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Gene deserts
Regions of >1 Mb that have no identifiable genes 3% of human genome is comprised of gene deserts
Do they exist simply because the genes are hard to identify (e.g. big genes)?
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1. 2. 3. 4. 5. 6.
Restriction enzymes
Gel electrophoresis Molecular cloning: isolate, amplify and purify fragments
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Characterizing DNA molecules through analysis of their sequences, not through a phenotype
1. 2. 3. 4. 5.
Where do we begin
1.
A genomic library
Ligate
Transform
2.
A cDNA library
DNA copied from all of the RNA transcripts in the tissue/cell of interest
Genomic libraries
Complete genomic library
Collection of clones that contain one copy of every sequence in the entire genome
Genomic equivalent number of clones in a perfect library To determine number of clones needed, divide the length of the genome by the average size of insert fragments
Clones from a genomic library with 20 kb inserts that are homologous to this region
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Converting RNA transcripts to cDNA: Obtaining mRNA from red blood cell precursors
Eukaryotic mRNAs have poly A tails at 3 end
mRNAs purified by affinity to oligo(dT) single strand DNA fragments of 20 nucleotides made of dT only
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Creating the second DNA strand complementary to the first cDNA strand
mRNA digested with RNAse 3 end of cDNA folds back and acts as a primer for 2nd strand synthesis In the presence of dNTPs and DNA polymerase, the first cDNA strand acts as a template for synthesis of the second cDNA strand Double-stranded cDNA can be cloned into a plasmid
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Fig. 9.8c, d
Recognition sites for restriction enzymes are usually 4 8 bp of double-strand DNA (see Table 9.1)
Often palindromic base sequences of each strand are identical when read 5'-to-3' Each enzyme cuts at same place relative to its specific recognition sequence (Figure 9.2)
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Restriction enzymes produce restriction fragments with either blunt or sticky ends
Blunt ends cuts are straight through both DNA strands at the line of symmetry Sticky ends cuts are displaced equally on either side of line of symmetry Ends have either 5' overhangs or 3' overhangs
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6-base recognition site occurs every 46 bp, average restriction fragment size is 4100 bp (4.1 kb)
3 billion bp genome/4100 = 700,000 fragments
8-base recognition site occurs every 48 bp, average restriction fragment size is 65,500 bp (65.5 kb)
3 billion bp genome/65,500 = 46,000 fragments
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Determine size of unknown fragments by comparison to migration of DNA markers of known size
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(c) Use process of elimination to derive the only possible arrangement that accounts for all the observed fragments
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Genomes of animals, plants, and microorganisms are too large to analyze using simple techniques such as gel electrophoresis and restriction mapping Cloning is a means to purify a specific DNA fragment away from all other fragments, and make many identical copies of the fragment The cloned fragment can then be analyzed by restriction mapping and DNA sequencing
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Polymerase chain reaction Purification and amplification of previously sequenced genomic regions
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Reverse translation generating a degenerate DNA sequence that contains all possible codons for a specific amino acid sequence
Fig. 9.10b
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Southern blots allow visualization of rare DNA fragments in complex samples (cont)
DNA is transferred from gel to nitrocellulose membrane by blotting DNA fragments on the membrane (blot) are in the same migration pattern as in the gel
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Southern blots allow visualization of rare DNA fragments in complex samples (cont)
After electrophoresis, gel is treated with NaOH to denature the transferred DNA and the blot is treated with uv and high temperature to attach single-stranded DNA
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Southern blots allow visualization of rare DNA fragments in complex samples (cont)
After hybridization of probe to the blot, autoradiography reveals fragments in restriction digests that have sequences complementary to the probe
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Two oligonucleotide primers (16 26 nt) are needed for PCR reactions
Region between the two primers will be synthesized
One primer is complementary to one strand of DNA at one end of the target region
The other primer is complementary to the other strand of DNA at the other end of the target region
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PCR consists of repeated cycles of DNA synthesis, with three steps in each cycle
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PCR Videos
http://www.youtube.com/watch?v=eEcy9k_KsDI&feature=player_embedded
http://www.youtube.com/watch?v=HMC7c2T8fVk&feature=player_embedded
http://www.youtube.com/watch?v=ZmqqRPISg0g&feature=player_embedded
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All four ddNTP reactions are run together in a single lane on a gel
After electrophoresis, fragments flow through a fluorescence detector and the color of the fragment is digitally recorded
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Each lane displays the sequence obtained from a separate DNA sample and primer Each fragment has terminated with a specific ddNTP labeled with a specific fluorescence
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RefSeq species reference genome sequence, a single, complete, annotated version of the species genome
Is not from one individual, but is a composite from several individuals
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Computerized analysis of chip hybridizations can be used to compare mRNA expression in two types of cells
Thousands of genes can be simultaneously analyzed
In this example, genes whose expression was altered by treatment with an experimental cancer drug were identified using a DNA chip
Visualizing genes of the human RefSeq genome with the UCSC Genome Browser
Fig. 9.16a
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A gene desert
Fig. 9.16b
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Fig. 9.16c
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Homologous sequences in two species that show evidence of being derived from a common ancestor
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An oligonucleotide array
DNA arrays have thousands of fragments of known nucleotide sequence spotted at precise locations on a solid support Arrays can be hybridized with fluorescent or radioactive DNA or RNA probes
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Used to interrogate target samples for SNPs or gene expression Can analyze >106 SNPs a day
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