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. Although the double helices are always locally aligned, the DNA inside viruses does not represent real liquid crystals, because it lacks fluidity. This packing can change from hexagonal to cholesteric to isotropic at different stages of the phage functioning. Double-stranded DNA is stored inside the capsid in the form of a spool, which can have different types of coiling leading to different types of liquid-crystalline packing. In viruses and bacteriophages, the DNA or RNA is surrounded by a protein capsid, sometimes further enveloped by a lipid membrane. In 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. This definition applies to many situations in vitro and is also close to the definition of DNA condensation in bacteria as "adoption of relatively concentrated, compact state occupying a fraction of the volume available". Usually, DNA condensation is defined as "the collapse of extended DNA chains into compact, orderly particles containing only one or a few molecules". To cope with volume constraints, DNA can pack itself in the appropriate solution conditions with the help of ions and other molecules.
#Scaffold protein h1 free#
For real polymers such as DNA, this gives only a very rough estimate what is important, is that the space available for the DNA in vivo is much smaller than the space that it would occupy in the case of a free diffusion in the solution. Mathematically, for a non-interacting flexible chain randomly diffusing in 3D, the end-to-end distance would scale as a square root of the polymer length. Like a garden hose, unpacked DNA would randomly occupy a much larger volume than when it is orderly packed. This means that at large distances DNA can be considered as a flexible rope, and on a short scale as a stiff rod. Under physiological conditions (e.g., near-neutral pH and physiological salt concentrations), the persistence length of dsDNA is generally around 50 nm, which corresponds to approximately 150 base pairs. The persistence length of double-stranded DNA (dsDNA) is a measure of its stiffness or flexibility, which depends on the DNA sequence and the surrounding environment, including factors like salt concentration, pH, and temperature. DNA is one of the stiffest natural polymers, yet it is also one of the longest molecules. Many features of the DNA double helix contribute to its large stiffness, including the mechanical properties of the sugar-phosphate backbone, electrostatic repulsion between phosphates (DNA bears on average one elementary negative charge per each 0.17 nm of the double helix), stacking interactions between the bases of each individual strand, and strand-strand interactions. ĭNA 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. In addition, DNA condensation has many potential applications in medicine and biotechnology. Therefore, DNA condensation in vitro serves as a model system for many processes of physics, biochemistry and biology. Condensed DNA often has surprising properties, which one would not predict from classical concepts of dilute solutions. Mechanistic details of DNA packing are essential for its functioning in the process of gene regulation in living systems. Condensation of Adenine and Guanine forming a phosphodiester bond, the basis of the nucleic acid backbone.ĭNA condensation refers to the process of compacting DNA molecules in vitro or in vivo. Pyrophosphate leaving group in a condensation reaction forming the ribose-phosphate polymer.
0 kommentar(er)
