The nucleoid (meaning nucleus-like) is an irregularly-shaped region within the cell of a prokaryote that contains all or most of the genetic material. In contrast to the nucleus of a eukaryotic cell, it is not surrounded by a nuclear membrane. The genome of prokaryotic organisms generally is a circular, double-stranded piece of DNA, of which multiple copies may exist at any time. The length of a genome widely varies, but generally is at least a few million base pairs.
A genophore is the DNA of a prokaryote. It is commonly referred to as a prokaryotic chromosome. The term "chromosome" is misleading for a genophore because the genophore lacks chromatin. The genophore is compacted through a mechanism known as supercoiling, whereas a chromosome is additionally compacted via chromatin. Nevertheless many prokaryotic organisms employ some specialized proteins (that can be considered as "histone-like" proteins) in order to spatially organize the genetic material so that picturing the nucleoid as an unorganized blob turns out to be quite misleading.
The genophore is circular in most prokaryotes, and linear in very few. The circular nature of the genophore allows replication to occur without telomeres. Genophores are generally of a much smaller size than Eukaryotic chromosomes. A genophore can be as small as 580,073 base pairs (Mycoplasma genitalium) while the genophore of the model organism E. Coli is about 4,600,000 bp. Many eukaryotes (such as plants and animals) carry genophores in organelles such as mitochondria and chloroplasts. These organelles are very similar to true prokaryotes.
The nucleoid can be clearly visualized on an electron micrograph at high magnification, where, although its appearance may differ, it is clearly visible against the cytosol. Sometimes even strands of what is thought to be DNA are visible. By staining with the Feulgen stain, which specifically stains DNA, the nucleoid can also be seen under a light microscope. The DNA-intercalating stains DAPI and ethidium bromide are widely used for fluorescence microscopy of nucleoids.
Experimental evidence suggests that the nucleoid is largely composed of DNA, about 60%, with a small amount of RNA and protein. The latter two constituents are likely to be mainly messenger RNA and the transcription factor proteins found regulating the bacterial genome. Proteins that carry out the dynamic spatial organization of the nucleic acid are known as nucleoid proteins or nucleoid-associated proteins (NAPs) and are distinct from histones of eukaryotic nuclei. In contrast to histones, the DNA-binding proteins of the nucleoid do not form nucleosomes, in which DNA is wrapped around a protein core. Instead, these proteins often use other mechanisms to promote compaction such as DNA looping. The most studied NAPs are HU, H-NS, Fis, CbpA, Dps that organize the genome by driving events such as DNA bending, bridging, and aggregation. These proteins can form clusters (like H-NS does) in order to locally compact specific genomic regions, or be scattered throughout the chromosome (HU, Fis) and they seem to be involved also in coordinating transcription events, spatially sequestering specific genes and participating in their regulation.