Primer Design for RNA/DNA amplification (Bioinformatics S9E1)
Channel: Danny Arends
Date: 2021-12-27

Answers to lecture 8 and introduction into Computer Aided Primer Design for polymerase chain reaction (PCR) amplification of RNA/DNA. The lecture starts at 26:44

Lectures @ https://dannyarends.nl/bioinformatik/
Programming Assignments and Answers @ https://dannyarends.nl/bioinfo/
Playlist: https://www.youtube.com/playlist?list=PLhR2Go-lh6X5A5WbiO3SPHuoWbwpNznUl

Chapters:
00:00 Welcome and Overview of the lecture
01:34 Answers to the assignments of lecture 8 - QTL mapping
02:20 Overview of the data Genotypes and Phenotypes
04:41 First things first, loading the data into R
07:48 Quick quality check (QC): Missing data per marker and per individual
14:00 Mapping quantitative traits using means and T-tests in R
25:04 Overview of the lecture and Viewer Drawing
26:44 Start of the Polymerase Chain Reaction (PCR) lecture - History
34:38 What do we need for Polymerase Chain Reaction (PCR)
37:05 Cycle step 1: Denaturation of template DNA (~90°C)
38:06 Cycle step 2: Annealing of forward and reverse primers to the template DNA (~54°C)
38:42 Cycle step 3: Extension of the DNA by the heat stable polymerase  (~72°C)
40:05 Exponential amplification in each Polymerase Chain Reaction (PCR) cycle
41:09 The first few PCR cycles in detail, less products than expected
42:56 Overview - What makes a good DNA primer ?
45:58 Primer design rule 1 - Primer should be unique
47:47 Primer length and it's impact on annealing temperature
49:16 Primer design rule 2 - Primer base pair composition
50:51 Annealing temperature and melting temperature of primers
54:52 Primer design rule 3 - Prevent secondary structures in or between primers
57:23 Primer design rule 4 - Primers work in pairs, ensure PCR suitability for both
58:15 Overview of primer design considerations and criteria

This is a live-stream recording of the MSc and PhD lecture series: Bioinformatics for plant and animal sciences, given digitally during the Covid19 pandemic at the Humboldt University in Berlin organized and lectured by Dr Danny Arends.

Thanks for taking an interest in my channel 😄If you've made it this far down, support me by giving a like or subscribing. Join me during my live streams Thursday afternoons on Twitch @ https://www.twitch.tv/dannyarends

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