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CAPS,molecular marker or biochemical buffer? 2019-01-18 11:07:29

In biochemical experiments,the abbreviation “CAPS” is appeared frequently,and it has two completely different meanings.


1. Molecular Markers-Cleaved Amplified Polymorphic Sequences

CAPS buffer,Cleaved Amplified Polymorphic Sequences,also known as RFLP-PCR,which is mainly used for restriction analysis of PCR-amplified DNA fragments. It is a technique for designing specific primers based on EST or published gene sequences,and combining specific PCR with restriction enzyme digestion to detect polymorphism.


With the development of molecular biology technology,DNA molecular marker technology has also developed rapidly. There are dozens of molecular markers,such as RFLP,AFLP,STS,CAPS,SCAR,SSR,SNP,RAPD,ISSR,TRAP,etc.,they are widely used in genetic breeding,genome mapping,gene mapping,species phylogenetic identification,gene bank construction,gene cloning and so on. Different molecular markers have different advantages and disadvantages,and their main applications are also different. CAPS has the advantages of co-dominance,site specificity,simple operation and low cost,and has been widely used in plant genotyping,localization,cloning,molecular identification and genetic diversity of animals,identification of varieties,linkage maps and identification of microorganisms. It has the following characteristics:
(1) There are many combinations of primers and restriction enzymes,which increases the chance of revealing polymorphisms,and is easy to operate and can be analyzed by agarose gel electrophoresis;
(2) In eukaryotes,the CAPS marker is codominant,which can distinguish between homozygous genotypes and heterozygous genotypes;
(3) The amount of DNA required is small,and the concentration of DNA is not critical;
(4) The primers used are longer,the amplification results are more stable,and the step of membrane transfer in RFLP analysis is avoided,and the accuracy of RFLP analysis can be maintained;
(5) The operation is simple,fast and highly automated.

Although the CAPS marker has many advantages,because it must use a restriction enzyme,the screening of a suitable enzyme combination is labor-intensive,and the number of mutant cleavage sites has been found to be limited,which limits its large-scale development and application.


2. Biochemical buffer——N-Cyclohexyl-3-aminopropanesulfonic acid
The molecular formula of CAPS is C9H19NO3S,pKa value is 10.4 at 25°C,buffer range is 9.7~11.1. Although CAPS is not introduced by Good et al.,it is also called as Good’s Buffer sometime. Its application areas are as follows:
(1) Used as a transfer buffer for diffusion blotting and electroblotting;
(2) Binding buffer and eluent in cation exchange chromatography;
(3) Running buffer in capillary electrophoresis;
(4) Effective crystallization solution for various proteins;
(5) enzyme assay buffer
(6) Support alkaline phosphatase activity and inhibit the growth of Aeromonas spp. at pH 10.5;
(7) suitable for use with the Bicinchoninic Acid (BCA) Assay.
The recipe of CAPS buffer,50X:

Dissolve 111 g of CAPS (3-[Cyclohexylamino]-1-propanesulfonic acid) in H2O,and adjust the pH to 10.5 with NaOH. Raise the final volume to 1 liter with H2O. The final concentration will be 500 mM CAPS.


Edited by Suzhou Yacoo Science Co.,Ltd.
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