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 DNA molecules in vitro or in vivo.[1] Mechanistic details of DNA packing are essential for its functioning in the process of gene regulation in living systems. Condensed DNA often has surprising properties, which one would not predict from classical concepts of dilute solutions. Therefore, DNA condensation in vitro serves as a 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 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. DNA is one of the stiffest natural polymers, yet it is also one of the longest molecules. 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. 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.[1] This means that at large distances DNA can be considered as a flexible rope, and on a short scale as a stiff rod. Like a garden hose, unpacked DNA would randomly occupy a much larger volume than when it is orderly packed. 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. 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. To cope with volume constraints, DNA can pack itself in the appropriate solution conditions with the help of ions and other molecules. Usually, DNA condensation is defined as "the collapse of extended DNA chains into compact, orderly particles containing only one or a few molecules".[3] 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".[4] 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.[1]
^ abcdTeif, VB; Bohinc, K (2011). "Condensed DNA: condensing the concepts". Progress in Biophysics and Molecular Biology. 105 (3): 208–22. doi:10.1016/j.pbiomolbio.2010.07.002. PMID 20638406.
^Bloomfield, VA (1996). "DNA condensation". Current Opinion in Structural Biology. 6 (3): 334–41. doi:10.1016/S0959-440X(96)80052-2. PMID 8804837.
^Bloomfield, VA (1997). "DNA condensation by multivalent cations". Biopolymers. 44 (3): 269–82. CiteSeerX 10.1.1.475.3765. doi:10.1002/(SICI)1097-0282(1997)44:3<269::AID-BIP6>3.0.CO;2-T. PMID 9591479.
^Zimmerman, SB; Murphy, LD (1996). "Macromolecular crowding and the mandatory condensation of DNA in bacteria". FEBS Letters. 390 (3): 245–8. doi:10.1016/0014-5793(96)00725-9. PMID 8706869.
DNAcondensation refers to the process of compacting DNA molecules in vitro or in vivo. Mechanistic details of DNA packing are essential for its functioning...
nucleoid forms by condensation and functional arrangement with the help of chromosomal architectural proteins and RNA molecules as well as DNA supercoiling...
Genomic DNA is tightly and orderly packed in the process called DNAcondensation, to fit the small available volumes of the cell. In eukaryotes, DNA is located...
after interphase, DNA has already been replicated when the cell enters prophase. The main occurrences in prophase are the condensation of the chromatin...
and DNA is negatively charged. This allows histones to make a strong ionic bond to DNA form a nucleosome. The most basic level of DNAcondensation is the...
chromosome is a package of DNA with part or all of the genetic material of an organism. In most chromosomes, the very long thin DNA fibers are coated with...
protein folding and DNA melting, liquid crystal-like transitions in the process of DNAcondensation, and cooperative ligand binding to DNA and proteins with...
have shown that deficient DNA repair, allowing greater accumulation of DNA damages, causes premature aging; and that increased DNA repair facilitates greater...
transfer, and thus Darwinian evolution. Nam et al. demonstrated the direct condensation of nucleobases with ribose to give ribonucleosides in aqueous microdroplets...
Eukaryotic DNA replication is a conserved mechanism that restricts DNA replication to once per cell cycle. Eukaryotic DNA replication of chromosomal DNA is central...
B-type lamins that are resistant to cleavage by caspases show decreased DNAcondensation and apoptotic “blebbing” formation, thereby underscoring the important...
Bacic A, McFadden GI, Waller RF (December 2012). "Loss of nucleosomal DNAcondensation coincides with appearance of a novel nuclear protein in dinoflagellates"...
transferase (TdT), also known as DNA nucleotidylexotransferase (DNTT) or terminal transferase, is a specialized DNA polymerase expressed in immature,...
guanine (G). In RNA, uracil binds to adenine via two hydrogen bonds. In DNA, the uracil nucleobase is replaced by thymine (T). Uracil is a demethylated...
in sunscreens and cosmetics. It is an ester formed by the Knoevenagel condensation of 2-ethylhexyl cyanoacetate with benzophenone. It is a viscous, oily...
the counterion condensation theories. Hansen, Per Lyngs; Podgornik, Rudi; Parsegian, V. Adrian (2001-07-23). "Osmotic properties of DNA: Critical evaluation...
recognized as saccharification. Hydrolysis reactions can be the reverse of a condensation reaction in which two molecules join into a larger one and eject a water...
Bacic A, McFadden GI, Waller RF (December 2012). "Loss of nucleosomal DNAcondensation coincides with appearance of a novel nuclear protein in dinoflagellates"...
to billions of copies of a specific DNA sample rapidly, allowing scientists to amplify a very small sample of DNA (or a part of it) sufficiently to enable...
Chromatin is a complex of DNA and protein found in eukaryotic cells. The primary function is to package long DNA molecules into more compact, denser structures...
phosphodiester bond. Sometimes the DNA polymerase will incorporate a ddNTP and the absence of the 3' OH group will interrupt the condensation reaction between the 5'...
and the DNAcondensation buffer (Buffer EC) to achieve high transfection efficiency. In the first step of Effectene–DNA complex formation, the DNA is condensed...
"Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci. U.S.A. 99 (26): 16899–903. Bibcode:2002PNAS...
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