YEASEN Agarose

YEASEN Agarose

— Directly Addressing Electrophoresis Pain Points, Running a Good Gel

Agarose is a purified linear galactan hydrophilic colloid extracted from agar or agar-containing seaweed. Structurally, it is a linear polymer composed of β-D-galactopyranosyl (1-4) linked to 3,6-anhydro-α-L-galactopyranosyl residues. As a gel reagent, it is commonly used for routine nucleic acid analysis through gel electrophoresis or blotting methods (such as Northern or Southern), and it is also suitable for protein applications, such as radial immunodiffusion (RID) experiments.
Agarose gel electrophoresis is an electrophoretic method that uses agarose as the support medium, including gel preparation, sample loading, and electrophoresis. The main difference in the analysis principle from other support material electrophoresis is that it has a dual role of "molecular sieve" and "electrophoresis". When the gel is placed in an electric field, charged nucleic acids migrate through the gel pores towards the positive pole. After electrophoresis under different conditions for an appropriate amount of time, nucleic acid fragments of different sizes and conformations will be located at different positions in the gel, thus achieving separation.

Fig.1 Steps for Nucleic Acid Electrophoresis Experiment Operation

Fig.2 Electrophoresis Migration Direction Diagram

How to Choose the Right Agarose?

Judge based on the basic parameters of agarose:

  • Sulfate Content — an indicator of purity;
  • Gel Strength — the external force required to break the gel;
  • Gel Point — the temperature at which a water-soluble agarose solution forms a gel upon cooling;
  • Electroendosmosis (EEO) — a type of electrokinetic motion where liquids penetrate the gel. The anionic groups within the agarose gel adsorb onto the matrix and do not migrate, but the dissociated cations will migrate towards the negative pole, thus generating electroosmosis. Since the electrophoretic migration of samples usually moves towards the positive pole, the internal convection caused by EEO can interfere with the separation efficiency. Based on the basic parameters of agarose, a high-quality agarose gel should have clear pores, be less prone to breaking, and have characteristics such as high purity (low sulfate content), high gel strength, relatively high gel point (quick solidification at room temperature), and low EEO.

Judge based on the separation range of agarose:

Agarose gels have a wide separation range and are commonly used for DNA gel recovery, DNA separation, and to confirm whether DNA is recombined, and whether plasmids and the like are cut open. Different sizes of target fragments correspond to different concentrations of agarose. According to the principle that high concentration is suitable for separating small fragments, you can refer to the following table to find the optimal gel concentration that suits your needs.

Agarose Concentration (%)

≥3

2-3

1-2

0.7-1

≤0.7

DNA Fragment Size (bp)

≤200

200-700

700-1500

1500-5000

≥5000

 

YEASEN High-Quality Agarose — Covering a Variety of Application Scenarios to Meet Your Needs

Product Name

Product Number

Product Specification

Application Scenario

Agarose

10208ES60/76

100 g / 500 g

Routine Nucleic Acid Electrophoresis

 

Product Advantages

Low electroendosmosis (EEO ≤ 0.13), resulting in excellent band separation, clear distinction, and faster migration.

Fig.3 Electrophoresis Diagram of Gels with Different Concentrations
Note: 0.75% agarose gel loaded with 1 kb ladder; 1% agarose gel loaded with 100 bp ladder, 1 kb ladder, 2000 DNA Marker, 5000 DNA Marker; 2% agarose gel loaded with 100 bp ladder, 2000 DNA Marker, 5000 DNA Marker. Sample volume: Marker neat liquid 2 μL diluted 5 times and then loaded with 10 μL. Electrophoresis programs for 0.75%, 1%, and 2% agarose gels are: 115 V for 45 min; 130 V for 40 min; 130 V for 50 min.

The gel pores are clear and straight, with high gel strength and less prone to breaking.

Note: The illustration is a product display of YEASEN Agarose (Cat#10208ES60).

High-Quality Agarose Usage Method

The concentration of agarose gel is usually chosen between 0.7% and 2%. The higher the concentration, the smaller the molecular pore size of the gel, the slower the DNA migration rate, and the higher the resolution. Conversely, the lower the concentration, the faster the DNA migration rate, and the lower the resolution. Choose the appropriate gel concentration and compatible electrophoresis buffer based on different experimental purposes.

Agarose Concentration

Effective Separation Range (bp)

Recommended Buffer

0.5%

2,000-50,000

1×TAE

0.8%

800-10,000

1×TAE

1.0%

400-8,000

1×TAE

1.2%

300-7,000

1×TAE

1.5%

200-3,000

1×TAE/0.5×TBE

2.0%

100-2,000

1×TAE/0.5×TBE

3.0%

25-1,000

0.5×TBE
TAE Buffer: TAE buffer contains acetic acid, EDTA, and Tris, suitable for rapid electrophoresis and separation of large DNA fragments. The presence of acetic acid lowers the pH value of the gel, helping to increase the electrophoresis speed.
TBE Buffer:TBE buffer contains boric acid, EDTA, and Tris, with a higher ion strength, suitable for high-resolution separation of small DNA fragments. The presence of borate ions enhances the stability of the gel, helping to improve separation efficiency. Therefore, when the gel concentration is high, TBE buffer should be used to facilitate the separation of bands.

Published Literature (Partial)

  • Li Z, Wang M, Fang H, et al. Solid-liquid interface adsorption of antibiotic resistance plasmids induced by nanoplastics aggravates gene pollution in aquatic ecosystems. Environ Pollut. 2023. doi:10.1016/j.envpol.2022.120456.IF=10.366(10208ES)
  • Wang M, Zhang S, Zheng G, et al. Gain-of-Function Mutation of Card14 Leads to Spontaneous Psoriasis-like Skin Inflammation through Enhanced Keratinocyte Response to IL-17A. Immunity. 2018;49(1):66-79.e5. doi:10.1016/j.immuni.2018.05.012.IF=19.734
  • Zhang Y, Ding H, Wang X, et al. MK2 promotes Tfcp2l1 degradation via β-TrCP ubiquitin ligase to regulate mouse embryonic stem cell self-renewal. Cell Rep. 2021;37(5):109949. doi:10.1016/j.celrep.2021.109949.IF=9.423
  • Zhu Z, Zhang L, Sheng R, Chen J. Microfluidic-Based Cationic Cholesterol Lipid siRNA Delivery Nanosystem: Highly Efficient In Vitro Gene Silencing and the Intracellular Behavior. Int J Mol Sci. 2022;23(7):3999. Published 2022 Apr 3. doi:10.3390/ijms23073999.IF=19.924
  • Zhao C, Yang D, Ye Y, et al. Inhibition of Pim-2 kinase by LT-171-861 promotes DNA damage and exhibits enhanced lethal effects with PARP inhibitor in multiple myeloma. Biochem Pharmacol. 2021;190:114648. doi:10.1016/j.bcp.2021.114648.IF=5.858
  • Yu J, Yang W, Xing S, et al. Blended gold/MnO2@BSA nanoparticles for fluorometric and magnetic resonance determination of ascorbic acid. Mikrochim Acta. 2019;186(2):89. Published 2019 Jan 10. doi:10.1007/s00604-018-3205-8.IF=5.479
  • Zheng X, Xu W, Sun R, Yin H, Dong C, Zeng H. Synergism between thioredoxin reductase inhibitor ethaselen and sodium selenite in inhibiting proliferation and inducing death of human non-small cell lung cancer cells. Chem Biol Interact. 2017;275:74-85. doi:10.1016/j.cbi.2017.07.020.IF=5.194
  • Zhou J, Xiong R, Zhou J, et al. Involvement of m6A regulatory factor IGF2BP1 in malignant transformation of human bronchial epithelial Beas-2B cells induced by tobacco carcinogen NNK. Toxicol Appl Pharmacol. 2022;436:115849. doi:10.1016/j.taap.2021.115849.IF=5.219
  • Zhou Y, Liu J, Cai S, Liu D, Jiang R, Wang Y. Protective effects of ginsenoside Rg1 on aging Sca-1⁺ hematopoietic cells. Mol Med Rep. 2015;12(3):3621-3628. doi:10.3892/mmr.2015.3884.IF=5.952

Related Product Selection Guide

Product Positioning

Product Name

Product Number

Product Specification

Application Scenario

Nucleic Acid Stains

YeaRed Nucleic Acid Gel Stain (10,000× in Water)

10202ES76

500 μL

Water-soluble, with the same spectral characteristics as EB, detected under 300 nm UV light excitation.

DNA Marker

GoldBand DL2000 DNA Marker

10501ES60/80

100 T/10×100 T

100-2000 bp

GoldBand DL5000 DNA Marker

10504ES60/80

100 T/10×100 T

100-5000 bp

GoldBand 100bp DNA Ladder

10507ES60/80

100 T/10×100 T

100-1,500 bp

GoldBand 1 kb DNA Ladder

10510ES60/80

100 T/10×100 T

250-12,000 bp