fragmenting genomic dna for cloning –random methods are best mechanical shearing: sonication,...
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Fragmenting genomic DNA for cloning
– Random methods are best•Mechanical shearing: sonication,
nebulizer•Nuclease treatment (usually restriction
digest): 4 base cutters, partial digest
– Large fragments better than small, fewer clones to get coverage of large genome
Random fragmentation of genomic DNA:
Hydrodynamic shear (physical breakage)-- sonication (vibrating metal probe)-- nebulization (like asthma inhalers)-- passage through small needle orifice
DNA must be repaired with DNA polymerase after these treatments
Enzymatic breakage-- Restriction enzyme (4 cutter, partial
digest)CviJ (pyGCpy and puGCpu)
-- DNAse I (semi-random cleavage)
Partial digest
Size fractionate
Block EcoRI sites
Add linkers
Digest with EcoRI
Ligate to lambda
Package
Early library
construction
Improved library
construction
Partial digest: Sau3A (BamHI compatible ends
Phosphatase
Ligate to lambda
Package
Improved lambdas for libraries• More restriction sites
• Sequences for phage RNA polymerase transcription (useful for probe synthesis)
But….
• Cosmids• BACs• PACs• YACs
…can be used for cloning larger DNAs using similar methods…
Why use lambda libraries?
• Cosmids replicate as high copy number plasmids--tend to be unstable, deleting insert DNA (to reduce drag on cells)
• BAC and YAC libraries difficult to prepare
• larger-sized DNA more difficult to work with
Cloning cDNAs
• Prepared by reverse transcription of mRNA
• Eukaryotic mRNAs--lack introns, often show variable splicing, cDNAs of these RNAs indicate how genes are actually expressed
• Individual mRNA abundance varies widely: to isolate low abundance mRNAs by cDNA cloning, need to make libraries
Key points of cDNA cloning
1) mRNA source (tissue type) matters a lot
2) mRNA must be of high quality (no Rnases….)
3) Rare mRNAs can be enriched
e.g. “Subtractive cloning”hybridize sample cDNA against immobilized RNA/cDNA from a “driver”, clone only those mRNAs that are not bound by the driver
This relies on differential mRNA expression between sample and “driver” mRNA populations
Gubler/Hoffman method (MC Chapter 11)
1) Synthesize first strand cDNA
2) Second strand cDNA
3) Methylate cDNA
4) Attach linkers or adaptors for cloning
5) Fractionate cDNA by size (select 2-8 kb)
6) Ligate cDNA into bacteriophage arms
cDNA synthesis
• Make the first DNA strand from the mRNA template using reverse transcriptase
• Remove the RNA
• Make the second DNA strand from the first DNA strand
Primers for “first strand” cDNA synthesis
1) Oligo dT (binds polyA tails)
2) Oligo dT with adaptors (restriction sites)
3) Primers linked to a plasmid
4) Random primers
But many cDNAs are not full-length--how get only full-length
cDNAs?Utilize the 5’ CAP structure on eukaryotic mRNAs:
ESTs: Expressed Sequence Tags
• Full length cDNAs hard to get, difficult to scale up
• But short cDNA sequences are often useful– ID and map specific genes– “High throughput” allows very fast
generation of 200-300 bp sequences, or ESTs
• Millions of ESTs in database• Useful in designing “microarrays” (later)
cDNA libraries: the easy way out
Pre-made cDNA libraries (organisms, tissues, variable conditions
Custom made cDNA libraries (you supply the mRNA)
“kits” for making your own cDNA library
(See Table 11-6 of Molecular Cloning for a directory)
Library construction
1) DNA (entire genome…)a) Fragment the DNAb) Clone in lambda phage vector
2) mRNA (only the expressed genes)a) First strand cDNAb) Second strand cDNAc) Expressed sequence tags (ESTs)
Screening libraries for specific genes
(finding the needle in the haystack)
I. Isolating individual clonesII. Screening by sequence
A. HybridizationB. PCR
III. Screening by protein structure/biological function
IV. Gene identification--diseases
Course reading #29
Improved library
construction
Partial digest: Sau3A (BamHI compatible ends)
Phosphatase
Ligate to lambda
Package
You want to clone a gene from the human genome…
So you follow the protocol for
Or…buy a kit/premade library…
Basic “lytic” phage life cycle
Lawn of E. coli
100’s to 1000’s of plaques (individual phage infections)
But…which lambda clone (plaque) has the gene of interest????
How many recombinant DNA molecules are required in a library to get complete coverage of a genome?
N = ln(1-p)
ln(1-f)
p = probability of getting a specific piece of DNA
f = fractional size of clone DNA relative to genome
N = number of clones needed
N = ln(1 - 0.99)
ln[1 - (1.7 x 104 / 3 x 109)]
p = probability of getting a specific piece of DNA = 99%f = fractional size of clone DNA relative to genome = 17000 base pairs (lambda capacity) / 3 x 10 9)
N = number of clones needed = 810,000
N = ln(1 - p)
ln(1 - f)
= 810,000
cDNA cloning: this calculation is harder…
Screen by hybridization
Very fast
Applicable to a large number of clones
Can identify clones that are not full length
But you need to know at least some of the sequence of the gene you are after (more on this later)
1) Known sequences: eg. previously cloned cDNA to locate position in genome (identical match exists in library--stringent hybridization conditions)
2) Probes for non-identical but related sequences: finding a related gene in another species (non-identical match--reduce stringency of hybridization)
3) Probing for a gene from a sequenced protein: eg.
his-phe-pro-phe-met
4) Screen by PCR
Design of nucleic acid probes
make synthetic “mixed probe” (typically 16-mers)
“guessmers”: long, degenerate oligo probes
• 40-60 nts, alternative to short, “mixed probe”• Codon uncertainty mostly ignored
– Most common codon used– Increased length improves specificity
• Inosine substitutions at uncertain positions– Inosine pairs with all 4 bases
• Low stringency hybridizations
“Colony hybridization” for ID of clones(like Southern blotting but without DNA isolation/gel electrophoresis)
Plaque-lift hybridization--using a lambda library
Can do this multiple times (replicate experiments)
Alternative to plating: arrayed libraries
• Individual clones of library spotted onto membranes in high density arrays (tens of thousands of genes)
• Membranes probed as described (a la microarrays)
• Standardizable, centralizable
Using genomic DNA libraries for mapping: Chromosome “walking”
• Prior to sequencing
• It is possible to determine the order of clones in a contiguous sequence (contig)
• Genes whose general location is known (by genetic mapping), but whose function is not known, can be found by starting with the genetic marker clone and “walking” away from it
Chromosome walking: how are individual clones in a genomic library positioned relative to each
other?
The data The genome “assembly”
• Probing can be restricted to one direction with RNA probes generated from clone ends
• Beware of “warping” to another chromosome because of repetitive sequence probes
• Use YAC and BAC libraries to take larger steps
Chromosome walking
Improved lambdas for libraries• More restriction sites
• Sequences for phage RNA polymerase transcription (useful for probe synthesis)
Expression libraries--alternative to hybridization
• Gene product (protein) is made (by E. coli) and detected by variety of methods
• Eukaryotic genes: cDNA library is essential (no introns, gene size small)
Screening:• Immunological• Functional
Detect antibody with secondary antibody conjugated to reporter enzyme for visualization
The plaque lift: kind of like a Western blot
Functional cloning
• Genetic complementation:– Cloned DNA sequence corrects defect in
host strain• Gain of function
– Cloned DNA confers new function to host
Both of these require cloned DNA to be transcribed, translated into functional protein in host (eukaryotic protein in E. coli could cause problems)
And you need a good assay for expression!
Functional complementation: shaker gene
Shaker-2 mice have defects in the inner ear, poor balance, and deafness
The shaker 2 gene encodes myosin XVMutations in the human homolog can cause deafness
Subtractive cloning– Remove cDNAs that are common to two
sources– Useful for isolation and detections of
differentially expressed rare cDNAs
– Example: differential expression from physiological change
– “driver” DNA - immobilized– “test” cDNA (single stranded): labelled and
then annealed to driver DNA– Remaining DNA has no counterpart in the
driver cells--probe library to locate genes– Or use the remaining DNA to probe a
microarray