Investigation of Ternary Complexes: DNA–Phosphatidylcholine Liposomes–Mg2+ by Freeze-Fracture Method and Their Role in the Formation of Some Cell Structures

Holes in the Nuclear Membrane as an Illustration of Gaps in the Understanding of the Biology by Biologists

At the moment, the conditions are in place to describe how to construct nuclear pores and how they work, missing only real understanding of process. The DNA-RNA-protein paradigm proposed by Crick 53 years ago (Symp Soc Exp Biol 12:138-163, 1958; Nature 227:561-563, 1970) severely hampers our understanding of nuclear pore structure and assembly because the problem lies outside paradigm. DNA in this scheme only plays the role of information storage from which information is transferred to RNA, then from RNA to proteins after which proteins perform all of the functions in the cell. Although it is known that DNA is able to build nucleosomes in vivo, many in vitro structures types of origami (Rothemund, Nature 440:297-302, 2006), the DNA is considered to be exotic as structural material for cells. The structural role of RNA is difficult to ignore, in connections with their participation in structures of ribosomes, ribonucleoproteins, and ribozymes, but imagine that DNA performs an important structural role in the cell is impossible in opinion of many authors. So, when there was a problem in explaining the origin of the nuclear pore, all efforts of biologists were directed to proteins such as nucleoporins, especially when taking into account that there are 30 nucleoporins and only one DNA. Here, I try to explain the typical mistakes of the old approach to such a complex problem as nuclear pore structure and assembly.

Isolation of chromatin DNA tightly bound to the nuclear envelope of HeLa cells

Recent discovery of the role of nuclear pores in transcription, predicted by our early DNA-membrane complex (DMC) model, makes membrane-bound DNA (MBD) isolation from the cell nucleus and analysis of the MBD actual. The method of MBD isolation proposed by us retains DMC integrity during isolation. We used HeLa cells for DMC extraction. Changing the ionic composition of the isolation medium and replacing DNase I, used commonly for chromatin destruction, with a set of restriction enzymes allowed us to isolate the MBD. Treatment of a nuclear membrane with proteinase K and ultrasound has been used to increase the yield of MBD. Electron microscopic analysis of the purified fraction of isolated DMC supports our previous model of nuclear envelope lipid-chromatin interaction in the nuclear pore assembly.

The mechanism of a nuclear pore assembly: a molecular biophysics view

The basic problem of nuclear pore assembly is the big perinuclear space that must be overcome for nuclear membrane fusion and pore creation. Our investigations of ternary complexes: DNA-PC liposomes-Mg²⁺, and modern conceptions of nuclear pore structure allowed us to introduce a new mechanism of nuclear pore assembly. DNA-induced fusion of liposomes (membrane vesicles) with a single-lipid bilayer or two closely located nuclear membranes is considered. After such fusion on the lipid bilayer surface, traces of a complex of ssDNA with lipids were revealed. At fusion of two identical small liposomes (membrane vesicles) < 100 nm in diameter, a "big" liposome (vesicle) with ssDNA on the vesicle equator is formed. ssDNA occurrence on liposome surface gives a biphasic character to the fusion kinetics. The "big" membrane vesicle surrounded by ssDNA is the base of nuclear pore assembly. Its contact with the nuclear envelope leads to fast fusion of half of the vesicles with one nuclear membrane; then ensues a fusion delay when ssDNA reaches the membrane. The next step is to turn inside out the second vesicle half and its fusion to other nuclear membrane. A hole is formed between the two membranes, and nucleoporins begin pore complex assembly around the ssDNA. The surface tension of vesicles and nuclear membranes along with the kinetic energy of a liquid inside a vesicle play the main roles in this process. Special cases of nuclear pore formation are considered: pore formation on both nuclear envelope sides, the difference of pores formed in various cell-cycle phases and linear nuclear pore clusters.

Chemical vectors for gene delivery: uptake and intracellular trafficking. Curr Opin Biotechnol. 2010;21:640-645. [PMID: 20674331 DOI: 10.1016/j.copbio.2010.07.003]

Chemical vectors for non-viral gene delivery are based on engineered DNA nanoparticles produced with various range of macromolecules suitable to mimic some viral functions required for gene transfer. Many efforts have been undertaken these past years to identify cellular barriers that have to be passed for this issue. Here, we summarize the current status of knowledge on the uptake mechanism of DNA nanoparticles made with polymers and liposomes, their endosomal escape, cytosolic diffusion, and nuclear import of pDNA. Studies reported these past years regarding pDNA nanoparticles endocytosis indicated that there is no clear evident relationship between the ways of entry and the transfection efficiency. By contrast, the sequestration of pDNA in intracellular vesicles and the low number of pDNA close to the nuclear envelop are identified as the major intracellular barriers. So, intensive investigations to increase the cytosolic delivery of pDNA and its migration toward nuclear pores make sense to bring the transfection efficiency closer to that of viruses.