Structural characterization of cationic lipid-tRNA complexes

Abstract

Despite considerable interest and investigations on cationic lipid–DNA complexes, reports on lipid–RNA interaction are very limited. In contrast to lipid–DNA complexes where lipid binding induces partial B to A and B to C conformational changes, lipid–tRNA complexation preserves tRNA folded state. This study is the first attempt to investigate the binding of cationic lipid with transfer RNA and the effect of lipid complexation on tRNA aggregation and condensation. We examine the interaction of tRNA with cholesterol (Chol), 1,2-dioleoyl-3-trimethylammonium-propane (DOTAP), dioctadecyldimethylammoniumbromide (DDAB) and dioleoylphosphatidylethanolamine (DOPE), at physiological condition, using constant tRNA concentration and various lipid contents. FTIR, UV-visible, CD spectroscopic methods and atomic force microscopy (AFM) were used to analyze lipid binding site, the binding constant and the effects of lipid interaction on tRNA stability, conformation and condensation. Structural analysis showed lipid–tRNA interactions with G–C and A–U base pairs as well as the backbone phosphate group with overall binding constants of KChol = 5.94 (± 0.8) × 104 M–1, KDDAB = 8.33 (± 0.90) × 105 M–1, KDOTAP = 1.05 (± 0.30) × 105 M–1 and KDOPE = 2.75 (± 0.50) × 104 M–1. The order of stability of lipid–tRNA complexation is DDAB > DOTAP > Chol > DOPE. Hydrophobic interactions between lipid aliphatic tails and tRNA were observed. RNA remains in A-family structure, while biopolymer aggregation and condensation occurred at high lipid concentrations.

Multivariate Analysis for Fourier Transform Infrared Spectra of Complex Biological Systems and Processes

“…Firstly, the analysis was made on each type of oocyte taken at the different maturation stages. For the SN oocytes, the component carrying the highest discrimination weight resulted that at 2938 cm -1 , likely due to cholesterol and / or phospholipids [76,77], in agreement with what found by the direct inspection of the spectra.…”

“…SN oocytes were found to be characterized -during maturation up to MII -by a significant increase of the 2937 cm -1 component that could be likely due to cholesterol and/or phospholipids ( Figure 3B) [76,77]. As discussed for NSN oocytes, the observed changes could reflect variations in the membrane properties, again highlighting the crucial role of lipids as markers of oocyte developmental competence [8,78].…”

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).…”

Physicochemical properties of polymers: An important system to overcome the cell barriers in gene transfection

“…Maintaining the Bform of the cellular DNA structure is also important issue especially after binding. For example, some lipid formulations induce partial changes of B to A and B to C conformational forms in the DNA structure 76 . Positively charged polyplexes interact with negatively charged proteoglycans of the cell membranes followed by endocytosis.…”