• Size of the DNA fragments can be prepared by different type of restriction enzymes.
• However, cDNA are of suitable size for cloning without further manipulation.
• If one is interested in the amino acid sequence of a protein – this information can be obtained using cloned cDNA.
• If one is interested in the whole gene including regulatory sequences, the genomic
DNA will be the suitable choice.

• cDNA is the abbreviation for complementary DNA or copy DNA
• A cDNA library is a set of clones representing as many as possible of the mRNAs in a given cell type at a given time
– Such a library can contain tens of thousands of different clones

• Isolation of poly(A) mRNA.
• Synthesis of cDNA by reverse transcription.
• cDNA molecules are joined to vector DNA to create cDNA library.
• Screen library for desired cDNA clone.

Poly(A) mRNA isolation
• Isolate total RNA
• Bind mRNA to oligo(dT) column
• Elute and discard rRNA and tRNA
• Elute poly(A) mRNA

• Central to successful cloning is the synthesis of cDNA from an mRNA template using reverse transcriptase (RT),
RNA-dependent DNA polymerase
– RT cannot initiate DNA synthesis without a primer
– Use the poly(A) tail at 3’ end of most eukaryotic mRNA so that oligo(dT) may serve as primer

• RT with oligo(dT) primer has made a single-stranded DNA from mRNA
• Need to start to remove the mRNA
• Partially degrade the mRNA using ribonuclease H (RNase H)
– Enzyme degrades RNA strand of an RNA-
DNA hybrid
– Remaining RNA fragments serve as primers for “second strand” DNA using nick translation

 The nick translation process simultaneously:
 Removes DNA ahead of a nick
 Synthesizes DNA behind nick
 Net result moves or translates the nick in the 5’ to 3’ direction
 Enzyme often used is E. coli
DNA polymerase I
 Has a 5’ to 3’ exonuclease activity
 Allows enzyme to degrade
DNA ahead of the nick

cDNA synthesis
• Reverse transcription using oligo(dT) primer linked with sequence recognized by Xho I
• Nick RNA strand using
RNaseH
• Second strand cDNA synthesis

Double stranded cDNA can be modified to be cloned into vector by adding adapters or linkers
• Blunt 3’ overhang using
Pfu polymerase
• Add Eco RI adapter.
• Digest with Xho I.
• cDNA contains one end compatible with Eco RI and
Xho I on the other end.

• Digest plasmid using
Eco RI and Xho I
• Ligate cDNA into digested plasmids
• Transformation – introduce recombinant plasmids into bacterial host cells.
• Select transformants using blue-white screening.

cDNA synthesis
• Reverse transcription using oligo(dT) primer
• RT does not always produce full length cDNA
• Nick RNA strand using
RNaseH
• Second strand cDNA synthesis using T4 DNA polymerase

1. Reverse transcription using oligo(dT) primer linked with sequence recognized by restriction endonuclease
2. RT synthesizes first strand of cDNA with 5methyl-dCTP
3. Biotin is attached to the end of mRNA
4. Rnase I degraded single stranded segments of
RNA
5. Full length RNA-DNA hybrid bind to streptavidin

6. Rnase H degrades the RNA of the RNA-DNA streptavidin hybrid
7.
A poly(dG) tail is added to the 3’ end
8. An oligo(dC) with sequence recognized by second restriction enzyme is added
9. Second cDNA strand is synthesized
10. Final full length of cDNA is cloned into vector

• Screening the library using nucleic acid hybridization is the most direct and very sensitive means for detecting the desired clones.
• This requires knowledge of the sequences of the gene being sought.
• In some case, part of the gene may have already been cloned, and this information can be used to search for flanking sequence.
• Information might come from genome sequence information of related organism.

• Double stranded DNA can be converted into single stranded DNA by heat or alkaline treatment. Heating breaks the H-bond but not phosphodiester bond.
• If the heated solution is rapidly cooled, the strands remain single stranded.
• If it is slowly cooled down, the helical conformation of DNA can be established.
• This process is called annealing .

• Retains both DNA polymerase and 3’ exonuclease activities but lacks of 5’ exonuclease activity.
• The 3’ exonuclease is retained because it reduces the misincorporation of erroneous dNTPs during the synthesis of new DNA strand.
• The 5’ exonuclease activity is abolished because it would degrade some of the newly synthesized
DNA.

• From each discrete colony formed on a master plate, a sample is transferred to a solid matrix, such as nitrocellulose or nylon membrane.
• The cells on the membrane are lysed, and the released DNA is denatured, deproteinized, and irreversibly bound to the membrane (crosslinking).
• A labeled DNA probe is added to the membrane under hybridization condition.
• After washing, exposing to an X-ray film, the colony carrying the gene can be identified.

Electrophoresis provides information on:
• Size of fragments. Fragments of known size provide comparison.
• Presence of specific sequences. These can be determined using probes.
DNA is denatured while in the gel, then transferred to a nylon filter to make a
“blot.”

 Probes are used to identify a desired clone from among the thousands of irrelevant ones
 Two types are widely used
 Polynucleotides also called oligonucleotides
 Antibodies

• First, cloned DNA from a closely related organisms (a heterologous probe) can be used.
• Hybridization conditions need to be adjusted.
• Second, probe can be synthesized based on the probable nucleotide sequence that is deduced from the known amino acid sequence of the protein encoded by the target gene.

Looking for a gene you want, might use homologous gene from another organism
 If already cloned
 Hope enough sequence similarity to permit hybridization
 Need to lower stringency of hybridization conditions to tolerate some mismatches

 Factors that promote separation of two strands in a DNA double helix:
 High temperature
 High organic solvent concentration
 Low salt concentration
 Adjust conditions until only perfectly matched
DNA strands form a duplex = high stringency
 Lowering these conditions lowers stringency until DNA strands with a few mismatches can hybridize

No homologous DNA from another organism?
 If amino acid sequence is known, deduce a set of nucleotide sequences to code for these amino acids
 Construct these nucleotide sequences chemically using the synthetic probes
 Why use several?
 Genetic code is degenerate with most amino acids having more than 1 nucleic acid triplet
 Must construct several different nucleotide sequences for most amino acids

• From each discrete colony formed on a master plate, a sample is transferred to a solid matrix, such as nitrocellulose or nylon membrane.
• The cells on the membrane are lysed, and their proteins are bound to the membrane.
• The membrane is treated with primary antibody that binds only to the target protein.
• Unbound primary antibody is washed away, and the membrane is treated with secondary antibody.
• Unbound secondary antibody is washed away and a colorimetric is carried out to identify the clone.

• From each discrete colony formed on a master plate, a sample is transferred to a solid matrix, such as nitrocellulose or nylon membrane.

• Defective host cell (A-) are transformed with plasmids from genomic library derived from wildtype strain.
• The transformed cells that carry a cloned gene that confers the A+ function will grow on minimal medium and selected.

l
 First phage vectors were constructed by Fred
Blattner and colleagues
 Removed middle region
 Retained genes needed for phage replication
 Could replace removed phage genes with foreign
DNA
 Originally named Charon phage
 More general term, replacement vectors
4-46

 Phage vectors can receive larger amounts of foreign
DNA
 Charon 4 can accept up to 20kb of DNA
 Traditional plasmid vectors take much less
 Phage vectors require a minimum size foreign DNA piece (12 kb) inserted to package into a phage particle
4-47

Cosmids are designed for cloning large DNA fragments
 Behave as plasmid and phage
 Contain

 cos sites, cohesive ends of phage DNA that allow the DNA to be packaged into a l phage head
Plasmid origin of replication permitting replication as plasmid in bacteria
 Nearly all l genome removed so there is room for large inserts (40-50 kb)
 So little phage DNA can’t replicate, but they are infectious carrying recombinant DNA into bacterial cells

 There are vectors designed for cloning genes into eukaryotic cells
 Other vectors are based on the Ti plasmid to carry genes into plant cells
 Yeast artificial chromosomes (YAC) and bacterial artificial chromosomes (BAC) are used for cloning huge pieces of DNA

• Cell suspension in electroporation cuvette
• Cells and DNA in the cuvette, prior, during, and after high-voltage electric field pulses
• Some cells acquire exogeneous DNA
• Increase in transformation frequency

 Helper cell self-transfers a conjugative, mobilizing plasmid with Tet r gene to a donor cell
 Donor cell contain nonconjugative, mobilizing plasmid with Kan r gene
 Subsequently, nonconjugative, mobilizing plasmid with Kan r gene is transported to a recipient cell
 Only recipient cell containing nonconjugative, mobilizing plasmid with Kan r gene can be grown in minimal medium with kanamycin