNA-polybasic complex yielded fragmentation of DNA covalent bonds and an oligonucleotide fragment remain bound to the polybasic compound.…”