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Brand of science/technology which deals with study of genomes (including molecular characterization and production of proteins, role in health and ease and effects of manipulation of these systems by agents



Procedures for finding exact order of nucleotides in DNA strand


Sequencing of virus genome

Sequenced virus first because of small genome
Sanger found genome of MS2 and phi-X174 phage


First cellular genome

Done on H. Influenzae
E. Coli popular bacteria but genome was twice as big
Started to understand protein and regulations from sequence


PLUS and MINUS method:

First method and required comparison of both + and - seq to find actual strand
Only for ssDNA


Maxim and Gilbert Method

Series of complex reactions
More difficult than inhibitor method
Can used for dsDNA


Sanger et al method

Used idea of inhibitors that can terminate elongation of DNA at specific points.
Remains the standard today


Sanger Method

Method based on DNA polymerase dependent syntehsis of complementary DNA strand in presence of dNTPS and ddNTPs
Synthesis is terminated when ddNTP is randomly added
Used gel electrophoresis too read out order


Modern Automated DNA sequencing

Advances in fluorescence detection allowed combining the four terminators into 1 reaction, they are labeled with different colored fluorescent dyes
Throughput increase with advent of capillary arrays allowing many samples to be analyzed in parallel


"Shotgun-cloning" Method

DNA sheared in to random fragments and ligated into plasmids
Generate thousands of plasmids each with random fragment
Library of plasmid are put into E. Coli so that each can be purified for sequencing
Each colony has different fragment


"Shotgun-cloning" Method (2)

Plasmids are isolated
Determine 500-100bp of sequence
Possible using primers complementary to plasmid area flanking either end of insert
Sequence 1000s of plasmid and stitch them together using computers for full genome


Limitations to whole genome shotgun-cloning method

Cloning Bias: Some genes toxic to E. Coli, results in gaps in assembled sequence
Project maintenance issues: Grown different colonies of E. Coli which is difficult
Slow and Expensive: Most advanced Sanger yields <100Kb per run, Typical genome has 5 million bp



Real time sequencing
Reaction can be performed in liquid or with DNA attached to slide or bead
No electrophoresis - instead readout of light production measured by camera


Ingredients of Pyrosequencing

Primer annealed to template
Mix of 4 enzymes and 2 chemicals:
DNA polymerase: extend primer with nucleotides
ATP sulfurylase: convert PPi and APS to ATP
Luciferase: convert ATP and luciferin to light
Apyrase - degrades unused NTP after each addition round
APS- adenosine phosphosulfate


Genome sequencing in microfabricated high-density picolitre reactors

DNA fragmented and primers are ligated to both ends
DNA attached to tiny beads under condition where one DNA fragment binds to one bead
Beads immersed in oil-water droplets and PCR used to amplify strands.
PCR primers complementary to primers attached to ends
Oil isolated droplets enable PCR on each each bead in isolation


Genome sequencing in microfabricated high-density picolitre reactors (2)

Beads placed in micro wells
Pyro enzymes is added to little beads
Reaction mixture (dNTPSs and apyrase) flowed over each well
Carry out many parallel pyrosequencing with a High Res camera recording each reaction


454 Pyrosequencing

Sequence DNA straight from bacteria no cloning for plasmid
No chromatography step
Massively parallel


Illumina/Solexa Sequencing

Differs from 454 in 2 major ways
Uses Sanger-like reaction using dye labeled reversilbe terminator NTPS
Amplifies DNA fragments on a surface of flow cell rather than a bead


454 vs Ilumina

Both needs sheering DNA into small pieces
Both need adapters which have primers ligated to strand
454 uses small beads and ilumina uses clusters of DNA strands
All start at a single piece of DNA that is amplified
Gives off light. In 454 intensity of one nucleotide is recorded at 1 at a time
Ilumina gives off coloured light but is added at the same time
454 is one by one, ilumina is parallel


Sequencing: next-next gen

Nano-Knife technology rubs small conductive blades over immobilized ssDNA
Determines sequence based on specific size and conductive changes of each base
May even detect modifications like methylations and protein binding


Bioinformatics: Locating Putative Genes

Annotation of DNA: understanding what the sequence means
computers look for patterns like regulatory seq, open-reading frames, rDNA and tRNA
Annotating new genomes takes longer than sequencing