4: Hybridization (PRELIMS) Flashcards
Vitro technique whereby ssDNA or RNA sequence called the probe is allowed to complementary base pair with DNA or RNA
Hybridization
What is the molecule that is allowed to complementary base pair with DNA or RNA?
Probe
Prior hybridization what do you need to do to the DNA?
Cut the DNA in short fragments
These are ssDNA/RNA molecule that can recognize and specifically bind to target DNA by complementary base pairing in mixture of biomolecule
Probe
Probes contain what molecule which can help to hybridize complementary DNA or RNA and resist nuclease degradation
Normal nitrogen bases
Enzyme that degrades DNA
Nuclease
Attaches to the Gene of Interest
Probe
T or F
Width of probe determine its specificity
F (LENGTH of probe determine its specificity)
Length of probe determines its what?
Specificity
T or F
Longer probe means more specific
T
This is for visualization of bound probe to target fragments in membrane
Probe labeling
What are the types of probe labeling?
- Enzyme
- Fluorescence
- Radiolabeled
In this type of probe labeling, a substrate is needed in order to catalyze reaction
Enzyme
In this type of probe labeling, light of a specific wavelength is emitted when excited by an external light source
Fluorescence
What is the positive result for Fluorescence type of probe labeling?
Fluorescent/Light formation
In this type of probe labeling, probe is labeled with radioactive isotope and is visualized using X-ray or CCD camera
Radiolabeled
T or F
UV light is used in visualizing radiolabeled type of probe
F (X-ray and CCD camera)
This process immobilizes the molecule of interest in support
Blotting
Gene of Interest + Membrane
Blotting
Uses hybridization technique for identification of specific nucleic acids
Blotting
What is the Target, Probe, and Purpose of Southern Blot hybridization technique?
Target: DNA
Probe: NA
Purpose: Gene structure
What is the Target, Probe, and Purpose of Northern Blot hybridization technique?
Target: RNA
Probe: NA
Purpose: Transcript structure, Gene expression
What is the Target, Probe, and Purpose of Western Blot hybridization technique?
Target: Protein
Probe: Protein (globulin)
Purpose: Protein processing gene
What is the Target, Probe, and Purpose of Eastern Blot hybridization technique?
Target: Protein
Probe: Protein
Purpose: Modification of WB using Enzymatic digestion
What is the Target, Probe, and Purpose of South-Western Blot hybridization technique?
Target: Protein
Probe: DNA
Purpose: DNA binding proteins, Gene
What is the Target, Probe, and Purpose of Far-Eastern Blot hybridization technique?
Target: Lipids
Probe: None
Purpose: Transfer of HPLC, Separated lipids to PDM for analysis by mass spectrophotometry
Enumerate all hybridization technique
- Southern Blot
- Northern Blot
- Western Blot
- Eastern Blot
- South-Western Blot
- Far-eastern Blot
This is a hybridization technique that allows the detection of given DNA sequence
Southern Blot
T or F
Southern blot can be used to identify heterogenous sequences of genomic DNA or facilitate gene mapping
F (can be used to identify HOMOGENOUS sequences of genomic DNA)
Use this card to familiarize the process of southern blotting
- Purify DNA
- Restriction Digestion
- Gel Electrophoresis
- Depurination
- Denaturation
- Blotting
- Saturation
- Fixation
- Hybridization
- Detection
1st and crucial step in southern blotting
Purify genomic DNA from eukaryotic cells or bacteria
2nd step in southern blotting wherein DNA is cut into smaller fragments by restriction enzymes
Restriction digestion/fragmentation
3rd step in southern blotting where there is separation of fragments according to their molecular weight
Gel Electrophoresis
How many percent of gel is used in Gel electrophoresis?
0.7 - 2%
meansyung size ng DNA is large; .8 to 2
What are the two types of gel used in Gel electrophoresis?
Agarose or Acrylamide
In the Gel electrophoresis part of southern blotting, sample is stained with what substance and subjected to what device?
Stained with Ethidium Bromide and Subjected to fluorescence under UV Light
After Gel electrophoresis in southern blotting, sample undergoes what?
Depurination
4th step of souther blotting wherein the DNA is apurinated or removing purines with DNA using diluted HCL
Depurination
What substance is used in depurination of DNA?
diluted HCl
T or F
In depurination part of southern blotting, you will be left with pyrimidines and some remnants of purines
F (left with PYRIMIDINES only since purines were removed during this step)
After depurination of sample in southern blotting, what is the next step?
Denaturation
What substance is used in denaturation part of southern blotting?
NaOH (Alkaline Solution)
What is the purpose of denaturation in southern blotting?
Break H-bonds to turn double stranded DNA to single stranded
After depurinating and denaturation, what step is done wherein the fragmented DNA is transferred into membrane
Blotting
In blotting, what are the 4 membrane types used?
- Nitrocellulose
- Nylon
- Modified Cellulose
- PVDF (polvinyl difluoride)
Membrane Types:
Usually used in southern blotting
Nitrocellulose
Membrane Type:
Used in northern blot; most sensitive
Nylon
Membrane Type:
What is used in modified cellulose?
Diethylaminoethyl or cARBOXYMETHYL
Membrane Type:
Used in western blot
PVDF
In blotting, what are the methods of transferring?
- Capillary
- Electroblotting
- Vacuum
Method of transferring:
Uses capillary action
Capillary
T or F
In capillary method of transferring, the movement of the fluid is downward
F (UPWARD)
Method of transferring:
Uses electric currents based on electrodes
Electroblotting
T or F
Nucleic acid are normally negatively charged
T
Method of transferring:
Nitrocellulose is placed under the gel through suction
Vacuum
In vacuum method of transferring, what solution is used to saturate?
NaCl
T or F
The recommended method of transferring is vacuum since it removes air bubbles
T
What is the process that prevents probe from binding to non-specific sites on the membrane surface?
Prehybridization
Prehybridization
What is the buffer solution used in southern blot?
Denhardt solution; Ficoll, Polyvinyl, Pyrolidine, Bovine serum
After blotting in southern blotting, what is the next step?
Saturation
NaCl
What are the 2 techniques of fixation in southern blotting?
- Drying at 80 degrees celsius
- UV radiation
After the fixation part in souther blotting, what is the next step wherein the probes is attached to the gene of interest?
Hybridization
T or F
Hybridization in southern blotting last 2-10 hours
F (last 1-16 HOURS)
After the process of hybridization in souther blotting, what is the next step?
Washing and autoradiography
In the washing part of southern blot, what substances are used?
Buffer, NaCl, Detergent
If the DNA is not washed in southern blotting, what result can this lead to?
False-positive result
Last step of southern blot is what?
Detection
In detection process of southern blot, what enables autoradiographic detection?
Radioactive probes
This hybridization technique allows detection of RNA molecules in a mixture of heterogenous NRA
Northern Blot
Use this card to familiarize process of Northern blot
- Extract and purify mRNA from cells
- Separate by gel electrophoresis
- Depurination
- Blotting
- Fixation
- Addition of probe/Hybridization
- Washing
- Detection
The northern blot almost has the same process as southern blot except for what step?
Denaturation (since RNA is already single stranded, no need to break H-bond)
In the blotting process of northern blot, what filter paper is used?
Aminobenyloxymethyl filter paper (ABOM filter paper–hirap na hirap ako memorize)
What fixation technique is used in northern blot?
Drying at 80 degrees c
What buffer solution is used in prehybridization of northern blot?
Salmon Sperm DNA EWWWWWWW
Hybridization technique where target proteins are transferred to hydrophobic membrane after the SDS-PAGE and detected using antibodies
Western Blot
Use this card to familiarize the process of western blot
- Load and Separate protein sample on SDS-PAGE
- PAGE –> Nitrocellulose membrane of PVDF
- Block the membrane w/ neutral protein
- Probing with antibody
- Detection of band
In western blot, where do you load and separate protein samples?
SDS-PAGE
After loading and separating in SDS-PAGE, what is the next step
Western blot
PAGE / fractionated proteins is electrophoretically transferred onto
nitrocellulose membrane of PVDF
OR
PAGE –> nitrocellulose membrane of PVDF
What are the 3 transfer buffers used in western blot?
- 25 mM. TRIS HCl
- 192 mM Lycine
- 20% methanol
After transfer into membrane in western blot, what is the next step?
Block membrane w/ neutral protein
T or F
You block membrane with an acidic protein
F (NEUTRAL protein)
This step in western blot, prevents non-specific binding of antibodies to membrane
Blocking w/ neutral protein
What are the 3 neutral proteins used in blocking process of western blot?
- 1-3% BSA
- 1-5% Skim milk
- PBS-Tween 20
After blocking process in western blocking, what is the next step?
Probing/Hybridization
In western blot, probing is done with an?
Antibody
T or F
In western blot, probing with antibody is only a one step process
F (two-step since you incubate with primary and secondary antibody)
In western blot, specifically in probing process, you first incubate membrane with what?
Primary antibody specific to target protein
Low amount of primary antibody indicates what result?
False-negative result
High amount of primary antibody indicates what result in western blot?
High non-specific reaction
In western blot, specifically in probing process, after incubating w/ primary what is the next antibody you use?
HRP - Labeled Secondary antibody specific to primary antibody
These 2 are example of secondary antibodies used to probe in western blot
- HRP
- Alkaline phosphatase
What is the last step in western blot?
Detection of band
In the last step of western blot which is detection of band, what do you use to incubate blot?
Chemiluminescent HRP Subtrate; Diaaminobenzidine, TMB, BCIP, NBT
How is the band detected in western blot?(
XRAY, CCD camera
T or F
In western blot, specifically in last step which is detection of band, an enzyme attached to antibody catalyzes reaction
T
Hybridization technique where target DNA, protein, or RNA is deposited directly on membrane
DOT Blot
T or F
In DOT Blot, there is gel resolution of target fragments
F (NO gel resolution of target fragments)
Use this card to familiarize yourself with the process of DOT Blot
- Purification of RNA/DNA
- Apply directly to the small dots
- Denature DNA (70-80 c)
- Add labeled probe
- Incubation for complementary binding
- Wash excess probe
- Visualization of result
T or F
Dot blot is denatured at 80-90 degrees c
F (70-80 degrees c)
What is the membrane used in DOT Blot?
Nitrocellulose or Nylon
What is the positive result of a DOT Blot?
Black dot
What is the advantage of DOT Blot from other techniques?
Simple; easy to use
This is a cytogenetic technique used to detect and localize the presence or absence of specific DNA sequences on chromosomes
Fluorescent in Situ Hybridization
FISH tilapia, talaping talapong talap-talap
–> Method for visualizing specific location on chromosome (by fluorescent complementary probes)
–> Fluorescent probes that bind to only parts of chromosomes
Fluorescent in Situ Hybridization
T or F
There is cell lysis in Fluorescent in Situ Hybridization
F (NO cell lysis in Fluorescent in Situ Hybridization)