Hi Dr.

Article Designing, optimization and validation of tetra-primer ARMS ...

BR

Hi Dr. see the link below

http://primer1.soton.ac.uk/primer1.html

Article Designing, optimization and validation of tetra-primer ARMS ...

https://youtu.be/mPqgd82CvsU

Hi Dear

I agree with Dr sadi

Follow

Hi Dr.

https://www.researchgate.net/publication/263427189_Designing_optimization_and_validation_of_tetra-primer_ARMS_PCR_protocol_for_genotyping_mutations_in_caprine_Fec_genes

As a general rule for ARMS primer design, if the 3' terminal mismatch is a weak one, a strong secondary mismatch is engineered. If it is a strong one, a weak secondary mismatch is introduced. Try putting the mismatch at the second nucleotide in the first instance and test the primer for specificity and generation of product. The position of the mismatch can be altered if the primer does not work, or the strength of the mismatch increased if non-specific bands are observed. According to Little in Current Protocols in Human Genetics (28), the strength of mismatch pairings are; maximum, GA, CT, TT; strong, CC; medium, AA, GG; Weak, CA, GT; none, AT, GC

Follow

Agree with previous answers

https://www.google.com/url?sa=t&source=web&rct=j&url=https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5811069/&ved=2ahUKEwiXv9OPlqTqAhUmsKQKHWdGDKkQFjALegQIAhAB&usg=AOvVaw1cpf92EoHaIFaMDGAG7MIQ

ARMS primer design

General principles of designing a PCR primer as discussed in chapter 3 also apply to the ARMS primers. The ARMS PCR requires a pair of primers including a common and an ARMS primer. The common primer is like any other PCR primer. But the ARMS primer has the following special features:

1. The primer is usually 30 bases in length.

2. The nucleotide at the 3’ end of the primer should be complementary to the target nucleotide i.e. G for C or C for G and T for A or A for T. Mismatch at this position can dramatically reduce the amplification. A:G, G:A, and C:C mismatches have the worst effect whereas the other mismatches have varying degrees of effect. For example in a mutation with A-T substitution the ARMS primer for the mutant allele should have the last nucleotide complementary to the nucleotide T i.e. it should have A. The primer for the normal allele at the same position should be complementary to the nucleotide A i.e. it should have T (Fig. 7.1).

3. An additional mismatch at one of the last five nucleotides of the ARMS primer further increases its specificity.

4. It is customary to include an internal PCR control in ARMS reactions. A pair of primers is designed to amplify a region of the gene of interest that usually is free of mutations. An amplification of the internal control region and no amplification by the ARMS primer indicate a true negative. In a false negative result neither the ARMS primer nor the internal control shows any amplification. There could be several reasons for the false negative result e.g. too little or too much DNA, poor

quality of DNA template, failure to add primer, Taq, or other reagents and presence of PCR inhibitors.

5. The sensitivity and specificity of an ARMS reaction can be controlled by stringent reaction conditions. Good primer design, higher annealing temperature and limited number of cycles are important in avoiding false results. The number of cycles should be just enough to give a clear positive result. Increasing the number of cycles un-necessarily can cause false positives. The usual length of ARMS primer is 30 bases. Primers of this length have a high Tm and annealing temperature and are therefore more specific.

http://grcpk.com/wp-content/uploads/2014/10/7.-ARMS.pdf

Follow

https://www.researchgate.net/publication/263427189_Designing_optimization_and_validation_of_tetra-primer_ARMS_PCR_protocol_for_genotyping_mutations_in_caprine_Fec_genes

Ayser Ashour ,

Thanks a lot for your comment and contributions.

Hadaf Kadhim ,

Thanks a lot for your contributions.

Ahmed Abdulkareem Almuteari ,

Thanks a lot for your comment and contributions.

Alaa Shahid Jassim Al-Bdery ,

Thanks a lot for your comment and contributions.

Rana A. Ghaleb ,

Thanks a lot for your comment and contributions.

Batool Shakir Abed Almjalawi ,

Thanks a lot for your comment and contributions.

Hiba J. Hamza ,

Thanks a lot for your comment and contributions.

Rahem Alziadi ,

Thanks a lot for your comment and contributions.

Basim Mohammed Hanon ,

Thanks a lot for your comment and contributions.

Fatima Malik Abood ,

Thanks a lot for your comment and contributions.

Saade Abdalkareem Jasim ,

Thanks a lot for your comment and contributions.

Lubna Abdulazeem ,

Thanks a lot for your comment and contributions.

Follow

Look to links on ARMS-PCR

https://www.researchgate.net/publication/272076871_Modified_Tetra-Primer_ARMS_PCR_as_a_Single-Nucleotide_Polymorphism_Genotyping_Tool

Designing tool: http://primer1.soton.ac.uk/primer1.html

Article Modified Tetra-Primer ARMS PCR as a Single-Nucleotide Polymer...

https://www.researchgate.net/deref/https%3A%2F%2Fyoutu.be%2FmPqgd82CvsU

Taisir Abdulelah Kadhim ,

Thank you very much for your contributions.

Isam Alkhalifawi ,

Thank you very much for your contributions.

Hazim A. N. Alhadrawi ,

Thank you very much for your contributions.

Follow

Marwa A. Al-Asady ,

Thank you very much for your contributions.

Hello dear dr

I agree with dr.Lubna

Follow

file:///C:/Users/DRHASA~1/AppData/Local/Temp/FecBMetaGene.pdf

https://www.thermofisher.com/iq/en/home/life-science/oligonucleotides-primers-probes-genes/custom-dna-oligos/oligo-technical-resources.html?gclid=CjwKCAjw_-D3BRBIEiwAjVMy7FabwQSGE60K6BS6hmcO1yB5sxu9j7ShJYw9JuGozWU0u08fysE09hoCfh4QAvD_BwE&s_kwcid=AL!3652!3!264260522316!p!!g!!how%20to%20design%20a%20primer&ef_id=CjwKCAjw_-D3BRBIEiwAjVMy7FabwQSGE60K6BS6hmcO1yB5sxu9j7ShJYw9JuGozWU0u08fysE09hoCfh4QAvD_BwE:G:s&s_kwcid=AL!3652!3!264260522316!p!!g!!how%20to%20design%20a%20primer&cid=bid_mol_pch_r01_co_cp1358_pjt0000_bid00000_0se_gaw_ta_awa_awa

Hi

https://www.googleadservices.com/pagead/aclk?sa=L&ai=DChcSEwj3rOrPg6XqAhUC4O0KHRfQBGYYABAAGgJkZw&ohost=www.google.com&cid=CAESQeD2AwSniuZ7-EAyc2FkFnHFvn5TOkigwxX294T5Oyku18n_jL9uKcliUYPQPioUqEBYptEhSwB8AFD-2FebzvQG&sig=AOD64_2fNwRvKccYptbjoTJFc1HZ9EEsUw&q&adurl&ved=2ahUKEwi8quLPg6XqAhWKRBUIHdGLCywQ0Qx6BAgPEAE

Follow

I agree with Dr. Hiba

https://www.researchgate.net/deref/https%3A%2F%2Fyoutu.be%2FmPqgd82CvsU

Follow

Article Designing, optimization and validation of tetra-primer ARMS ...

https://www.researchgate.net/deref/https%3A%2F%2Fwww.thermofisher.com%2Fiq%2Fen%2Fhome%2Flife-science%2Foligonucleotides-primers-probes-genes%2Fcustom-dna-oligos%2Foligo-technical-resources.html%3Fgclid%3DCjwKCAjw_-D3BRBIEiwAjVMy7FabwQSGE60K6BS6hmcO1yB5sxu9j7ShJYw9JuGozWU0u08fysE09hoCfh4QAvD_BwE%26s_kwcid%3DAL!3652!3!264260522316!p

Yazi Abdullah Jassim ,

Thank you very much for your contributions.

Gunel T. Imanova ,

Thank you very much for your contributions.

Shaimaa Obaid Hasson ,

Thank you very much for your contributions.

Salim Hussein Hassan ,

Thank you very much for your contributions.

Saad Abd Al-Aziz ,

Thank you very much for your contributions.

Samah Ahmed Kadhum Al-jebory ,

Thank you very much for your contributions.

Rand Jabbar ,

Thank you very much for your contributions.

Alyaa Saad ,

Thank you very much for your contributions.

Hasanain Shareef ,

Thank you very much for your contributions.

Nada Khazal K. Hindi ,

Thank you very much for your contributions.

Assist.Prof.Dr. Mays Hadi Jebur ,

Thank you very much for your contributions.

Follow

Article Designing, optimization and validation of tetra-primer ARMS ...

Article Designing, optimization and validation of tetra-primer ARMS ...

Rasha Hadi Saleh ,

Thank you very much for your contributions.

Designing, optimization and validation of tetra-primer ARMS PCR protocol for genotyping mutations in caprine Fec genes

Huda Hadi Al-Hasnawy ,

Thank you very much for your contributions.

Hello dr

Follow

Nada Khazal K. Hindi و

Thank you very much for your contributions.

Dear Dr.

https://www.youtube.com/watch?v=mPqgd82CvsU

Article Designing, optimization and validation of tetra-primer ARMS ...

http://helix.wustl.edu/dcaps/dcaps.html  to design primers

https://www.researchgate.net/publication/272076871_Modified_Tetra-Primer_ARMS_PCR_as_a_Single-Nucleotide_Polymorphism_Genotyping_Tool

Designing tool : http://primer1.soton.ac.uk/primer1.html

Article Modified Tetra-Primer ARMS PCR as a Single-Nucleotide Polymo...

Ali Hussein Al-Marzoqi ,

Thank you very much for your contributions.

Follow

Dear Rana H. Raheema ,

Thank you very much for your contributions

https://www.researchgate.net/deref/https%3A%2F%2Fwww.youtube.com%2Fwatch%3Fv%3DmPqgd82CvsU

Dear Mayada Darweesh ,

Thank you very much for your contributions .

https://www.youtube.com/watch?v=mPqgd82CvsU

Fadyia Mahdi Alameedy ,

Thank you very much for your contributions .

In ARMS-PCR, 2 pairs of primers in a single PCR tube, can simultaneously amplify both mutant and normal alleles as well as allow amplification of an internal DNA control. This technique has been applied to study different mutations. tetra-primer PCR in which allele-specific amplification is achieved in a single PCR reaction using two outer primers and two allele-specific inner primers. combined tetra-primer PCR with ARMS to form the tetra-primer ARMS-PCR or T-ARMS technique by introducing deliberate mismatches at position − 2 from the 3′ end of inner primers to improve allele specificity. In a single step reaction, the outer primers amplify a large fragment of the target gene, irrespective of its genotype although each inner primer combines with a particular opposite outer primer to generate smaller allele-specific amplicons, which are of different sizes and can easily be discriminated on gel electrophoresis either as homozygous or heterozygous.

link: Article Designing, optimization and validation of tetra-primer ARMS ...

I have designed the primer by

ARMS PCR Primers were designed using Primer1(http://primer1.soton.ac.uk/primer1.html) only Inner forward and inner reverse primers were selected for allele specificity. For reference

Follow

Dear Roma Lal,

Thank you very much for your contributions

Dear Taisir Abdulelah Kadhim ,

Thank you very much for your contributions