Search results
Results from the WOW.Com Content Network
Specifically, it is the phosphodiester bonds that link the 3' carbon atom of one sugar molecule and the 5' carbon atom of another (hence the name 3', 5' phosphodiester linkage used with reference to this kind of bond in DNA and RNA chains). [3] The involved saccharide groups are deoxyribose in DNA and ribose in RNA.
DNA ligase is a type of enzyme that facilitates the joining of DNA strands together by catalyzing the formation of a phosphodiester bond.It plays a role in repairing single-strand breaks in duplex DNA in living organisms, but some forms (such as DNA ligase IV) may specifically repair double-strand breaks (i.e. a break in both complementary strands of DNA).
The mechanism of the ligation reaction was first elucidated in the laboratory of I. Robert Lehman. [4] [5] Two fragments of DNA may be joined by DNA ligase which catalyzes the formation of a phosphodiester bond between the 3'-hydroxyl group (-OH) at one end of a strand of DNA and the 5'-phosphate group (-PO4) of another.
Minimalistic mechanism of DNA nick sealing by DNA ligase. In order to join these fragments, the ligase progresses through three steps: Addition of an adenosine monophosphate (AMP) group to the enzyme, referred to as adenylylation, Adenosine monophosphate transfer to the DNA and; Nick sealing, or phosphodiester bond formation. [5] [6]
2) A two-step "associative" (addition-elimination or A N + D N) mechanism that proceeds via a pentavalent phosphorane intermediate. [13] This is represented by the blue dashed lines in the figure at right. 3) A one-step fully synchronous mechanism analogous to S N 2 substitution. Bond formation and breakage occur simultaneously and at the same ...
This mechanism, as well as others, allows for cross-regulation of the cAMP and cGMP pathways. PDE12 cleaves 2',5'-phosphodiester bond linking adenosines of the 5'-triphosphorylated oligoadenylates. [9] [10] PDE12 is not a member of the cyclic nucleotide phosphodiesterase superfamily that contains PDE1 through PDE11.
This is typically via hydrolysis of a small pendant chemical group on one of the molecules, typically resulting in the formation of new C-O, C-S, or C-N bonds. For example, DNA ligase can join two complementary fragments of nucleic acid by forming phosphodiester bonds, and repair single stranded breaks that arise in double stranded DNA during ...
In order for the phosphodiester bond to be formed, the DNA-AMP intermediate must be cleaved off. To accomplish this task, there is a nucleophilic attack on the 5’-phosphate from the upstream 3’-hydroxyl which results in the formation of the phosphodiester bond.