Characterization of specific noncovalent complexes between guanidinium derivatives and single-stranded DNA by MALDI

Abstract

Noncovalently bound complexes between highly basic sites of 12 guanidinium compounds and single-stranded DNA were studied using matrix-assisted laser desorption/ionization (MALDI) mass spectrometry. 6-Aza-2-thiothymine (ATT) was used as the matrix in the presence of ammonium citrate, and spectra were recorded in the positive ion mode. Detailed control experiments confirmed unambiguously the high selectivity and specificity of the guanidinium moiety for phosphate groups of DNA. The results verify the binding stoichiometry and show preferential binding of hydrophobic binders (pyrene and anthracene guanidinium derivatives) to all sequences examined. In addition, we demonstrate that electrostatic noncovalent interactions are strengthened with phosphorothioate analogs of DNA. These results clearly highlight the structure-directing role of the self-assembling organic species and strongly emphasize the significance of concentration, hydrophobicity, hydrogen-bonding, and pi-pi interactions of the artificial receptor in the formation of these noncovalent complexes. Because of the ability of DNA-binding compounds to influence gene expression, and therefore cell proliferation and differentiation, the interactions described above could be important in providing a better understanding of the mechanism of action of these noncovalent genetic regulators.

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

“…This suggests that the geometry of the complex can play a role and/or that forces other than ionic ones are involved. Vasseur et al [19]âusedâMALDI-TOFâtoâobserveâcomplexesâbetween single-stranded oligonucleotide and guanidine derivatives (guanidine being the basic site of the arginine residues). They showed that the presence of an aromatic ring permitted a better interaction, pointing out the importance of complementary hydrophobic forces and -stacking.…”

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

“…Noncovalent complexes involving polybasic peptides and DNA have been detected by MALDI-TOF [13][14][15][16][17][18]. The first observation of such complexes was reported by Juhasz and Biemann [13]: highly acidic compounds (such as DNA) were detected as noncovalent complexes with a peptide or a small protein rich in arginine, lysine and/or histidine.…”

“…Subsequently, Woods et al [15] used this matrix to observe complexes between various basic peptides and single/ double stranded DNA. ATT (at times in the presence of ammonium citrate) has been successfully used also to observe other complexes involving DNA and derivatives of guanidinium (which is the basic site of the arginine residues) [16] or peptides [17,18], or between two peptides bound by ionic bonds [8, 20 -22]. In all these reports focusing on acid/base interactions, guanidinium seemed to play an important role as the basic site.…”

New features of DNA damage by acid hydrolysis in MALDI-TOF mass spectrum

“…Recently, 21mers RNA was first successfully sequenced by acid hydrolysis with MALDI MS [8]. (3) Non-covalent binding [9][10][11] interactions between RNA, single/double stranded DNA, quadruplex DNA or hairpin DNA and peptides, polyamine, guanidinium derivatives, acridine, or stilbazolium ligands have been successfully analyzed. However, even with the advantages of the rapidity, simplicity, and using primarily single charged ions, MALDI MS is less frequently used to study non-covalent complexes than ESI MS. (4) Quantitative analysis.…”