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Formamide is a constituent of cryoprotectant vitrification mixtures used for cryopreservation of tissues and organs. Formamide is also used as an RNA stabiliser in gel electrophoresis by deionizing RNA. In capillary electrophoresis, it is used for stabilizing (single) strands of denatured DNA.
The E. Coli DnaG primase is a 581 residue monomeric protein with three functional domains, according to proteolysis studies. There is an N-terminal Zinc-binding domain (residues 1–110) where a zinc ion is tetrahedrally coordinated between one histidine and three cysteine residues, which plays a role in recognizing sequence specific DNA binding sites.
In biochemistry, denaturation is a process in which proteins or nucleic acids lose folded structure present in their native state due to various factors, including application of some external stress or compound, such as a strong acid or base, a concentrated inorganic salt, an organic solvent (e.g., alcohol or chloroform), agitation and radiation, or heat. [3]
When subjected to denaturing factors like increased heat or chemicals like formamide in low levels, DNA is partially denatured in a predictable pattern based on its nucleotide content in different regions. [1] This allows unique fingerprints or ‘barcodes' to be generated for molecules with different sequences not unlike restriction mapping.
There are two main types of primase: DnaG found in most bacteria, and the AEP (Archaeo-Eukaryote Primase) superfamily found in archaean and eukaryotic primases. While bacterial primases (DnaG-type) are composed of a single protein unit (a monomer) and synthesize RNA primers, AEP primases are usually composed of two different primase units (a heterodimer) and synthesize two-part primers with ...
For DNA oligonucleotides, i.e. short sequences of DNA, the thermodynamics of hybridization can be accurately described as a two-state process. In this approximation one neglects the possibility of intermediate partial binding states in the formation of a double strand state from two single stranded oligonucleotides.
DnaB helicase is an enzyme in bacteria which opens the replication fork during DNA replication.Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerisation of the N-terminal domain has been observed and may occur during the enzymatic cycle. [1]
DNA synthesis is initiated by the RNA polymerase primase, which makes an RNA primer with a free 3'OH. [23] This primer is attached to the single-stranded DNA template, and DNA polymerase elongates the chain by incorporating nucleotides; DNA polymerase also proofreads the newly synthesized DNA strand. [23]