Ribonucleic acid (RNA) condensation by thermal cycling with metal cations: yield of nanoparticles and their applicability for transfection

To the present, different efficient but expensive, multistage, and time-consuming technologies have been developed to deliver ribonucleic acids (RNA) into eukaryotic cells. Here, we report a simple and feasible solution to design RNA nanocarriers based on nucleic acid condensation by bi- and trivalent metal ions during thermal cycling. Efficient RNA conversion to nanoparticles with small size (10-50 nm) suitable for transfection was achieved using cations Ni²⁺, Co²⁺ or Cu²⁺ alone or in combination with Ca²⁺ at the specially selected concentrations (2.0 mM-3.5 mM), low ionic strength, and narrow pH range (8.0-8.5). Other ions - Mn²⁺, Zn²⁺, Tb³⁺, or Gd³⁺ - caused RNA-cleaving effect that was abolished in the presence of Ni²⁺, Co²⁺, Zn²⁺, or Cu²⁺. Naked RNA-metal ion nanoparticles were extremely unstable in phosphate buffer and sensitive to serum ribonucleases (RNases), and this problem was solved by treatment with polyarginines-16 and 8. Polyarginine-stabilized nanoparticles, containing malachite green (MG) aptamer RNA and metal cations, crossed the cell membrane, dissociated in the cytoplasm, and preserved the functionality of transported RNA, as judged from efficient transfection of human embryonic kidney 293 cells. The technology, involving RNA condensation by metal cations, can be used as a cheap alternative to produce nanoscale carriers to deliver various RNAs into cells in vitro and in vivo.Communicated by Ramaswamy H. Sarma.

Preparation and Properties of Nanoparticles, tRNA-Bivalent Metal Cation (Me2+) Complexes, and Prospects of Their Practical Use

The patterns of formation of RNA nanoparticles (NPs) during thermal cycling of bacterial total tRNA in the presence of cations Ca²⁺, Mn²⁺, Ni²⁺, Zn²⁺, Co²⁺, and Cu²⁺ were studied. The optimal conditions for the production of NPs were found, and it was revealed that their size depends on the ratio of the concentrations of Me²⁺ and tRNA. The concentration of reagents for obtaining NPs of small size (from 5 to 100 nm) was selected. It was shown that tRNA-based nanoparticles can comprise short (20-50 nt) ribooligonucleotides, including aptamers and siRNAs. The stability of NPs during storage in buffer solutions of various composition was studied. It was found that the initial suspensions of NPs are quite stable, but they are rapidly destroyed in PBS buffer (pH 7.4). A simple and effective stabilizer (polyarginine) was found, the additives of which ensure the preservation of nanoparticles in PBS buffer for more than 5 h. Nanoparticles modified with the stabilizer are resistant to blood serum nucleases and can be used for transfection.

New insight into formation of DNA-containing microparticles during PCR: the scaffolding role of magnesium pyrophosphate crystals

This work aims to study molecular mechanisms involved in the formation of DNA-containing microparticles and nanoparticles during PCR. Both pyrophosphate and Mg(2+) ions proved to play an important role in the generation of DNA microparticles (MPs) with a unique and sophisticated structure in PCR with Taq polymerase. Thus, the addition of Tli thermostable pyrophosphatase to a PCR mixture inhibited this process and caused the destruction of synthesized DNA MPs. Thermal cycling of Na-pyrophosphate (Na-PPi)- and Mg(2+)-containing mixtures (without DNA polymerase and dNTPs) under the standard PCR regime yielded crystalline oval or lenticular microdisks and 3D MPs composed from magnesium pyrophosphate (Mg-PPi). As shown by scanning electron microscopy (SEM), the produced Mg-PPi microparticles consisted of intersecting disks or their segments. They were morphologically similar but simpler than DNA-containing MPs generated in PCR. The incorporation of dNTPs, primers, or dsDNA into Mg-pyrophosphate particles resulted in the structural diversification of 3D microparticles. Thus, the unusual and complex structure of DNA MPs generated in PCR is governed by the unique feature of Mg-pyrophosphate to form supramolecular particles during thermal cycling. We hypothesize the Mg-pyrophosphate particles that are produced during thermal cycling serve as scaffolds for amplicon DNA condensation.