Lab - Modx (Prelim)
Lab - Modx (Prelim)
ANALYTICAL PHASE
DNA and RNA Extraction
● Majority of incubation s teps m ust be kept at lower
temperature to inhibit possible nuclease activity while
s toring DNA or RNA samples on ice
● It is recommended to do initial DNA damage repair for
genomic DNA sequencing applications
● Test kits s hould be validated and m ethods s hould be
verified in performing the procedure
● Manualm ethods houlduseaprecipitationwashs tepswith
centrifugation of spin columns
M olecular Biology & Diagnostics M AKATAK 2
MATERIALS AND EQUIPMENT IN MOLECULAR DIAGNOSTICS MICROCENTRIFUGE TUBES
● Aka Eppendorf tubes
PERSONAL PROTECTIVE EQUIPMENT (PPE) ● Tapered,s peciallyengineeredtesttubesforcentrifugework,
● SAFETY GLASSES/GOGGLES designed to resist high G-forces induced by centrifugal
● GLOVES forces
● LABORATORY GOWN/COAT MIXERS
● LABORATORY FOOTWEAR VORTEX
SEROLOGICAL PIPETTES ● Stirs at controlled speeds to mix liquids
● Toaccuratelypipetterelatives mallvolumes,typically1-25m l SONICATOR
during experimentation ● Applies sound energy, used to fragment molecules of DNA
● Individuallywrapped,s terilepipettesareusedwhenworking ● Protein expression and purification
with cell cultures under aseptic conditions ● Uses:
MICROPIPETTES ○ Mix cells in suspensions
● Instrumentusedtom easureandextractverys mallamounts ○ Mix reagents of an assay to create homogenous
of liquids from a solution s olutions
● Differenttypeshavedifferentlevelsofaccuracy,butusuallyto VORTEX MIXER SONICATOR
the nearest microliter (uL) WATER BATH
● Often used to handle s mall amounts of s olutions in ● Container that uses water to heat or m aintain a constant
m olecular biology temperature in a
PLASTIC MICROPIPETTE TIPS ● highly controlled manner
● Disposable, autoclavable tips used to protect the ● Uses:
m icropipetter from contamination ○ To heat or thaw fragile biological s ubstances like
● Used and disposed after each use in order to prevent m ammalian cells
contamination and reduce sterile clean up and sterilization ○ To m aintain a m ore homogenous temperature control
AUTOCLAVE when working with nucleic acids and proteins
● Removes m icroorganisms (virus, bacteria, fungi, etc) and WATER BATH DRI BATH
s pores using high pressure and high temperature s team SHAKER
s terilization ● Usedtom ixoragitates olutions,oftenpriortoplacementin
● Sterile contaminated materials like biohazardous wastes the centrifuge or spectrophotometer
● Sterile glassware, plastics and pipettes for use in aseptic ● Uses:
techniques ○ To incubate antibodies, chemical reactions during
● Sterile liquids for use in experimentation experimentations for mixing and reproducible results
CENTRIFUGE ○ To aerate m edia while growing bacterial or yeast
● Is an apparatus that rotates at high s peed and s eparates cultures
s ubstances of different densities CO2 INCUBATOR
○ Microcentrifuge ● Sealed chamber with controls tom anagetemperatureand
■ Lightweight, s mall volume (0.2-2.0 m L), fast s ometime humidity and CO2 levels
acceleration for s hort intervals, uses Eppendorf ● Used to culture adherent cells under s pecific conditions
tubes m imicking normal or diseased in vivo environment
○ Ultracentrifuge PETRI DISHES/FLASK
■ Isolates mallerparticles,plasmids,DNA,RNAand ● Typeofglassorplastics hallowrounddisk/flaskcoatedwith
proteins a extracellular matrix (ECM) like material
● Uses: ● Uses:
○ Remove cell elements from blood to provide cell free ○ To culture mammalian cells in vitro
s erum or plasma ○ Can also hold culture m edium/agar to grow bacteria
○ Separate s ubcellular components (mitochondria, and viruses
nuclei, etc) MICROPLATE READER
○ Remove insoluble matter from extracted proteins ● Aka plate readers or microplate photometers
○ Pellet, DNA, RNA, proteins and lipids in isolation of ● Allows a variety of tests to be performed and measured
m acromolecules ● Multiwell plates (microplates)
MICROCENTRIFUGE ULTRACENTRIFUGE ● Uses:
MICROSCOPES ○ Quantify protein, gene expression and various
● Used to visualize objects and areas of objectsthatcannot m etabolic processes
be seen by the naked eye ○ Samples are measured by:
○ Fluorescence microscope ■ Absorbance – ELISA, protein and nucleic acid
■ Target proteins, cells or cellular components quantifications, enzyme activity assays
■ Uses fluorescent dyes/fluorochromes ■ Fluorescence–more expensive, more sensitive
○ Electron microscope ■ Luminescence–Optically simpler the fluorescence
■ Higher resolution (up to 100,000 magnification) pH METER
■ Cannot be used on live samples ● Indicates the acidity or alkalinity of as olutionexpressedin
C. HOMOGENIZATION
MATERIALS
● Specimen: fresh tissue or frozen tissue
● uffer agent
B
● Processofdisruptingbiologicalm embranesbringingtissue
○ TE buffer contains 10mM Tris and 1mM EDTA at pH
orcells ampletoahomogenousoruniforms tates uchthat
7.5-8.5
all fractions are identical in composition
● Additives
○ Mechanical method
○ NaCl: prevents DNA denaturation ○ Chemical method
○ Detergent: causes the cell to lyse m aking DNA ● Rotor-stator: contains a blade and perforated tube which
released in the solution rotates at high speed
● Others Procedure
○ EDTA:chelatingagentsthatblockstheactivityofDNase 1. Weigh all the tissue sample
enzyme 2. Grind or homogenize the tissue
○ MgCl2: protects DNA from mixing with other organelles 3. Centrifuge the sample at 10,000rpm for 10 minutes at 4C
○ Alcohol: allows precipitation of DNA 4. Collect the homogenate or the s upernatant into a
○ Proteinase K: digests contaminating proteins pre-chilled tube
○ Dithiothreitol: s tabilizes enzymes that possess free
s ulfhydryl groups D. MICROORGANISM
○ TritonX-100:lysingbacterialcellstoextractproteinand ● Somebacteriaandfungihavetoughcellwallsandm ustbe
other organelles broken down to release the nucleic acid and isolate the DNA
SAMPLE PREPARATION ○ Mechanical Method
A. DENSITY GRADIENT CENTRIFUGATION ○ Chemical Method
● Specimen:bloodinheparinwithphosphatebuffers alineor ■ 1% s odium dodecyl s ulfate + 0.2M NaOH +
acid citrate dextrose Tris-base, EDTA and glucose can break bacterial
● Based on s ize and density by employing a m edium of cell walls
graded densities that can s eparate peripheral blood ■ 8%s ucrose,8%tritonX-100,Tris-buffer,EDTAand
m ononuclear cell from other blood cells lysozyme treatment can release DNA immediately
● Ficoll-Paque: m ost common used gradient m edia for but should be precipitated with alcohol immediately
isolating mononuclear cells
○ Slow or s hort centrifugation, particles s eparate based ISOLATION METHODS
on size A. ORGANIC ISOLATION METHODS
○ Longorfastcentrifugation,particless eparatebasedon ● Hydrophobic contaminants s uch as lipids andlipoproteins
density s hould be dissolved
Procedure ● Uses high s alt, low pH and organic m ixtureofphenoland
1. Dilute blood sample to a 1:1 volume ratio chloroform for purification
2. Add 1 ml of density gradient medium to a fresh tube ● Phenol and chloroform form a biphasic emulsion when
3. Layer the diluted blood on top of the density gradient centrifuged; DNA will dissolve and isolated in the upper
4. Centrifuge at 400g for 30 minutes with brake off aqueous phase of the solution
5. After centrifugation, carefully harvest the m ononuclear ● Cetyltrimethylammonium bromide (CTAB): used as
cells on top of the gradient at the plasma layer of the tube pre-treatmentfors mallamountsofDNAfroms ampleswith
6. Wash the harvested cells twice in the appropriate buffer s mall quantity of DNA samples
M olecular Biology & Diagnostics M AKATAK 7
● RNase: enzyme used to degrade RNA contaminants
NA isolation
R
SAMPLE PREPARATION
A. GUANIDINIUM THIOCYANATE PHENOL-CHLOROFORM
EXTRACTION
● Widely used method for extraction
● Guanidinium thiocyanate is a chaotropic agent for protein
degradation