What does intercalation do to DNA?

2.1. Inhibition of DNA-dependent enzymes. Generally, intercalators cause enzyme inhibition by blocking the DNA sites competitively so that the enzyme cannot interact with the DNA, thereby affecting the DNA replication and transcription.

What do intercalating agents do?

A substance that inserts itself into the DNA structure of a cell and binds to the DNA. This causes DNA damage. In cancer treatment, DNA intercalating agents may kill cancer cells by damaging their DNA and stopping them from dividing.

How do intercalating agents bind to DNA?

Intercalating agents are hydrophobic heterocyclic ring molecules that resemble the ring structure of base pairs, and include ethidium bromide, acridine orange, and actinomycin D. Insertion of these agents distorts the DNA double helix, thereby interfering with DNA replication, transcription, and repair.

How does SYBR Green Intercalate?

SYBR® Green fluorescence increases up to 1,000-fold upon intercalation with dsDNA. As amplification proceeds, the amount of DNA product increases, and hence the number of SYBR® green molecules incorporated into DNA increases.

How does ethidium bromide make DNA visible?

Ethidium bromide is known as an intercalate agent as it inserts itself between the stacked bases of DNA. The ring structure of ethidium bromide resembles the rings of DNA bases and it is also hydrophobic. Ethidium bromide is fluorescent and is visible under UV light. This allows DNA to be visualized.

Why is ethidium bromide called an intercalating agent?

Ethidium is capable of forming close van der Walls contacts with the base pairs and that’s why it binds to the hydrophobic interior of the DNA molecule. Molecules that bind in this manner are called intercalating agents because they intercalate into the compact array of stacked bases.

Why is ethidium bromide mutagenic?

Because ethidium bromide can bind with DNA, it is highly toxic as a mutagen. It may potentially cause carcinogenic or teratogenic effects, although no scientific evidence showing either health effect has been found. Exposure routes of ethidium bromide are inhalation, ingestion, and skin absorption.

Why EtBr is used in gel electrophoresis?

Ethidium Bromide (EtBr) is sometimes added to running buffer during the separation of DNA fragments by agarose gel electrophoresis. It is used because upon binding of the molecule to the DNA and illumination with a UV light source, the DNA banding pattern can be visualized.

What makes a good Intercalator?

In order for an intercalator to fit between base pairs, the DNA must dynamically open a space between its base pairs by unwinding. These structural modifications can lead to functional changes, often to the inhibition of transcription and replication and DNA repair processes, which makes intercalators potent mutagens.

Why is TaqMan better than SYBR Green?

In quantitative gene expression analysis, two methods have more popularity, SYBR Green and TaqMan, SYBR Green is relatively cost benefit and easy to use and technically based on binding the fluorescent dye to double-stranded deoxyribonucleic acid (dsDNA) where TaqMan method has more expensive and based on dual labeled …

Is SYBR Green toxic?

Mutagenicity of these stains was not observed although their toxic concentration was reached. Thus, SYBR Gold and SYBR Green II do not show mutagenicity in our tests, even at toxic doses, and these DNA stains represent safer alternatives to ethidium bromide for nucleic acid visualization.

What is the role of intercalation in DNA?

Intercalation is a special binding mode where the planar aromatic moiety of a small molecule is inserted between a pair of base pairs, causing structural changes in the DNA and leading to its functional arrest. Enormous progress has been made to understand the nature of the intercalation process since its idealistic conception five decades ago.

How are intercalating agents used in the medical field?

Most of the intercalating agents are used clinically as the antibacterial, antiparasitic, and antitumor agents ( Berman and Young, 1981, Denny, 2002, Waring, 1981 ), as intercalation inhibits DNA replication and transcription process thereby inhibiting the cell division and growth ( Lenglet & David-Cordonnier, 2010 ).

When was intercalation first proposed as a mechanism?

Intercalation as a mechanism of interaction between cationic, planar, polycyclic aromatic systems of the correct size (on the order of a base pair) was first proposed by Leonard Lerman in 1961.

How does bleomycin act as an intercalator in DNA?

Bleomycin is a DNA intercalator. An intercalator is a molecule that binds DNA and inserts itself into DNA structure. Bleomycin binds to Fe 2+, and this complex leads to free radical formation when oxygen is added. These free radicals then intercalate between DNA strands, which produces single- and double-stranded breaks in DNA (Figure 20-4 ).