1 Put a DNA regulatory region upstream of a reporter gene to analyze its elements PCR Space for res....
-
Upload
camron-fox -
Category
Documents
-
view
218 -
download
0
Transcript of 1 Put a DNA regulatory region upstream of a reporter gene to analyze its elements PCR Space for res....
![Page 1: 1 Put a DNA regulatory region upstream of a reporter gene to analyze its elements PCR Space for res. enz. to bind (“elbow room”) Reporter gene Transfect.](https://reader035.fdocument.pub/reader035/viewer/2022062500/5697bf871a28abf838c8875c/html5/thumbnails/1.jpg)
1
Put a DNA regulatory region upstream of a reporter gene to analyze its elements
PCR
Space for res. enz. to bind(“elbow room”)
Reportergene
Transfect
Typical reporter vector features
Updated 11/15/10 4:51 PM
![Page 2: 1 Put a DNA regulatory region upstream of a reporter gene to analyze its elements PCR Space for res. enz. to bind (“elbow room”) Reporter gene Transfect.](https://reader035.fdocument.pub/reader035/viewer/2022062500/5697bf871a28abf838c8875c/html5/thumbnails/2.jpg)
2
Popular reporters to study promoter/enhancers
• Beta-galactosidase (β-gal) – detection by several different assays
• Chloramphenicol acetyl transferase (CAT) – detected by a sensitive radioactive assay
• Luciferase (firefly, Renilla [jellyfish]) – detection, easy dual, sensitive luminescent assay
• Green fluorescent protein (GFP, BFP, YFP)) – cytological, visible in living cells, fusion proteins, FACS
• Neomycin phosphotransferase (neo)–selectable drug resistance (geneticin or G418
resistance)
• similarly: resistance to hygromycin, puromycin, histidinol, bleomycin, zeostin
• Dihydrofolate reductase (DHFR) – selectable in dhfr- cells, amplifiable, fusion proteins work
• Suicide selection: Herpes simplex virus thymidine kinase (HSVTK)
FACS = fluorescence-activated cell sorter
![Page 3: 1 Put a DNA regulatory region upstream of a reporter gene to analyze its elements PCR Space for res. enz. to bind (“elbow room”) Reporter gene Transfect.](https://reader035.fdocument.pub/reader035/viewer/2022062500/5697bf871a28abf838c8875c/html5/thumbnails/3.jpg)
3
HSVTKGancilovir, ATP(non-toxic)
Gancilovir-PO4
Mammalian TKGangcylovir, ATP
toxicity, death
Use example: Site-directed recombination
Engineered chromosome: WT protein of interest HSVTK
lox
lox
Replacement plasmid:
Mut. protein of interest
gangcylovir
Mut. protein of interest
Select recombinants as HSVTK-, ganciclovir-resistant
Gangcyclovir selection AGAINST the presence of enzyme activity
(compare to 5-fluoro-orotic acid (FOA) resistance in yeast, URA3-)
CRE recombinase(cassette exchange)
(Ganciclovir itself is not toxic)
![Page 4: 1 Put a DNA regulatory region upstream of a reporter gene to analyze its elements PCR Space for res. enz. to bind (“elbow room”) Reporter gene Transfect.](https://reader035.fdocument.pub/reader035/viewer/2022062500/5697bf871a28abf838c8875c/html5/thumbnails/4.jpg)
4
diacetylated
monoacetylated
Testing for a cell-specific promoter: chloramphenicol acetyl transferase (CAT) reporter assay
Thin layer chromatography (TLC)
CAT cDNA is from a prokaryotic source. CAT is not foundin mammalian cells.Therefore low backgrounds.
A B
14C-chloramphenicol
unacetylatedPositive controlNegative control
Applied Molec. Genet., U. Ariz
![Page 5: 1 Put a DNA regulatory region upstream of a reporter gene to analyze its elements PCR Space for res. enz. to bind (“elbow room”) Reporter gene Transfect.](https://reader035.fdocument.pub/reader035/viewer/2022062500/5697bf871a28abf838c8875c/html5/thumbnails/5.jpg)
5
Reporter enzyme substrates for different purposes
• ONPG (ortho-nitrophenyl-beta-galactoside) – spectrophotometric measurement (420 nm – blue color – simplest)
• X-gal (5-Bromo-4-chloro-3-indolyl-ß-D-galactoside) – blue precipitate - for cytology or colony detection
• Umbelliferyl–galactoside (-> umbelliferone, fluorescent, reading in a fluorimeter allows more sensitive quantification than spectrophotometry)
• Galacton-STAR or some such (-> chemiluminescent product = emission of light, so lower background than fluorescence)
• Lactose (glucose-beta-galactose disaccharide) – allows growth if hydrolyzed; growth phenotype. For microbial cells usually.
Substrates for beta-galactosidase, for example:
![Page 6: 1 Put a DNA regulatory region upstream of a reporter gene to analyze its elements PCR Space for res. enz. to bind (“elbow room”) Reporter gene Transfect.](https://reader035.fdocument.pub/reader035/viewer/2022062500/5697bf871a28abf838c8875c/html5/thumbnails/6.jpg)
6
Mapping transcriptional elements upstream of a promoter:
Mapping with restrictionenzyme mediated deletions
Conclusion:
Light units of luciferase in hepatocytes
luciferase reporter cDNA gene
Applied Molec. Genet., U. Ariz
![Page 7: 1 Put a DNA regulatory region upstream of a reporter gene to analyze its elements PCR Space for res. enz. to bind (“elbow room”) Reporter gene Transfect.](https://reader035.fdocument.pub/reader035/viewer/2022062500/5697bf871a28abf838c8875c/html5/thumbnails/7.jpg)
7Footprinting: detects sites on DNA to which protein are bound
Naked DNA DNA + DNA-binding proteinP
opul
atio
n of
mol
ecul
es
missing
Pop
ulat
ion
of m
olec
ules
Partial DNase
Gel electrophoresis.autoradiography
Footprint
32P end-label(e.g., by phosphorylation of the 5’ OH with polynucleotide kinase and
gamma 32P-ATP)
Many unlabeled fragments are present but not seen
![Page 8: 1 Put a DNA regulatory region upstream of a reporter gene to analyze its elements PCR Space for res. enz. to bind (“elbow room”) Reporter gene Transfect.](https://reader035.fdocument.pub/reader035/viewer/2022062500/5697bf871a28abf838c8875c/html5/thumbnails/8.jpg)
8
Note uneven cleavage of naked DNA by DNase
DNA footprint data
Note enhanced cleavage (sensitization) as well as protection
![Page 9: 1 Put a DNA regulatory region upstream of a reporter gene to analyze its elements PCR Space for res. enz. to bind (“elbow room”) Reporter gene Transfect.](https://reader035.fdocument.pub/reader035/viewer/2022062500/5697bf871a28abf838c8875c/html5/thumbnails/9.jpg)
9
(EMSA = electrophoretic mobility shift assay)
(shift)
(supershift)
1 2 3 4 5
DNA element
Applied Molec. Genet. U. Arizona
Protein-DNA binding: EMSA or gel shift
(Even though the hexagon looks like a protein here)
competitor
![Page 10: 1 Put a DNA regulatory region upstream of a reporter gene to analyze its elements PCR Space for res. enz. to bind (“elbow room”) Reporter gene Transfect.](https://reader035.fdocument.pub/reader035/viewer/2022062500/5697bf871a28abf838c8875c/html5/thumbnails/10.jpg)
10
http://brc.se.fju.edu.tw/protein/interact/binding.htm
(EMSA = electrophoretic mobility shift assay)
Protein-DNA binding: EMSA or gel shift
![Page 11: 1 Put a DNA regulatory region upstream of a reporter gene to analyze its elements PCR Space for res. enz. to bind (“elbow room”) Reporter gene Transfect.](https://reader035.fdocument.pub/reader035/viewer/2022062500/5697bf871a28abf838c8875c/html5/thumbnails/11.jpg)
11
(surpershifted complex is not competed by NON-specific probe)
(competed only by specific probe)
(two molecules of protein bound)
Protein DNA complexes migrate more slowly than naked DNA
Gel shifts (EMSA
Super-shift
![Page 12: 1 Put a DNA regulatory region upstream of a reporter gene to analyze its elements PCR Space for res. enz. to bind (“elbow room”) Reporter gene Transfect.](https://reader035.fdocument.pub/reader035/viewer/2022062500/5697bf871a28abf838c8875c/html5/thumbnails/12.jpg)
12
SELEX for protein binding sites on nucleic acids
Systematic Evolution of Ligands by Exponential Enrichment
Synthesize ~1014 oligomers with a random central section (e.g., 20-mer=1013)
Incubate with a protein of interest
Separate the protein-DNA complexes from the free DNA:e.g., using EMSA, IP, nitrocellulose, protein on beads in a column
Dissociate complex,PCR amplify the bound DNA fraction
Reiterate the cycle 5 to 10 times.If 99.9% efficient:enough
( = 1 microgram =~ several $100)
Last step: clone and sequence the “winners”
![Page 13: 1 Put a DNA regulatory region upstream of a reporter gene to analyze its elements PCR Space for res. enz. to bind (“elbow room”) Reporter gene Transfect.](https://reader035.fdocument.pub/reader035/viewer/2022062500/5697bf871a28abf838c8875c/html5/thumbnails/13.jpg)
13
Binding to protein of interest
RThttp://www.molmed.uni-luebeck.de/T.%20Restle/Bilder/SELEX.jpg
Practical capacity ($700):
1014 random sequences
(random ~21-mer = 421)
![Page 14: 1 Put a DNA regulatory region upstream of a reporter gene to analyze its elements PCR Space for res. enz. to bind (“elbow room”) Reporter gene Transfect.](https://reader035.fdocument.pub/reader035/viewer/2022062500/5697bf871a28abf838c8875c/html5/thumbnails/14.jpg)
14
= 3 x 1014 molecules, or enough for 30-fold coverage
10 ug
molecules= 3E+13
X 6.00E+17 molecules per umole
= 0.00005 umoles of the 60-mer
~20000 daltons19800 =X MW of a nucleotide=@330 ug/umole
60 nt
20 nt variable region + two 20 primer templates = 60 nt total length
420 = ~1013 unique sequences
![Page 15: 1 Put a DNA regulatory region upstream of a reporter gene to analyze its elements PCR Space for res. enz. to bind (“elbow room”) Reporter gene Transfect.](https://reader035.fdocument.pub/reader035/viewer/2022062500/5697bf871a28abf838c8875c/html5/thumbnails/15.jpg)
15PUM2, a novel murine puf protein, and its consensus RNA-binding siteWhite EK, Moore-Jarrett T, Ruley HE. RNA. 2001 Dec;7(12):1855-66.
Consensus:
Binding site for a “puf “ protein, implicated in mRNA degradation
Code
Integer
Base Name Meaning
Complement
A 1 Adenine A T
C 2 Cytosine C G
G 3 Guanine G C
T 4 Thymine T A
U 4 Uracil U A
R 5 (PuRine) G|A Y
Y 6 (PYrimidine) T|C R
K 7 (Keto) G|T M
M 8 (AMino) A|C K
S 9 Strong interaction (3 H bonds) G|C S
W 10 Weak interaction (2 H bonds) A|T W
B 11 Not-A (B follows A) G|T|C V
D 12 Not-C (D follows C) G|A|T H
H 13 Not-G (H follows G) A|T|C D
V 14 Not-T (or U) (V follows U) G|A|C B
N,X 15 ANy nucleotide G|A|T|C N
- 16 Gap of indeterminate length Gap -
Description
Nucleic acid degenerate base abbreviations (FYI)20-mer
![Page 16: 1 Put a DNA regulatory region upstream of a reporter gene to analyze its elements PCR Space for res. enz. to bind (“elbow room”) Reporter gene Transfect.](https://reader035.fdocument.pub/reader035/viewer/2022062500/5697bf871a28abf838c8875c/html5/thumbnails/16.jpg)
16
TPA = Tissue plasminogen activator, dissolves clots
Problem: Cleared quickly from bloodstream by liver
Bind to hepatocytes in liver via TPA’s kringle domain
Want to isolate a TPA mutant protein with less affinity for hepatocytes
Must be still enzymatically active of course.
![Page 17: 1 Put a DNA regulatory region upstream of a reporter gene to analyze its elements PCR Space for res. enz. to bind (“elbow room”) Reporter gene Transfect.](https://reader035.fdocument.pub/reader035/viewer/2022062500/5697bf871a28abf838c8875c/html5/thumbnails/17.jpg)
17
![Page 18: 1 Put a DNA regulatory region upstream of a reporter gene to analyze its elements PCR Space for res. enz. to bind (“elbow room”) Reporter gene Transfect.](https://reader035.fdocument.pub/reader035/viewer/2022062500/5697bf871a28abf838c8875c/html5/thumbnails/18.jpg)
18Goal: to improve tissue plasminogen activator as a therapeutic “clot-busting” treatmentMeans: Reduce or eiminate the binding of tPA to liver cells, as this clears it from the blood
Authors here use a mammalian cells as the carrier of the DNA and the cell surface as a display site. Display was via a fusion protein to a membrane anchor protein, DAF (peptide, really).DAF = “decay accelerating factor”
What did they do?Cassette mutagenesis.
What region?333 bp K1 (kringle-1), known to bind the MAb387, which competes for hepatocyte binding (so assuming it is the same target epitope).
How did they get kringle mutated?Error-prone PCR
How did they isolate just the kringle 1 region? PCR fragment.
How did they get the mutagenized fragment back in?Introduced restriction sites at the ends, w/o affecting the coding.
![Page 19: 1 Put a DNA regulatory region upstream of a reporter gene to analyze its elements PCR Space for res. enz. to bind (“elbow room”) Reporter gene Transfect.](https://reader035.fdocument.pub/reader035/viewer/2022062500/5697bf871a28abf838c8875c/html5/thumbnails/19.jpg)
19
hepatocyte
mAb
mAb competes with hepatocyte for binding
tPA
tPAtPA
Kringle domain (~100 Aas)
K
K
K
![Page 20: 1 Put a DNA regulatory region upstream of a reporter gene to analyze its elements PCR Space for res. enz. to bind (“elbow room”) Reporter gene Transfect.](https://reader035.fdocument.pub/reader035/viewer/2022062500/5697bf871a28abf838c8875c/html5/thumbnails/20.jpg)
20
Got this far(two topics through next graphic)
![Page 21: 1 Put a DNA regulatory region upstream of a reporter gene to analyze its elements PCR Space for res. enz. to bind (“elbow room”) Reporter gene Transfect.](https://reader035.fdocument.pub/reader035/viewer/2022062500/5697bf871a28abf838c8875c/html5/thumbnails/21.jpg)
21
What did they put the mutagenized fragment into?DAF – TPA fusion protein gene
How did they get it into into cells?Electroporation
What cells did they use as hosts?293 carrying SV40 large T antigen
How many copies per cell. And why is that important? One, by electroporation at low DNA concentration. [In a transient transfection!]Binding is dominant. Lack of binding (what they are after) is recessive.
How did they select cells making MAb387-non-binding TPA?FACS:Recover cells that bind fluorescent mAb vs. protease domainbut low binding to fluorescent mAb vs. kringle domain
![Page 22: 1 Put a DNA regulatory region upstream of a reporter gene to analyze its elements PCR Space for res. enz. to bind (“elbow room”) Reporter gene Transfect.](https://reader035.fdocument.pub/reader035/viewer/2022062500/5697bf871a28abf838c8875c/html5/thumbnails/22.jpg)
22
Tracked down vector: contains SV40 ori and is transfected into 293 cells making SV40 T-antigen. So plasmid replicates during the transient transfection higher signal.
![Page 23: 1 Put a DNA regulatory region upstream of a reporter gene to analyze its elements PCR Space for res. enz. to bind (“elbow room”) Reporter gene Transfect.](https://reader035.fdocument.pub/reader035/viewer/2022062500/5697bf871a28abf838c8875c/html5/thumbnails/23.jpg)
23
For reiteration of the process
Sort the cells with low fluorescence
,
![Page 24: 1 Put a DNA regulatory region upstream of a reporter gene to analyze its elements PCR Space for res. enz. to bind (“elbow room”) Reporter gene Transfect.](https://reader035.fdocument.pub/reader035/viewer/2022062500/5697bf871a28abf838c8875c/html5/thumbnails/24.jpg)
24
How did they recover the plasmid carrying the mutant TPA gene from the selected cells?
Hirt extraction: Like a plasmid prep, lyse cells gently, high MW DNA entangles and forms a “clot”.Centrifuge. Chromosomal DNA soft pellet; plasmid DNA circles stay in supernatant.
Then re-transfect, re-sort in FACS.
After 2 sorting rounds, test individual E. coli clones: 60% are binding-negative.
![Page 25: 1 Put a DNA regulatory region upstream of a reporter gene to analyze its elements PCR Space for res. enz. to bind (“elbow room”) Reporter gene Transfect.](https://reader035.fdocument.pub/reader035/viewer/2022062500/5697bf871a28abf838c8875c/html5/thumbnails/25.jpg)
25
MAb to protease domain
MAb to kringle-1 domain
enriched
Low kringle-1 reactivity
FITC = fluorescein reagent. PE = phycoerythrin (fluorescent protein)
No good
good good good good
Collect these
![Page 26: 1 Put a DNA regulatory region upstream of a reporter gene to analyze its elements PCR Space for res. enz. to bind (“elbow room”) Reporter gene Transfect.](https://reader035.fdocument.pub/reader035/viewer/2022062500/5697bf871a28abf838c8875c/html5/thumbnails/26.jpg)
26
Hepatoma cell binding. How?
Clone mutated regions into regular TPA gene for testing (no DAF, protein now secreted)
Label WT TPA with fluorescein (FITC, conjugated chemically) Mix with hepatoma cells and analyze on a flow cytometer (FACS w/o the sorter part).
See specific and non-specific binding. Subtract non-specific binding: the amount not competed by excess un-labeled wt TPA.
FITC = fluorescein isothiocyanate
![Page 27: 1 Put a DNA regulatory region upstream of a reporter gene to analyze its elements PCR Space for res. enz. to bind (“elbow room”) Reporter gene Transfect.](https://reader035.fdocument.pub/reader035/viewer/2022062500/5697bf871a28abf838c8875c/html5/thumbnails/27.jpg)
27
WT
Compete. So still bind.
But still haveprotease activity
Hepatoma cell binding assay:measure competition for binding of fluorescently labeled WT TPA
Can’t compete (good)No competitor
Binding assay, initial condition
![Page 28: 1 Put a DNA regulatory region upstream of a reporter gene to analyze its elements PCR Space for res. enz. to bind (“elbow room”) Reporter gene Transfect.](https://reader035.fdocument.pub/reader035/viewer/2022062500/5697bf871a28abf838c8875c/html5/thumbnails/28.jpg)
28
![Page 29: 1 Put a DNA regulatory region upstream of a reporter gene to analyze its elements PCR Space for res. enz. to bind (“elbow room”) Reporter gene Transfect.](https://reader035.fdocument.pub/reader035/viewer/2022062500/5697bf871a28abf838c8875c/html5/thumbnails/29.jpg)
29