© 1999 Robert A. Freitas Jr. All Rights Reserved.

Robert A. Freitas Jr., Nanomedicine, Volume I: Basic Capabilities, Landes Bioscience, Georgetown, TX, 1999

8.5.4.6 Nuclear Matrix and Transcript Domains

Like the cytoskeleton of the cell, the nucleus is thought to possess a nuclear skeleton comprised of a network of insoluble protein fibers known as the nuclear matrix.^{1134,3418-3423} This finely branched meshwork of superfine filaments attaches to the nuclear lamina or cortex (Section 8.5.4.3) and extends to the nucleolus. Assuming ~10⁶ filaments each averaging ~50 nm long gives a total fiber length L_fiber ~ 50,000 microns, which for a D ~ 8 micron diameter nucleus implies a mean grid spacing of:

{Eqn. 8.7}

Typical mesh spacings seen in electron micrographs do indeed range from ~50-100 nm.¹¹³² The filaments are constructed from a variety of nuclear matrix proteins (NMPs). More than a dozen NMPs have been identified, many of them cell-specific;^3421,3422 also, NMPs released by cancer cells differ from those released by normal cells of the same type.^3422,3423

The nuclear matrix organizes thousands of DNA replication sites during mitosis, and provides architectural order during interphase for RNA metabolism (wherein mRNA molecules are synthesized, spliced, and made ready for export to the protein-synthesizing machinery in the cytoplasm).¹¹³⁵ The regions where RNA metabolism occurs are called transcript domains.^{1133,1135,2021} A human nucleus typically has 20-40 transcript domains, each ranging in diameter from ~0.5 to 3 microns and aligned in a planar horizontal array in the "lower" portion of the nucleus (Fig. 8.49); "lower" is toward the ventral surface of a cell that is adherent to the glass plate used in the microscopic study.¹¹³⁵ A single nucleolus occupies the "upper" or "lower" portions of the nucleus with equal frequency; its position is established by sequence-specific DNA binding proteins.¹¹³⁹ The outermost edge of a transcript domain lies an average of ~0.8 microns (range 0.5-1.2 microns) from the inside surface of the nuclear cortex or nuclear envelope. Located in the core of each domain is a protein called SC-35 that is required for the assembly of the molecular machinery that splices the introns out of mRNA,³⁴²⁴ and each domain is surrounded by a discrete border of high-density chromatin -- with a given chromosome always occupying the same general location in the nucleus at each mitotic phase. All 20-40 transcript domains collectively occupy ~5% of the total nuclear volume, whereas the specific RNA accumulations occupy no more than 1%.

However, nuclear matrix elements may not be necessary for physical support inside each chromosomal territory. Several theoretic descriptions of chromosome structure have been compared to experimental data, and one such description, the Random-Walk/Giant-Loop (RWGL) model,^2466,3416 proposes that huge 35 million base-pair (Mbp) loops are bound to a nuclear matrix that permeates the region. More recently, polymer dynamics simulations of chromosomal territories performed by Munkel, Langowski and Knoch^{1013,2464,2465,3417} suggest that a Multi-Loop-Subcompartment (MLS) model is in better accord with experiment. In the MLS model, chromatin fiber is folded into ~120 Kbp sized loops which are organized into rosettes of 1-2 Mbp. The rosettes (which may be structural units for replication, etc.) are interconnected by a piece of chromatin of similar base pair content so that no protein matrix is needed for structural support. The MLS model agrees with the metaphase organization proposed by Pienta and Coffey.²⁴⁶⁷ The MLS rosettes are clearly visible in Figure 8.50, which shows human chromosome 15 in its highly condensed metaphase state, as it might appear during mitosis. Figure 8.51 shows two polymer dynamics simulations of the 3-5 micron³ territory of human chromosome 15 in its relaxed state between cell divisions, using the RWGL model (left) and the MLS model (right). The numerous apparently matrix-free voids up to ~0.5 micron in diameter that appear in the MLS simulation are presumably largely filled by another chromosome (not shown). (Sometimes the two copies of chromosome 15 are adjacent, but most of the time they are separated.) However, numerous ~0.1 micron voids do exist (c.f. 100-nm keyhole passage; Section 5.3.1.2), and dynamic processes may temporarily open still larger spaces possibly large enough for a medical nanorobot to seek slow, relatively safe and unobstructed passage, but the theoretical pathways of spheres, diffusion and percolation through territories remain to be studied [T. Knoch, personal communication, 1999].

Last updated on 20 February 2003