Probing tRNA interaction with biogenic polyamines

Abstract

Biogenic polyamines are found to modulate protein synthesis at different levels. This effect may be explained by the ability of polyamines to bind and influence the secondary structure of tRNA, mRNA, and rRNA. We report the interaction between tRNA and the three biogenic polyamines putrescine, spermidine, spermine, and cobalt(III)hexamine at physiological conditions, using FTIR spectroscopy, capillary electrophoresis, and molecular modeling. The results indicated that tRNA was stabilized at low biogenic polyamine concentration, as a consequence of polyamine interaction with the backbone phosphate group. The main tRNA reactive sites for biogenic polyamine at low concentration were guanine-N7/O6, uracil-O2/O4, adenine-N3, and 29OH of the ribose. At high polyamine concentration, the interaction involves guanine-N7/O6, adenine-N7, uracil-O2 reactive sites, and the backbone phosphate group. The participation of the polycation primary amino group, in the interaction and the presence of the hydrophobic contact, are also shown. The binding affinity of biogenic polyamine to tRNA molecule was in the order of spermine > spermidine > putrescine with K Spm = 8.7 3 10 5 M À1, K Spd = 6.1 3 10 5 M À1 , and K Put = 1.0 3 10 5 M À1 , which correlates with their positively charged amino group content. Hill analysis showed positive cooperativity for the biogenic polyamines and negative cooperativity for cobalt-hexamine. Cobalt(III)hexamine contains high-and low-affinity sites in tRNA with K 1 = 3.2 3 10 5 M À1 and K 2 = 1.7 3 10 5 M À1 , that have been attributed to the interactions with guanine-N7 sites and the backbone PO 2 group, respectively. This mechanism of tRNA binding could explain the condensation phenomenon observed at high Co(III) content, as previously shown in the Co(III)-DNA complexes.

Mitochondrial ribonuclease P structure provides insight into the evolution of catalytic strategies for precursor-tRNA 5′ processing

“…Mg(II) was previously shown to activate PRORP1 catalysis (2). To further analyze the metal dependence, we examined the activation of PRORP1 by other divalent cations in the presence of the magnesium hexahydrate mimic, cobalt(III) hexammine (21), to stabilize the tertiary structure of pre-tRNA. PRORP1 with a stoichiometric zinc ion (Table S2) cannot catalyze pre-tRNA cleavage, indicating that the bound Zn(II) is a structural cofactor (Fig.…”

Effect of PEG and mPEG-Anthracene on tRNA Aggregation and Particle Formation

“…Similar spectral changes were observed for the backbone PO 2 stretching vibrations in the IR spectra of dendrimer−tRNA, biogenic polyamine−tRNA, and cationic lipid−tRNA complexes, where strong ligand−phosphate binding occurred. 13,31,32 Hydrophobic Contacts. A possible impact of PEG−tRNA interaction on polymer antisymmetric and symmetric CH 2 stretching vibration in the region of 3000−2800 cm in PEG 6000-tRNA and free mPEG-anthracene with CH 2 bands at 2944, 2883, and 2857 cm −1 shifted to 2940 and 2886 cm −1 (2957 did not shift) in mPEG-anthracene-tRNA adducts (spectra not shown).…”

Effect of Synthetic Polymers on tRNA Nanoparticle Formation

“…Synthetic polymer complexes with DNA and tRNA via hydrophilic, hydrophobic contacts, groove binding and phosphate interaction [25][26][27][28][29]. The infrared spectra and difference spectra of the free tRNA showed major alterations of tRNA in-plane vibrations and the backbone phosphate asymmetric and symmetric stretching bands [30][31][32][33][34][35], upon polymer complexation ( Figure 2-panels A and B). Low concentration (0.125 mM) of synthetic polymers PEG-3350, PEG-6000, mPEG-PAMAM-G3, mPEG-PAMAM-G4 and PAMAM-G4 induced minor changes of tRNA vibrational frequencies, while at high polymer content (1 mM) major alterations of tRNA inplane and the backbone vibrational frequencies (Figure 2-panels A and B).…”