DNA Facts

Some useful facts about DNA (taken from Wikipedia unless otherwise noted)

mass of DNA: 1 bp 660 Daltons (660 g/mol)

molarity of 1 ug/ul of single base-pairs = 1.5 mM (divide by fragment length to get molarity of fragments)

DNA per mammalian cell: 6 pg

length of DNA (diploid human) per cell: 2 m

Human Genome

human genome: 3.1 Gb, so 6 billion bp in normal diploid

human chromosomes: 23 pairs (22 automosomes and X and Y chromosomes)

human mitochondria genome: 16.5 kbp, encodes 13 proteins; 1% of cellular DNA (1000 - 10,000 copies per cell)

Rodent Genomes

rat genome: 2.87 Gb

rat chromosomes: 21 pairs

mouse genome: 2.73 Gb

mouse chromosomes: 20 pairs

Nucleosomes

Approximately 30 million nucleosomes per human cell (~ 1 / 200 bp)

147 bp wrapped (1.67 left-handed superhelical turns) around histone octamer (2 copies each H2A, H2B, H3, and H4).

The nucleosome contains over 120 direct protein-DNA interactions and several hundred water-mediated ones.

Linker DNA between nucleosomes 10-80 bp

ideal MNase mononucleosomal digest -> 3 x 10⁷ fragments per cell (3 x 10¹³ for 1 million cells); if 4 x 10⁵ transcription start sites (TSS) of 2000 bp length, so ~10 nucleosomes/TSS, then ~ 4 x10⁶ (~10%) of mononucleosomal fragments will be of interest.

Acetylation sites: "On average, 5 to 9 lysine residues of H2B, H3, and H4 were acetylated while a higher number (10 to 11 sites) of modifications was observed for H2A [but may be more]" PMID 37011222 ; so total of 50 - 76 acetylation sites per nucleosome.