Comprehensive Overview of DNA Ligase: Mechanisms, Types, and Applications

What is DNA Ligase?

DNA ligase forms a phosphodiester bond between two DNA fragments. DNA ligase does not require a template because DNA ligase joins two nicks in a DNA double strand at the same time. DNA ligase is an enzyme that repairs DNA breaks by joining the 5´-phosphorylated ends of broken DNA to the 3´-OH ends, repairing breaks in the phosphate backbone of DNA. In vivo, ligases are essential for the repair of many forms of DNA, including the repair of DNA strand incisions, single-strand breaks in double-stranded DNA molecules, Okazaki fragments formed during DNA replication, and the repair of incision and double-strand break junctions during repair events. In vitro, ligases (especially T4 DNA ligase) are key reagents in many molecular biology experiments, including vector and insert fragment ligation for recombinant plasmid construction, junction ligation in next-generation sequencing (NGS) library construction, and cyclization of double-stranded DNA.

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DNA Ligase Function

DNA ligase functions primarily by sealing nicks in the DNA backbone, which are gaps that arise during DNA replication and repair. These nicks are covalent bonds where the phosphodiester linkage between adjacent nucleotides is incomplete. The ligase enzyme acts by facilitating the formation of a stable phosphodiester bond between the 5'-phosphate and 3'-hydroxyl termini of adjacent DNA strands. This function is crucial for processes such as DNA replication, where lagging strand synthesis creates Okazaki fragments that must be joined to form a continuous DNA strand.

DNA Ligase Mechanism

The catalytic mechanism of DNA ligase involves a three-step process:

• Adenylation: The enzyme binds an ATP or NAD+ molecule, leading to the formation of a ligase-AMP intermediate. The highly conserved lysine residue in the enzyme attacks the 5'-phosphate of ATP or NAD+, releasing pyrophosphate (PPi).
• Transfer of AMP: The AMP is transferred from the adenylated ligase to the 5'-phosphate of the DNA strand, creating an adenylated DNA intermediate.
• Phosphodiester Bond Formation: Finally, the enzyme catalyzes the formation of a phosphodiester bond between the 5'-phosphate of the adenylated DNA strand and the 3'-hydroxyl group of the adjacent DNA strand, releasing AMP in the process.

This mechanism, shared among various DNA ligases, underscores the enzyme's universal role in DNA manipulation across different organisms. Factors affecting the ligation efficiency include the following three (1) the temperature of the ligation reaction: the optimal reaction temperature of DNA ligase is 37°C, but at this temperature, the hydrogen bonding of sticky ends is very unstable, so the optimal temperature for ligating sticky ends is generally considered to be more appropriate at 4-16°C. For flat ends there is no need to consider the hydrogen bonding problem, and higher temperatures can be used to give better performance of enzyme activity; (2) enzyme concentration; (3) pH.

Types of DNA Ligase

Adenosine Triphosphate (ATP)-dependent DNA Ligase

ATP-dependent DNA ligases that use the energy of ATP to catalyze the formation of a phosphodiester bond between two nucleotide strands.

(1) T4 DNA Ligase

T4 DNA ligase is an ATP-dependent DNA ligase.

• T4 DNA ligase catalyzes the formation of a phosphodiester bond between adjacent 5′-phosphate groups and 3′-hydroxyl groups on two DNA double strands, which can join the flat ends of double-stranded DNA, compatible sticky ends, and single-stranded cuts therein.
• T4 DNA ligase can repair single-stranded incisions in DNA/RNA or double-stranded RNA heteroduplexes.
• Reaction conditions for T4 DNA ligase: warming at 16°C and incubation at 65°C for 10 minutes for inactivation.

(2) T7 DNA Ligase

T7 DNA ligase is derived from T7 phage and is an ATP-dependent DNA ligase.

• T7 DNA ligase catalyzes the formation of phosphodiester bonds between the sticky ends and the adjacent 5' phosphate termini and 3' hydroxyl groups of the incised double-stranded DNA.
• T7 DNA ligase repairs single-stranded incisions in DNA/RNA heteroduplexes.
• T7 DNA ligase reaction conditions: warming at 25°C and incubation at 65°C for 10 minutes to inactivate.

(3) T3 DNA Ligase

T3 DNA ligase is derived from T3 phage and is an ATP-dependent DNA ligase.

• T3 DNA ligase can effectively catalyze the ligation of sticky-end and flat-end double-stranded DNA molecules as well as the repair of defects in double-stranded DNA or DNA/RNA heterozygous strands.
• Defect repair of DNA/RNA heterozygous strands by T3 DNA ligase can be both RNA and RNA ligation.
• Reaction conditions for T3 DNA ligase: warming at 25°C and incubation at 65°C for 10 minutes for inactivation.
• High salt tolerance of T3 DNA ligase: 2 times more tolerant to NaCl than T4 DNA ligase in the reaction.

(4) SplintR Ligase

SplintR ligase, also known as PBCV DNA ligase and Chorella virus DNA ligase, is an ATP-dependent DNA ligase.

• SplintR Ligase efficiently catalyzes the joining reaction of two adjacent DNA single strands paired with a complementary RNA single strand.
• The optimal reaction temperature for SplintR ligase is 25 degrees Celsius, which can be optimized between 16-37 degrees Celsius, with 37 degrees Celsius significantly improving the specificity of the reaction; it is inactivated at 65°C for 20min.
• SplintR Ligase is very sensitive to monovalent cations (e.g., the concentration of NaCl or KCl should be less than 50 mM), and the ligation efficiency decreases with decreasing length of the splinted RNA, and is zero when the length is < 10 nt.

Nicotinamide Adenine Dinucleotide (NAD)-dependent DNA Ligase

NAD+-dependent DNA ligases that utilize the energy of nicotinamide adenine dinucleotide (NAD+) to catalyze the formation of a phosphodiester bond between two nucleotide strands.

(1) E. coli DNA Ligase

E. coli DNA ligase is cofactor and Mg2+ dependent with NAD+ (nicotinamide adenine dinucleotide).

• E. coli DNA ligase catalyzes sticky end joining of double-stranded DNA or repair of indentations in double-stranded DNA and DNA/RNA heterodimeric strands.
• E. coli DNA Ligase does not perform ligation of flat-ended double-stranded DNA under conventional conditions. It can also catalyze the ligation reaction of flat-ended double-stranded DNA with the addition of 10-15% PEG and appropriately high concentrations of monovalent cations.
• E. coli DNA Ligase is active from 4-37°C. It is inactivated by incubation at 16°C and 65°C for 20 minutes.

(2) Taq DNA Ligase

Taq DNA Ligase uses NAD+ as a cofactor and is active in the range of 45°C-65°C. It catalyzes the repair of deletions in double-stranded DNA. It catalyzes the repair of indentations in double-stranded DNA early.

DNA Ligase in DNA Replication

In the complex process of DNA replication, DNA ligase plays a crucial role in ensuring the integrity and continuity of the newly synthesized DNA strand. This enzyme is indispensable for sealing the nicks that occur during DNA replication, particularly on the lagging strand. During DNA replication, the DNA polymerase enzyme synthesizes the new DNA strand in a discontinuous fashion on the lagging strand. This occurs in the form of short segments known as Okazaki fragments, which are produced as DNA polymerase moves away from the replication fork. Each Okazaki fragment is synthesized in the 5' to 3' direction, creating a series of separate DNA segments that need to be joined together to form a continuous strand.

Schematic diagram of the involvement of ligase in DNA replication.

DNA Ligase vs DNA Polymerase

While both DNA ligase and DNA polymerase are essential for DNA replication, they perform distinct functions:

• Different Formation Methods: DNA ligase forms a phosphodiester bond between two DNA fragments. dna polymerase can only form a phosphodiester bond by adding a single nucleotide to an already existing DNA fragment.
• Different Templates: DNA ligase does not need a template, because DNA ligase is the DNA double-stranded two gaps connected at the same time. DNA polymerase is a DNA strand as a template, the individual nucleotides through the phosphodiester bond to form a DNA strand and the template strand complementary to the DNA strand.
• Different Applications: DNA ligase is mainly used in genetic engineering, the restriction endonuclease "cut" out of the sticky ends reassembled, so it is also known as the "gene needle and thread". DNA polymerase plays a role in the replication of DNA, mainly connecting DNA fragments with individual deoxyribonucleotides. DNA polymerase plays a role in DNA replication, mainly by connecting DNA fragments to the phosphodiester bonds between individual deoxyribonucleotides.

Applications of DNA Ligase

DNA ligase's versatility extends beyond cellular processes into various biotechnological applications:

• Molecular Cloning: DNA ligase is used to insert foreign DNA fragments into plasmid vectors, facilitating the cloning and propagation of recombinant DNA.
• Mutation Detection: Ligase-based assays help detect mutations and verify DNA sequences by ensuring the accurate joining of DNA fragments.
• DNA Assembly: Enzymes like T4 DNA ligase are employed in synthetic biology to assemble large DNA constructs from smaller fragments.
• Next-Generation Sequencing: DNA ligase plays a role in preparing DNA libraries for sequencing by ensuring the accurate joining of sequencing adapters to DNA fragments.

Comprehensive Overview of DNA Ligase: Mechanisms, Types, and Applications

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