DNA condensation

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Pyrophosphate leaving group in a condensation reaction forming the ribose-phosphate polymer. Condensation of Adenine and Guanine forming a phosphodiester bond, the basis of the nucleic acid backbone.

DNA condensation refers to the process of compacting

model system for many processes of physics, biochemistry and biology.[2] In addition, DNA condensation has many potential applications in medicine and biotechnology.[1]

DNA diameter is about 2 nm, while the length of a stretched single molecule may be up to several dozens of centimetres depending on the organism. Many features of the DNA double helix contribute to its large stiffness, including the mechanical properties of the sugar-phosphate backbone, electrostatic repulsion between

eukaryotes, the DNA size and the number of other participating players are much larger, and a DNA molecule forms millions of ordered nucleoprotein particles, the nucleosomes, which is just the first of many levels of DNA packing.[1]

In life

In viruses

In

liquid crystals, because it lacks fluidity. On the other hand, DNA condensed in vitro, e.g., with the help of polyamines also present in viruses, is both locally ordered and fluid.[1]

In bacteria

Basic units of genomic organization in bacteria and eukaryotes.
Main article: Nucleoid § Condensation and organization

Bacterial DNA is packed with the help of

bacterial chromosome. Bacterial nucleoid evolutionary represents an intermediate engineering solution between the protein-free DNA packing in viruses and protein-determined packing in eukaryotes.[1]

Sister chromosomes in the bacterium Escherichia coli are induced by stressful conditions to condense and undergo pairing.[6] Stress-induced condensation occurs by a non-random, zipper-like convergence of sister chromosomes. This convergence appears to depend on the ability of identical double-stranded DNA molecules to specifically identify each other, a process that culminates in the proximity of homologous sites along the paired chromosomes. Diverse stress conditions appear to prime bacteria to effectively cope with severe DNA damages such as double-strand breaks. The apposition of homologous sites associated with stress-induced chromosome condensation helps explain how repair of double-strand breaks and other damages occurs.[6]

In eukaryotes

Different levels of DNA condensation in eukaryotes. (1) Single DNA strand. (2) Chromatin strand (DNA with histones). (3) Chromatin during interphase with centromere. (4) Two copies of condensed chromatin together during prophase. (5) Chromosome during metaphase.
Main article: chromatin

Eukaryotic DNA with a typical length of dozens of centimeters should be orderly packed to be readily accessible inside the micrometer-size nucleus. In most eukaryotes, DNA is arranged in the cell nucleus with the help of histones. In this case, the basic level of DNA compaction is the nucleosome, where the double helix is wrapped around the histone octamer containing two copies of each

genes, which are characterized by a less compact structure called euchromatin, and to alleviate protein access in more tightly packed regions called heterochromatin. During the cell division, chromatin compaction increases even more to form chromosomes, which can cope with large mechanical forces dragging them into each of the two daughter cells.[1] Many aspects of transcription are controlled by chemical modification on the histone proteins, known as the histone code
.

Chromosome scaffold has important role to hold the chromatin into compact chromosome. Chromosome scaffold is made of proteins including condensin, topoisomerase IIα and kinesin family member 4 (KIF4)[7]

dinoflagellate histone-like proteins (HLPs) for packaging instead. It is unknown how they control access to genes; those do retain histone have a special histone code.[9][10]

In archaea

Depending on the organism, an archaeon may use a bacteria-like HU system or a eukaryote-like nucleosome system for packaging.[11]

In vitro

DNA condensation can be induced in vitro either by applying external force to bring the double helices together, or by inducing attractive interactions between the DNA segments. The former can be achieved e.g. with the help of the osmotic pressure exerted by crowding neutral polymers in the presence of monovalent salts. In this case, the forces pushing the double helices together are coming from entropic random collisions with the crowding polymers surrounding DNA condensates, and salt is required to neutralize DNA charges and decrease DNA-DNA repulsion. The second possibility can be realized by inducing attractive interactions between the DNA segments by multivalent cationic charged ligands (multivalent

proteins).[1]

Physics

Condensation of long double-helical DNAs is a sharp phase transition, which takes place within a narrow interval of condensing agent concentrations.[ref] Since the double helices come very closely to each other in the condensed phase, this leads to the restructuring of water molecules, which gives rise to the so-called hydration forces.[ref] To understand attraction between negatively charged DNA molecules, one also must account for correlations between counterions in the solution.[ref] DNA condensation by proteins can exhibit hysteresis, which can be explained using a modified Ising model.[12]

Role in gene regulation

Nowadays descriptions of gene regulation are based on the approximations of

dilute solutions, although it is clear that these assumptions are in fact violated in chromatin. The dilute-solution approximation is violated for two reasons. First, the chromatin content is far from being dilute, and second, the numbers of the participating molecules are sometimes so small, that it does not make sense to talk about the bulk concentrations. Further differences from dilute solutions arise due to the different binding affinities of proteins to condensed and uncondensed DNA. Thus in condensed DNA both the reaction rates can be changed and their dependence on the concentrations of reactants may become nonlinear.[1]

See also

References

  1. ^
    PMID 20638406
    .
  2. PMID 8804837
    .
  3. PMID 9591479
    .
  4. PMID 8706869
    .
  5. PMID 26942688
    .
  6. ^
    PMID 23884460
    .
  7. ^ Chromosome Scaffold is a Double-Stranded Assembly of Scaffold Proteins, by Poonperm et al, Nature scientific reports
  8. PMID 20400466
    .
  9. PMID 26646152
    .
  10. PMID 30558155
    .
  11. S2CID 85874882
    .
  12. PMID 27091987
    .

Further reading
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