In-pond Race way systems for Aquaculture (IPRS).pptx
rdt ppt.pptx
1. GURU NANAK INSTITUTE OF PHARMACEUTICAL SCIENCE AND
TECHNOLOGY
TOPIC : Characteristics and mechanism of action of ligase enzymes
NAME OF THE STUDENT : ANKIT GHOSH
UNIVERSITY ROLL NUMBER : 31308421036
ACADEMIC SESSION : 2023-24
PAPER NAME : RECOMBINANT DNA
TECHNOLOGY
PAPER CODE : CMc 501
Maulana Abul Kalam Azad University of Technology
2. B. Sc./ SEM 5/2023-24 / RECOMBINANT DNA TECHNOLOGY / CMc 501 /Presentation_1
ligase is an enzyme that can catalyze the joining (ligation) of two molecules by
forming a new chemical bond.
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.
DNA ligases are the ligases that join or bind the two DNA fragments (also
known as Okazaki fragments) by forming a phosphodiester bond.
DNA Ligase is needed for DNA replication as well as the DNA repairing
process.
DNA Ligase is widely utilized in laboratories for carrying out recombinant
DNA experiments.
The most widely utilized ligase in a science laboratory is the DNA ligase.
3. B. Sc./ SEM 5/2023-24 / RECOMBINANT DNA TECHNOLOGY / CMc 501 /Presentation_1
The DNA ligase is a class of the enzyme that helps in the formation of phosphodiester
bond between the 5’ end of one side to the 3’ end of another side using an energy
molecule (ATP or NAD+ ).
DNA ligase catalyzes the formation of phosphodiester bond between two
deoxynucleotide residues of two DNA strands.
DNA ligase enzyme requires a free hydroxyl group at the 3´ -end of one DNA chain and
a phosphate group at the 5´-end of the other and requires energy in the process.
E. coli and other bacterial DNA ligase utilizes NAD+ as energy donor, whereas in T4
bacteriophage, T4 DNA ligase uses ATP as cofactor.
All the eukaryotic enzyme works efficiently at body temperature (37°C). However,
some of the DNA ligases like the T4 DNA ligase work efficiently at 16°C temperature,
in vitro. Even, the ligation can also be achieved at 4°C during in Vitro reaction
4. B. Sc./ SEM 5 /2023-24 / RECOMBINANT DNA TECHNOLOGY / CMc 501 /Presentation_1
1. The 5’ end of the DNA breaks is called “donor” while the 3’ ends are called
“acceptor”.
2. The catalytic reaction of ligation is started with the recognition of the ligation site as
nick.
3. The reaction starts with the nucleophilic attack.
In the first step, one ATP or NAD+ (in case of bacterial ligase) energy molecules react
with ligase enzyme and helps in forming the enzyme-AMP complex linked to amino
group of the lysine. The AMP attached with the lysine amino acid present in the active
site of the enzyme by releasing the PPi. Thus, the active centre of the enzyme becomes
adenylated by addition of AMP to its lysine and starts the enzymatic reaction. The bond
formed between the lysine of enzyme and the AMP is called the phospho-amide bond.
In the second step, the active site of the enzyme with the AMP moiety activates the
phosphate group at the 5´-end of the DNA molecule to be joined [and releases the AMP
from the lysine and attached it with the phosphate of the donor]. Thus the ligase enzyme
transfers the AMP to the 5’ phosphate end.
The final step is a nucleophilic attack by the 3´-hydroxyl group on this activated
phosphorus atom. Now the enzyme attaches the 5’ to the 3’ by creating the
phosphodiester bond and releases the AMP from the active site.
5. B. Sc./ SEM 5/2023-24 / RECOMBINANT DNA TECHNOLOGY / CMc 501 /Presentation_1
• Ligates the cohesive blunt ends as well as sticky ends.
• Ligate single-stranded as well as double-stranded DNA.
• Used in a ligase chain reaction
• Used during the DNA repair mechanism
• Use during DNA replication
• Used to insert a gene in the plasmid
PROCESS OF BLUNT END LIGATION
PROCESS OF STICKY END LIGATION
6. B. Sc./ SEM 5/2023-24 / RECOMBINANT DNA TECHNOLOGY / CMc 501 /Presentation_1
• Shuman S (June 2009). "DNA ligases: progress and prospects". The Journal of
Biological Chemistry. 284 (26):
1736517369. doi:10.1074/jbc.R900017200. PMC 2719376. PMID 19329793.
• Lehman IR (November 1974). "DNA ligase: structure, mechanism, and
function". Science. 186 (4166): 790–
7. Bibcode:1974Sci...186..790L. doi:10.1126/science.186.4166.790. PMID 4377758. S2
CID 86549159.
• Holliday, G. L., Rahman, S. A., Furnham, N., & Thornton, J. M. (2014). Exploring the
biological and chemical complexity of the ligases. Journal of molecular biology, 426(10),
2098–2111. https://doi.org/10.1016/j.jmb.2014.03.008
