Recombinant DNA

Farid khan
Recombinant DNA
Cloning Technology
台大農藝系遺傳學 601 20000 Chapter 7 slide 1

DNA Cloning
1. The goal of molecular cloning is large amounts of pure
DNA that can be further manipulated and studied.
2. Summary of the procedure:
a. Isolate DNA from the organism.
b. Use restriction enzymes to cut the DNA, and ligate fragments
into a cloning vector.
c. Transform recombinant DNA into a host, which will replicate
the DNA (molecular cloning) and pass copies to all progeny.

Restriction Enzymes
1. Restriction endonucleases (restriction enzymes) each recognize a
specific DNA sequence (restriction site), and break a phosphodiester
linkage between a 3’ carbon and phosphate within that sequence.
2. Restriction enzymes are used to create DNA fragments for cloning, and
to analyze positions of restriction sites in cloned or genomic DNA.
3. Restriction enzymes are a bacterial defense against viral DNA.
Restriction sites in the bacterial chromosome are methylated, and thus
protected.
4. A restriction enzyme has a threeletter name derived from the genus
and species of the organism from which it was isolated; it is underlined
or italicized. Roman numerals and sometimes letters designating a
particular bacterial strain may follow.
5. Many restriction sites are palindromes of 4, 6 or 8base pairs, but
others are not completely symmetrical (Figure 7.1 and Table 7.1).

Fig. 7.1 Restriction site in DNA, showing symmetry of the sequence around the
center point

Peter J. Russell, iGenetics: Copyright © Pearson Education, Inc., publishing as Benjamin Cummings.
6. Based on probability, a specific short DNA sequence will
occur more frequently than longer one. In a 50% GC
organism with random distribution of bases, the
probability of a specific base at a given position is ¼, so
frequency of a partuclar restriction site is (¼)n, where n is
the number of the base pairs in the recognition sequence.
7. Some restriction enzymes produce blunt ends, where both
DNA strands are cut between the same base pairs. Others
create sticky (staggered) ends.
8. Sticky ends are useful in cloning, because complementary
sequences hydrogenbond (anneal) and are held together
so DNA ligase can covalently link them.
9. All copies of a DNA sequence will contain the same
restriction sites, and will be cut into identical fragments.

Fig. 7.2 Examples of how restriction enzymes cleave DNA

Fig. 7.3 Cleavage of DNA by the restriction enzyme EcoRI

Cloning Vectors and DNA Cloning
Animation: DNA Cloning in a Plasmid Vector
1. Several types of cloning vectors have been constructed, each with different molecular properties and
cloning capacity.
2. Plasmid cloning vectors are derived from natural plasmids, circles of dsDNA that include origin
sequences (ori) needed for replication in bacterial cells. An E. coli plasmid vector, for example,
must contain these features:
a. An ori sequence for replication.
b. A selectable marker, such as antibiotic resistance.
c. Unique restriction sites, so that a particular restriction enzyme cuts only once in the plasmid. A fragment of
insert DNA cut with the same enzyme is commonly inserted into the unique restriction site.
3. An example of a typical E. coli cloning vector is pUC19 (2,686bp). The pUC19 plasmid features:
a. High copy number in E. coli, with nearly a hundred copies per cell, provides a good yield of cloned DNA.
b. Its selectable marker is ampR.
c. It has a cluster of unique restriction sites, called the polylinker (multiple cloning site).
d. The polylinker is part of the lacZ (βgalactosidase) gene. The pUC19 plasmid will complement a lacZ E. coli,
allowing it to become lacZ+. When DNA is cloned into the polylinker, lacZ is disrupted, preventing
complementation from occurring.
e. Xgal, a chromogenic analog of lactose, turns blue whenβgalactosidase is present, and remains white in its
absence, so bluewhite screening can indicate which colonies contain recombinant plasmids (Figure 7.4).

Fig. 7.4 The plasmid cloning vector pUC19

4. DNA can be inserted into a cloning vector by restriction digestion and then ligation
(Figure 7.5).
a. Cut pUC19 (the vector plasmid) with a restriction enzyme that has a unique site in the
polylinker.
b. Cut the DNA to be cloned (insert DNA) with the same enzyme.
c. Mix insert DNA with pUC19 DNA and allow random joining of fragments to occur.
d. Resulting plasmids are transformed into E. coli either through chemical treatment of the cells
or by electroporation. The cells are grown on media plates containing ampicillin and Xgal.
e. Ampicillinresistant colonies result from pUC19 sequences. Blue colonies contain only the
vector with its ends rejoined, while white colonies often contain pUC19 with its lacZ gene
inactivated by insert DNA.
f. If the 5’phosphates of vector DNA are removed by alkaline phosphatase, DNA ligase will not
rejoin their ends, and fewer blue colonies will result.
5. Many plasmid cloning vectors are available, with features including different arrays of
unique restriction sites in the polylinker, and phage promoters (e.g., T7, T3, SP6) that
can be used to control transcription of the cloned DNA.
6. Plasmid cloning vectors are available for many prokaryotic and eukaryotic organisms. In
some cases the plasmids are unable to replicate, but are maintained because they
integrate into the genome.
7. Size of the insert DNA is limited in plasmid cloning vectors, and plasmids carrying more
than 5–10 kb are often unstable.
Fig. 7.5 Insertion of a piece of DNA into the plasmid cloning vector pUC19

Phage λ Cloning Vectors
• There are versions of bacteriophage λ (lamda) with sequences for
lysogeny removed, so that only lytic infection is possible.
• Restriction sites in the λ DNA separate required bacteriophage genes
in the chromosome arms from the nonessential sequences in the
central region. The λ chromosome central region is replaced with
insert DNA, using restriction digestion and DNA ligation.
• When ligated DNA is mixed with phage λ proteins, phage heads
assemble and DNA is packaged, forming virus paritcles.
• Only phage with both arms of phage λ chromosome and a properly
sized (3752kb) central insert sequence are able to replicate by
infected E. coli. Progeny phages include insert DNA in their
chromosomes, so do their progeny in the following rounds of
infection, providing quantities of the insert DNA.
• Many versions of phage cloning vectors are available, with features
including and expanded array of restriction sites, systems for
expressing cloned genes and for creating plasmid subclones of the
insert DNA. 台大農藝系遺傳學 601 20000 Chapter 7 slide 13
Fig. 7.6 Scheme for using phage λ DNA as a cloning vector

Cosmid cloning vectors
1. Cosmids are constructed vector with features from both
plasmids and phages. These features include:
• An E. coli ori sequence.
• A selectable marker such as ampR
• Convenient restriction sites.
• A phage cos site, allowing the DNA to be pakaged into a
phage head for introduction into E. coli.
• Cosmid as small as 5kb are available, and 3247kb of
DNA can be inserted into them. Recombinant cosmids
< 37kb or > 52 kb cannot be packaged, don’t enter E.
coli, and therefore are not replicated.

Fig. 7.7 Cosmid cloning vector

Shuttle Vectors
1. A cloning vector capable of replicating in two or
more types of organism (e.g., E. coli and yeast) is
called a shuttle vector. Shuttle vectors may
replicate autonomously in both hosts, or integrate
into the host genome

Yeast Artificial Chromosomes (YACs)
1. YAC vectors function as artificial chromosomes in yeast. Their
features include (Figure 7.8)
a. Linear structure with a yeast telomere (TEL) at each end.
b. A yeast centromere sequence (CEN).
c. A marker gene on each arm that is selectable in yeast. (e.g. TRP1 and
URA3)
d. A yeast origin of replication known as autonomous replicating
sequence (ARS).
e. Unique restriction sites for inserting foreign DNA.
2. Several hundred kb of insert DNA can be cloned in a YAC. YAC
clones are made by:
• generatingYAC arms by restriction digest.
• Ligating with insert fragments up to 500 kb inlength.
• Transforming into yeast.
• Selecting for markers (e.g. TRP1 and URA3)
Fig. 7.8 Example of a yeast artificial chromosome (YAC) cloning vector

Bacterial Artificial Chromosomes (BACs)
1. BACs are used for cloning fragments up to about 200 kb
in E .coli. BAC vectors contain:
a. the ori of an E. coli plasmid called the F factor.
b. A multiple cloning sites.
c. A selectable marker.
d. Other features, “bells and whistles.”
2. BAC can be handles like regular bacterial plasmids, but
the F factor ori keeps copy number at one BAC molecule
per cell.

• iActivity: Building A Better Beer?

Recombinant DNA Libraries
1. It is sometimes useful to have a genomic library, a
collection of clones containing at least one copy
of every DNA sequence in a genome. Genomic
libraries are available for many organisms.
2. Chromosome libraries are collections of cloned
fragments of individual chromosomes.
3. Complementary DNA (cDNA) libraries are
cloned collections of DNA copied from a cell’s
mRNA.

Genomic Libraries
1. A genomic library is used to isolate and study a cloned DNA
containing a sequence of interest. Genomic libraries of eukaryotic
DNA are constructed by digesting genomic DNA with a restriction
enzyme, and ligating into a vector that can accommodate the genome
in a manageable number of clones.
2. There are three general ways to produce genomic libraries:
a. Complete digestion with restriction enzyme, cleave at all relevant
restriction sites. This has drawback:
1) Genes containning one or more sites for the restriction enzyme
will be cloned into two or more pieces.
2) To screen the entire genome, a very large number of clones
would have to be examined, because insert DNA size is relative
small.
b. Longer DNA fragments can be generated with mechanical sheering
(e.g passage through a syringe needle) rather than restriction enzyme
cutting. A disadvantage is the absence of uniform ends, require
enzymatic modification before insertion into a clonning vector.
a. Partial digestion with a restriction enzyme is controlled so that it cuts
only some of the available sites. Ideally, this results in cloninng a
population of overlapping fragments representing the entire genome
(Figure 7.9)
• Partially digested DNA molecules in a certain size range are
selected by density gradient centrifugation or agarose gel
electrophoresis.
• DNA fragments with sticky ends from restriction digestion can
be cloned directly. Sometimes two enzymes with compatible
sticky ends are used (e.g. BamHI and Sau3A), creating a hybrid
recognition site.
• Genomic sequences are not equally represented in the libraries,
because:
a) Regions of DNA with relevant restriction sites very close
together or very far apart are removed at the size selection.
b) Some regions of eukaryotic DNA prevent vector replication
in E. coli, and so are eliminated from the library.
1. The number of clones needed for a complete library can be calculated
based on the size of the genome and the average size of DNA
inserted into the vector. In practice, a library should contain many
times more than the calculated minimum number of clones.
Fig. 7.9 Use of partial digestion with a restriction enzyme to produce DNA fragments
of appropriate size for constructing a genomic library

Chromosome libraries
1. Screening the genomic library of an organism
with a large genome is laborious. Screening time
can be reduced if a gene has been localized to a
chromosome, by examining a library made from
only that chromosome. Human, for example,
have 24 different chromosome libraries (22
autosomes, X and Y).
2. Separating chromosome so they may be
individually cloned is accomplished with
techniques such as flow cytometry.
cDNA Libraries
1. A cell’s mRNA molecules can be copied to make complementary DNA
strands (cDNA) and the cDNA can then be cloned, creating a library
representing only the genes being expressed in the cells at that time.
2. The cDNA derives only from mature mRNA. Introns are not present.
3. The poly(A) tail at the 3’ end of the mRNA is useful for:
a. Isolating mRNA from cell lysates by passage over an oligo(dT)
column.
i. The mRNA’s poly(A) tail sticks to the poly(T) attached to the
column substrate.
ii. Other molecules pass through the column, but mRNAs are
retained.
iii. mRNAs are eluted with decreasing ionic strength buffer, resulting
in significant purification.
b. Priming the synthesis of cDNA, by providing a known 5’ sequence.

4. Synthesis of cDNA involves these steps (Figure 7.10):
a. A short oligo(dT) primer is used. It anneals to the mRNA’s
poly(A) tail, allowing reverse transcriptase to synthesize cDNA.
This creates a DNAmRNA hybrid.
b. RNase H degrades the mRNA strand, creating small RNA
fragments that serve as primers.
c. DNA polymerase I makes new DNA fragments, and DNA ligase
connects the new DNA fragments to make a complete chain.
d. The resulting cDNA is a doublestranded copy of the starting
mRNA.

Fig. 7.10 The synthesis of complementary DNA (cDNA) from a polyadenylated mRNA

5. A method for cloning cDNA involves (Figure 7.11):
a. Introducing restriction site linkers to the ends of the cDNA by
blunt end ligation.
b. Digestion with the cognate restriction enzyme to create sticky
ends.
c. Mixing cDNA with vector DNA cut with the same restriction
enzyme in the presence of DNA ligase.
d. Transforming into an E. coli host for cloning.
6. If the cDNA has sites for the same restriction enzyme
used in the polylinker, the cDNA will be cloned in pieces.
The problem is avoided by using polylinkers engineered
with appropriate ssDNA overhangs (sticky ends) so that
restriction digestion is unnecessary.

Fig. 7.11 The cloning of cDNA using BamHI linkers

Finding a Specific Clone in a Library
1. A number of techniques have been developed for
identifying the clone of interest in a cDNA
library. Some are discussed here.

Screening a cDNA library
1. One way to select a cDNA clone from the library is to detect a protein
product it is producing (Figure 7.12).
2. For protein to be produced, an expression vector is needed, in which the
cloned cDNA is inserted between a promoter and a transcription
terminator.
3. Labeled antibodies are used to detect the specific protein in a host
colony. An array of colonies is transferred to a membrane fiter, cells
are lysed and their proteins bind to the filter, which is incubated with
the relevant antibody.
4. Radioactively labeled antibody bound to colonies is detected by an
autoradiogram, in which the dry fiter is placed on X ray film in the dark
for a number of hours. Colonies with antibody bound will be visible as
dark spots on the film.
5. Once identified, the cDNA can be used to:
a. Analyze the genome of the same or another organism for homologous
sequences.
b. Isolate the nuclear gene for the mRNA from a genomic library.
c. Quantify mRNA synthesized from the gene.
Fig. 7.12 Screening for specific cDNA plasmids in a cDNA library by using an antibody
probe

Screening a Genomic Library
1. Finding a specific clone in a plasmid or cosmid genomic library is
similar to screening a cDNA library (Figure 7.13).
a. E. coli cells are transformed with the genomic library, and plated on
selective medium.
b. Colonies produced are replica plated onto a membrane filter on a plate
of selective medium, and cells grow on the filter.
c. Cells are lysed, DNA is denatured and bound tightly to the filter.
d. Filter is incubated with the labeled single-stranded cDNA probe, which
forms hybrids with complementary DNA molecules bound to the filter.
e. Filter is washed and the label is detected by autoradiography for a
radioactive probe, or chemiluminescent or colorimetric assay for
nonradioactive labeling.
f. Clones detected by the probe are then further characterized.
.
Fig. 7.13 Using DNA probes to screen plasmid or cosmid genomic libraries for specific
DNA sequences

2. Screening X genomic libraries uses a slightly different screening
method (Figure 7.14):
a. Phage are plated on a bacterial lawn, producing plaques that each

contain a different cloned DNA sequence.
b. Free DNA in the plaques binds a membrane filter placed on the
surface of the plate (a plaque lift).
c. DNA on the filter is denatured in situ, exposed to labeled probe, and
detected as appropriate for the type of label.
d. A number of plaque lifts can be made from the same plate, and
screened with different probes.
e. Once detected, insert DNAs are usually subclonecl into plasmids for
further analysis.

Box Fig. 7.1 Random primer method of radioactively labeling DNA

Fig. 7.14 Screening a bacteriophage λ library for a specific gene clone

Identifying Genes in Libraries by
Complementation of Mutations
1. Well-defined mutants may be used to clone genes by complementalion,
in which cloned genes overcome a defect in the mutant.
2. To clone a yeast gene by complementation:
a. A genomic library is made from the wild-type yeast strain in a yeast-E.
coli shuttle vector.
b. The library is transformed into a yeast strain with two mutations, one to
allow selection of transformants, and the other a mutation in the gene
for which the wild-type genes sought The ARGJ gene is an example
(Figure 7.15).
c. Transformed yeast with the wild-type phenotype restored for the gene
sought are selected and their plasmid DNA further characterized.

Fig. 7.15 Example of cloning a gene by complementation of mutations: the cloning of
the yeast ARG1 gene

Identifying Specific DNA Sequences in Libraries
Using Heterologous Probes
1. It is possible to identify specific genes in a
genomic library using cloned equivalent genes
(heterologous probes) from other organisms,
especially if the gene is highly conserved or the
species are closely related.

Identifying Genes or cDNAs in Libraries
Using Oligonucleotide Probes
1. Synthetic oligonucleotides are useful in probing libraries, sequence data
are available for part of the gene of interest. Knowledge of substitutions
produced by mutation also aids probe selection. Sequences for many
genes are available in GenBank.
2. Using the universal genetic code, the amino acid sequence is used to
design a DNA oligonucleotide probe. Degeneracy in the genetic code
means that a mixture of oligonucleotides must be prepared, each of
which encodes the target protein.
3. The library is probed with the oligonucleotide mixture to detect the gene
of interest. This is a powerful (but not perfect) technique for isolating
specific clones.

Analysis of Genes and Gene Transcripts
1. Cloned DNA is used in many types of experiments. Some are described here:
a. Restriction sites may be mapped in the insert DNA. Maps are used for subcloning
and for comparing the gene with the cDNA.
b. Cloned DNA can be used as a probe to characterize transcription of the
corresponding gene in cells. This yields information about:
i. Size of the initial gene.
ii. Processing steps in mature mRNA production.
iii. The amount of gene transcript.
iv. Timing of expression in the cell cycle.
v.Patterns of expression in different tissues and/or during development.
c. The complete DNA sequence may be determined and compared with other DNA
sequences in a computer database in order to:
i. Examine similarity between related genes.
ii. Gain clues about the function of an uncharacterized gene.
iii. Predict the polypeptide encoded by a gene.
Restriction Enzyme Analysis of Cloned DNA
Sequences
1. Cloned DNA can be cut with restriction enzymes and electrophoresed on agarose gels and
visualized with ethidium bromide, in order to map its restriction sites (Figure 7.16 and
Figure 7.17).
2. The DNA is cut with several different enzymes, and each cut is loaded in a lane of an
agarose gel. Electrical current drives the negatively charged DNA fragments through the
gel. Small molecules move more quickly than large ones, so the fragments are separated
by size.
3. DNA is stained with ethidium bromide, which fluoresces under UV light when complexed
with DNA. The gel is photographed, and the distance migrated by each band of identical
DNA molecules is measured and compared with a calibration curve to determine the size
of each fragment.
4. An example of restriction site mapping is shown in Figure 13.9. A real restriction map is
more complex to generate, involving more restriction sites, and more sites for each
enzyme.
5. Restriction mapping may be done with a circular plasmid, a cloned sequence, or a
fragment of plasmid prepared by gel cutting.

Fig. 7.16 Constructing a restriction map for EcoRI and BamHI in a DNA fragment

Animation: Restriction Mapping

Restriction Enzyme Analysis of Genes in the
Genome
1. Knowing the location of restriction sites in a genome region of interest may be
useful for analyzing intron organization or cloning parts of a gene into a vector.
2. The restriction site map can be determined using cDNA or the same gene from a
related species as probe. The process is as follows:
a. Genomic DNA samples are cut with different restriction enzymes.
b. Each sample is electrophoresed in an agarose gel, and stained with ethidium
bromide. Genomic DNA produces a large variety of fragments, which appear as a
smear on the gel.
c. DNA is denatured to single strands, and Southern blotting transfers the DNA to a
membrane filter (Figure 7.18). The DNA fragments on the filter are arranged just as
they were in the gel.
d. Labeled probe is added to the filter, where it will hybridize with any complementary
DNA fragments that were on the original gel. Bound DNA is visualized as
appropriate for the label type.
e. The bands showing a hybridization signal are compared with marker bands to
determine their size, and construction of a map is begun. Additional data from
individual and combined restriction digests may be needed to complete the map.

Fig. 7.18 Southern blot procedure

Analysis of Gene Transcripts
1. Northern blotting analyzes RNA much the same way that Southern
blotting does DNA:
a. RNA is extracted from the cell, undergoes gel electrophoresis and is
bound to a filter.
b. Hybridization between bound cellular RNA and a labeled probe
occurs. The sizes of the RNA fragments detected by the probe can be
determined.
2. Northern blot analysis is used for determining:
a. The size(s) of mRNA encoded by a gene. Northern blots have shown
that different mRNA species arise from the same region of DNA,
suggesting differential use of promoters and terminators, and/or
alternative mRNA processing.
b. Whether a specific mRNA is present in a cell type, and if so, at what
levels. Gene activity is measured in this way, and RNA sampling is
widely used to study development, tissue specialization, or the
response of cells to various physiological stimuli.

DNA Sequencing
Animation: Dideoxy DNA Sequencing
1. Once cloned, DNA fragments may be sequenced,
allowing identification of gene and regulatory
sequences, and comparison with homologous
genes from different organisms.

2. Dideoxy sequencing (Sanger, 1970s) is based on DNA
polymerase extending short primers, using either linear or
circular DNA as a template. In dideoxy sequencing
(Figure 7.19):
a. DNA is heat denatured, and a short oligonucleotide primer
(designed so 3’ end is near DNA sequence of interest) anneals to
one strand and serves as primer.
b. A reaction mix is set up with label on either the primer or
dNTP(s). The mix includes:
i. ssDNA template to be sequenced.
ii. Primer (anneals to template).
iii. DNA polymerase.
iv. The four deoxynucleotide (dNTP) precursors.
Fig. 7.19 Dideoxy DNA sequencing of a theoretical DNA fragment

c. The reaction mix is divided into four tubes, and to each is added
a small amount of a different dideoxynucleotide, so that one tube
receives ddCTP, another ddTTP, etc. (Figure 7.20).
d. Dideoxynucleotides lacks 3’OH, having only 3’H, and so are
unable to bond with the 5’phosphate of another nucleotide. A
phosphodiester linkage cannot form, and the chain terminates at
the site of insertion of the ddNTP.
e. The specific ddNTP in a reaction competes with its
corresponding NTP for incorporation into the growing DNA
chain.
f. The four reaction mixes, one for each ddNTP, are typically run in
adjacent lanes on a polyacrylamide gel. The label on the DNA
bands reveals their location, and therefore their sizes.
g. DNA sequence is determined by reading the sequencing ladder
from bottom to top to give the sequence of the newly synthesized
strand from 5’3’ (Figure 7.21).
Fig. 7.20 A dideoxynucleotide (ddNTP) DNA precursor

3. Automation based on the dideoxy method enables
rapid DNA sequencing. In the automated process:
a. Only one reaction mix is needed, containing all four
dideoxynucleotides, each tagged with a different color.
b. DNA fragments generated are separated by
electrophoresis in a single lane.
c. The gel is scanned by a laser device that determines
which fluorescent label is present at each nucleotide
position in the sequence, and sends the information to
a computer.

4. Computer programs can analyze DNA sequences using
new data along with databases of previously reported
sequences. Computer analysis is used to:
a. Look for restriction sites.
b. Compare a variety of sequences from the same or different
species.
c. Locate homologous regions.
d. Find transcription regulatory sequences.
e. Detect open reading frames and predict the amino acid sequence
encoded, including protein structure and function.

Polymerase Chain Reaction (PCR)
1. PCR starts with a mixture of DNA molecules and produces many copies of one
specific DNA sequence (amplimers). Mullis developed the technique in the
1980s.
2. PCR begins with DNA containing the sequence to be amplified, and a pair of
synthetic primers that flank the sequence. Steps in the process include (Figure
7.23):
a. Heat denature DNA (94–95°C).
b. Cool (37–65°C) and anneal primers to complementary sequences with their 3’ ends
facing each other, flanking the target DNA.
c. Extend the primers (70–75°C) with heatresistant DNA polymerase from the
thermophilic bacterium, Thermus aquaticus.
d. Repeat the cycle of denaturation and primer binding.
e. Extend again with Taq DNA polymerase. Products the length of the target sequence
begin to be produced.
f. Repeat the process, doubling the amount of target DNA with each round of
extension.
3. In 20 PCR cycles, millionfold amplification of the target sequence occurs. The
temperature changes are automated in a thermal cycler.
Fig. 7.23 The polymerase chain reaction (PCR) for selective amplification of DNA
sequences

4. Applications of PCR include:
a. Amplifying DNA for cloning.
b. Amplifying DNA from genomic DNA for sequencing without
cloning.
c. Mapping DNA segments.
d. Disease diagnosis.
e. Sex determination of embryos.
f. Forensics (the analysis of legal evidence).
g. The study of molecular evolution.

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台大農藝系 遺傳學 601 20000 Chapter 7 slide 1

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a. Phage are plated on a bacterial lawn, producing plaques that each

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台大農藝系遺傳學 601 20000 Chapter 7 slide 1

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