Kinetics and mechanism of DNA uptake into the cell nucleus

Abstract

Gene transfer to eukaryotic cells requires the uptake of exogenous DNA into the cell nucleus. Except during mitosis, molecular access to the nuclear interior is limited to passage through the nuclear pores. Here we demonstrate the nuclear uptake of extended linear DNA molecules by a combination of fluorescence microscopy and single-molecule manipulation techniques, using the latter to follow uptake kinetics of individual molecules in real time. The assays were carried out on nuclei reconstituted in vitro from extracts of Xenopus eggs, which provide both a complete complement of biochemical factors involved in nuclear protein import, and unobstructed access to the nuclear pores. We find that uptake of DNA is independent of ATP or GTP hydrolysis, but is blocked by wheat germ agglutinin. The kinetics are much slower than would be expected from hydrodynamic considerations. A fit of the data to a simple model suggests femto-Newton forces and a large friction relevant to the uptake process.A common component in many types of viral infection (1, 2), strategies for genetic therapy (3), and direct DNA vaccination (4) is the accumulation of exogenous DNA in a host cell nucleus. While much attention has been paid to viral invasion mechanisms for cellular entry, relatively little is known about the uptake of DNA into the nucleus itself, particularly as it is not a part of normal cellular physiology. In nondividing cells, molecular exchange across the nuclear envelope normally takes place through the nuclear pore complexes (NPCs). These large channels, whose physiological role is primarily in regulating traffic of proteins and protein-RNA complexes between the nucleus and cytoplasm (5-8), exhibit distinct modes of passive exchange for small molecules and peptide signal-mediated selective transport for larger ones (9). Several pathways for the latter have been identified, based on affinity for receptors of the karyopherin ␤͞importin ␤ (10, 11) and related families (12). Less is known about the biochemistry related to DNA uptake, even whether such exists at all. Indeed, a prominent feature of the viral mechanisms is their ability to co-opt the native protein import machinery by expression of appropriate nuclear localization signals (NLS; ref. 1).The size scales of the NPC make it an unlikely transporter for DNA. The upper cutoff for diffusive passage of colloidal gold particles is Ϸ9 nm, whereas the NLS-mediated mechanism displays an apparent cutoff at Ϸ25 nm diameter (13,14). This scale easily encompasses the size of most protein transport substrates, for which the molecular weight of the cargo-receptor complex will be in the low hundreds of kDa. A recent study of transport rates finds the passage of several molecules per second in the NLS-mediated mode (15). Tightly compacted messenger ribonucleoprotein (mRNP) particles have been observed to unwind during their export through NPCs, conforming to the restricted space within the pore (16). The virulence proteins VirD2 and VirE2 of Agrobacterium tumefaciens mediate the import o...

Illegitimate DNA integration in mammalian cells

“…Many transfection procedures have been developed that enable DNA to enter into the cytoplasm, but its passage into the nucleus is mainly mediated by cellular processes. 1,2 After its entry into the nucleus, a large proportion of the foreign DNA is rapidly degraded or diluted among subsequent cell divisions. 3 However, molecules containing an origin of replication (typically derived from viruses) can persist for long periods as extrachromosomally replicating episomes under certain conditions (such as expression of viral tumour antigens or association with the nuclear matrix).…”

A note on confined diffusion

“…In many instances, the particles' motion is strictly restricted to bounded domains. One can quote corralled motion of receptors on cell membrane [4,5,6], protein diffusion inside the cell nucleus [7], or transporter diffusion through nuclear pores [8,9]. In a typical experiment, trajectories of tracer particles are recorded and analysed in terms of position correlations or mean square displacement.…”

Controlling molecular transport through nanopores

“…The techniques described here can be used to shed light on the uptake of DNA into bacteria [97] or into the cell nucleus [98]. Owing to the vast variety of membrane proteins, there remain a vast number of processes that remain under intense investigation.…”