1. Source and structure

Both agar (Agar) and agarose (Agarose) are derived from the cell wall polysaccharides of red algae (e.g., cauliflower, aburella), but their chemical composition is very different. Agar is a natural mixture of agarose (about 70%) and agar gum (agaropectin, about 30%), the latter containing sulfate and carboxylic acid groups, with a negative charge; Agarose, on the other hand, is a neutral linear polysaccharide after repeated purification of agar gum, which is only composed of D-galactose and 3,6-dehydrated-L-galactose.

2. Physical and chemical properties

1. Solidification and melting temperature:

• The solidification temperature of agar is about 32-40°C, the melting temperature is more than 85°C, and the stability is strong at high temperatures, which is suitable for microbial culture media that needs to be heated repeatedly.

• Agarose has a lower solidification temperature (about 28-36°C) and a melting temperature of 62-65°C, making it more suitable for DNA electrophoresis (avoiding high temperature damage to nucleic acids).

2. Gel Strength and Transparency:

• The agar gel has high strength (≥900 g/cm²), but the transparency is poor, often milky white, and impurities in the colloid may interfere with optical detection;

• Agarose gel transparency is close to glass (light transmission >90%) but less strong (about 300 g/cm² of ordinary agarose), and the high-purity low-electroosmotic model reduces DNA tailing.

3. Electroosmotic effect:

• Because agar contains charged agar gum, it will produce strong electroosmotic flow during electrophoresis, resulting in the reverse migration of small molecule substances, which is completely unsuitable for nucleic acid separation;

• Agarose is desulfurized with very low electroosmotic effect (especially low melting point agarose) to ensure accurate separation of DNA bands by molecular weight.

3. Application scenarios

1. Agar:

• Microbial culture: 1.5-2% agar prepared solid medium to support the growth of bacterial colonies and resist high-temperature sterilization (121°C for 20 minutes without decomposition);

• Food industry: gelling agent for jelly and gummies, taking advantage of its high gel strength and acid and alkali resistance;

• Plant tissue culture: supports callus differentiation with the addition of hormones at a lower cost than agarose.

2. Agarose:

• Nucleic acid electrophoresis: 0.8-2% agarose gel to isolate DNA fragments, EB or GelRed staining followed by UV observation;

• Protein purification: 4% agarose microspheres (e.g., Sepharose) are used for affinity chromatography, conjugated antibodies, or nickel ion capture of target proteins;

• Cell 3D culture: Low melting point agarose (liquid at 37°C) encapsulates cells to simulate the in vivo microenvironment to study tumor invasion.

4. How to choose

1. Experimental purpose is preferred:

• Culture bacteria/fungi → select agar;

• Nucleic acid electrophoresis/protein purification → agarose selection.

2. Purity requirements:

• Industrial grade agar (ash <5%) for general microbiology experiments;

• Molecular biology experiments must use high-purity agarose (sulfate content <0.3%).

3. Gel strength:

• Need to support large volumes of media (e.g., large Petri dishes) → High gel-strength agar (e.g., 1.5% concentration);

• Chromosomal step assays requiring rapid solidification → Fast solidification of agarose (e.g., SeaKem LE).

4. Transparency Needs:

• Laser confocal observation of cells → low-background fluorescent agarose (e.g., NuSieve GTG);

• Common colony count → regular agar is sufficient.

5. Special Features:

• DNA recovery → low melting point agarose (melting temperature ≤ 65°C);

• Anti-regeneration (inhibition of repetitive gel coagulation) → Compound agar with carrageenan added.

6. Cost control:

• High-throughput screening → low-cost agar (about 1/10 the price of agarose);

• Precision Experiments → Invest in high-purity agarose (avoid impurity interference).

5. Common problems and solutions
Problem 1: Agar medium does not solidify Possible causes: insufficient concentration (<1%), pH <4.5 (acidic degradation), high temperature sterilization time is too long. </b12>