1. Recombinant DNA Technology (Part II)

2. Genomic VS cDNA Library
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.

3. Making cDNA Library
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

4. Making cDNA Library 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.

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

7. Making cDNA Library
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

8. Making cDNA Library
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

9. Making cDNA Library 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

10. cDNA synthesis
Reverse transcription using oligo(dT) primer linked with sequence recognized by XhoI
Nick RNA strand using RNaseH
Second strand cDNA synthesis

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

13. Digest plasmid using EcoRI and XhoI
Ligate cDNA into digested plasmids
Transformation – introduce recombinant plasmids into bacterial host cells.
Select transformants using blue-white screening.

14. 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

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

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

18. Screening the Library
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.

19. DNA hybridization assay
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.

20. DNA hybridization assay

21. Random-primer method

22. The Klenow fragment
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.

23. E. Coli DNA polymerase I

25. Random-primer method

27. Screening the Library
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.

30. Southern Blot 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.”

37. Identifying a specific clone with a specific probe
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

38. Possible sources of probes
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.

39. Polynucleotide probes
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

40. Control of Hybridization Stringency
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

41. Possible sources of probes
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

42. Screening by immunological assay
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.

44. Screening by protein activity
From each discrete colony formed on a master plate, a sample is transferred to a solid matrix, such as nitrocellulose or nylon membrane.

45. Screening by functional complementation
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.

46. l Phage Vectors
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

47. Vectors for cloning large pieces of DNA
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

52. Cosmid Vectors 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

54. Eukaryotic Vectors
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

55. Electroporation 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

56. Tripartite mating
Helper cell self-transfers a conjugative, mobilizing plasmid with Tetr gene to a donor cell
Donor cell contain nonconjugative, mobilizing plasmid with Kanr gene
Subsequently, nonconjugative, mobilizing plasmid with Kanr gene is transported to a recipient cell
Only recipient cell containing nonconjugative, mobilizing plasmid with Kanr gene can be grown in minimal medium with kanamycin