PCR Primer Design A to Z by Using NCBI Primer Blast | Bangla Tutorial | Dawn of Bioinformatics

Primers are short oligonucleotides that are important in DNA replication in living cells and also in PCR techniques in molecular biology. PCR has 3 basic steps - denaturation, annealing and extension. Primers are needed in the annealing step. They bind with the template DNA and help Taq polymerase to amplify the strand. The main property of primers is that they must correspond to sequences on the template molecule (must be complementary to template strand). The Criteria for a good primer include the followings -
• Length of 18-24 bases, sometimes 18-30 bases
• 40-60% G/C content
• Start and end with 1-2 G/C pairs
• The presence of G or C bases within the last five bases from the 3' end of primers (GC clamp) helps promote specific binding at the 3' end due to the stronger bonding of G and C bases. More than 3 G's or C's should be avoided in the last 5 bases at the 3' end of the primer .
• Melting temperature (Tm) of 55-65°C, sometimes 55-70°C is also considered
• Primer pairs should have a Tm within 5°C of each other
• Avoid intra-primer homology (more than 3 bases that complement within the primer) or inter-primer homology (forward and reverse primers having complementary sequences). These circumstances can lead to self-dimers or primer-dimers instead of annealing to the desired DNA sequences.
• Try to avoid runs of 4 or more of one base, or dinucleotide repeats (for example, ACCCC or ATATATAT).
• Try to avoid regions of secondary structure and have a balanced distribution of GC-rich and AT-rich domains.
• If you are using the primers for mutagenesis, try to have the mismatched bases towards the middle of the primer.
Link: www.ncbi.nlm.n...
Link2: insilico.ehu.es...

[@saddam_M]

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[@dawn_of_bioinformatics]

Thank you so much...asa kori new video khub tara tari e asbe..😊😊

[@bdsinfohub]

ধন্যবাদ দাদা প্রথমবার এইরকম ভালো লেকচার শুনলাম bioinformatics এ বাংলায়। Subscribe করলাম 🙏🏽

[@dawn_of_bioinformatics]

Thank you so much ❤️🙂

[@kironsheikh3901]

Thanks vaiya. Onek din theke erokom lecture khujchilm. Next a erokom aro video cai. Best Wishes for you❤️

[@dawn_of_bioinformatics]

Thank you so much...😊

[@mehedihasan-cu4uc]

Thank you vaiya,, I am student of final year undergraduate of Biochemistry and Molecular Biology at BSMRSTU. This video is very informative to me when I was learned PCR . I have benefited to watch your video.

[@dawn_of_bioinformatics]

Most welcome brother... 😍😍😍

[@shamimsnutritionlab]

Great lecture

[@dawn_of_bioinformatics]

😍😍😍😍

[@rameshbabu5347]

Thanks lot sir, very wonderful .

[@dawn_of_bioinformatics]

Welcome 🤗

[@lovetolearn1200]

ভাইয়া অনেক ইনফরমেটিভ ভিডিও, ধন্যবাদ ❤️🖤

[@dawn_of_bioinformatics]

😍😍

[@nazmunnahar2100]

Thank you so much

[@dawn_of_bioinformatics]

😍😍

[@mohaiminurrahman2763]

Thank you vaiya❤

[@dawn_of_bioinformatics]

Welcome 🤗

[@maksudulislamtonu2876]

Hey, just wanted to tell you how helpful this was. Thank you.

[@dawn_of_bioinformatics]

Welcome... 😊😊

[@ashikurrahman3307]

Simple and effective ....🙂

[@dawn_of_bioinformatics]

😊

[@aponpaul3892]

Thanks a lot bhaiya

[@dawn_of_bioinformatics]

Welcome..🙂

[@debabanighosh4950]

So good videos Bhai, if possible make some videos on machine learning, Python, R and in detail metagenomics data analysis in such a simple manner. Wishing you all good. Thanks.

[@dawn_of_bioinformatics]

Thank you 😊

[@minhaz7074]

DNA sequence theke gene bank accession number kivabe nite hoy. DNA sequence submit kore accession number neowar procedure

[@dawn_of_bioinformatics]

Eta bistarito vabe bolte hobe vaya

[@minhaz7074]

@@dawn_of_bioinformatics vaiya video banayen eta niye

[@anuradhapatil1114]

How to validate the MSP Primers before ordering them and can we do the 5 gene methylation in a single tube? can anyone explain about how to carry out?

[@dawn_of_bioinformatics]

🙂🙂🙂

[@souravroy9705]

Bhaiya apni length kibhabe pelen mne gene tar length

[@dawn_of_bioinformatics]

Eta to select kora jay download korar time e

[@eigahiga1919]

Please make a video on eukaryotic gene primer design

[@dawn_of_bioinformatics]

Ok I'll try

[@johoraislam3235]

How can I design RAPD primer?

[@dawn_of_bioinformatics]

It’s little bit complex

[@raselkhan1384]

can you help me designing primer for a particular SNP analysis? amplifying an area that contains a particular SNP?

[@dawn_of_bioinformatics]

Ok.. I'll make a video on it..

[@rameshbabu5347]

I also SNP

[@sadiasuha3356]

thank you vaiya ❤❤

[@dawn_of_bioinformatics]

Welcome ❤️❤️