Читать книгу Algorithms in Bioinformatics - Paul A. Gagniuc - Страница 58

To get a sense of genome size closer to our reference system, some transformations can express the mega base pairs as physical lengths. The linear length of a double-stranded DNA (dsDNA) molecule can be calculated by multiplying the average distance between bases (∼3.4 angstrom = 0.34 nm [179, 180]; 1 angstrom = 0.1 nm) by the total number of base pairs in a genome. Here, genomes are expressed in mega base pairs. Since 1Mbp is equal to one million base pairs, the size of a genome can be multiplied by one million and then multiplied further by the average distance between bases (0.34 nm). One meter is equal to 1 000 000 000 nanometers (1 × 10⁹). Thus, the result expressed in nanometers is divided by 1 × 10⁹ for conversion to meters.

Depending on the organism, cells of different tissues can be characterized based on the number of sets of chromosomes present: monoploid (one set of chromosomes), diploid (two sets), triploid (three sets), tetraploid (four sets), pentaploid (five sets), and so on. For instance, the human genome contains 3.1 Gbp (3100 Mbp). Thus, in a human haploid (or monoploid) cell (e.g. a single set of chromosomes found in a gamete), the unfolded length of a single set of chromosomes, arranged linearly one after the other, would show an approximate length of:

Thus, a single set of human chromosomes (n = 23 Chr) can theoretically unfold up to 1 m. However, the human body is constituted mainly of somatic cells (diploid cells – two sets of chromosomes/cell). For a diploid cell (2n = 46 Chr), the linear length of all 46 dsDNA molecules is calculated as above and the result in multiplied by two:

Therefore, the two sets (2n = 46 Chr) of human chromosomes found inside a somatic cell can theoretically unfold up to 2.1 m. The linear length of dsDNA molecules from all chromosomes of a somatic cell and the estimated average number of somatic cells in the human body, can be used for various mental experiments (e.g. comparisons between DNA lengths and cosmic distances). These calculations can be empirically extended for ssDNA molecules placed linearly one after the other. For instance, the 2.1 m of dsDNA from a somatic cell, of course, doubles if the ssDNA approach is considered (2.1 m × 2 DNA strands = 4.2 m of ssDNA). The implementation found in Additional algorithm 2.1 uses the above formula to convert the number of bases of a genome to physical length expressed in meters. Important: For convenience, from this point on all notations “b”, “kb”, “Mb”, “Gb” will refer to dsDNA (double stranded DNA).