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Lab - Modx (Prelim)

Modx lab
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0% found this document useful (0 votes)
11 views

Lab - Modx (Prelim)

Modx lab
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as PDF, TXT or read online on Scribd
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‭Molecular Biology & Diagnostics‬

‭Our Lady of Fatima University – Pampanga‬


‭College of Medical Laboratory Science‬
‭PRELIM‬
‭Autoclave:‬
‭MOLECULAR LABORATORY SAFETY GUIDELINES‬ ‭●‬ ‭used for sterilizing equipment used in the laboratory‬
‭https://www.youtube.com/watch?v=srURYFGb10k‬
‭MOLECULAR BIOLOGY‬ ‭Micropipette:‬
‭●‬ ‭used‬ ‭to‬‭m easure‬‭out‬‭and‬‭transfer‬‭s mall‬‭quantities‬‭of‬‭liquid‬
‭GENERAL CHARACTERISTICS‬ ‭in‬ ‭m icroliters‬ ‭or‬ ‭m illiliters‬ ‭accurately;‬ ‭s hould‬ ‭be‬ ‭used‬ ‭in‬
‭●‬ ‭ ranch‬‭of‬‭biology‬‭that‬‭deals‬‭with‬‭the‬‭s tructure‬‭and‬‭function‬‭of‬
B ‭aseptic conditions‬
‭the macromolecules‬ ‭Micropipette tips:‬
‭●‬ ‭Responsible‬ ‭for‬ ‭the‬ ‭development‬ ‭and‬ ‭performance‬ ‭of‬ ‭●‬ ‭disposable,‬ ‭autoclavable‬ ‭tips‬ ‭used‬ ‭to‬ ‭protect‬ ‭the‬
‭m olecular diagnostic test for nucleic acid‬ ‭m icropipette‬ ‭from‬ ‭contamination‬ ‭but‬ ‭it‬ ‭m ust‬ ‭be‬ ‭disposed‬
‭●‬ ‭target found in a variant of settings‬ ‭each use‬
‭EQUIPMENT‬ ‭P10‬ ‭dispenses 0.5-10ul‬‭(white)‬
‭Thermocycler:‬ ‭P20‬ ‭dispenses 2-20ul (yellow)‬
‭●‬ ‭apparatus‬‭that‬‭is‬‭used‬‭to‬‭amplify‬‭s egments‬‭of‬‭nucleic‬‭acids‬ ‭P200‬ ‭dispenses 20-200ul (yellow)‬
‭and‬ ‭has‬ ‭the‬ ‭capacity‬ ‭to‬ ‭change‬ ‭temperature‬ ‭based‬ ‭on‬ ‭its‬ ‭P1000‬ ‭dispenses 200-1000ul (blue)‬
‭pre-programmed steps‬ ‭P5000‬ ‭dispenses 1000-5000ul (white)‬
‭UV Transilluminator:‬ ‭Other materials‬
‭●‬ ‭allows‬ ‭the‬ ‭visualization‬ ‭of‬ ‭target‬ ‭DNA‬ ‭and‬ ‭proteins‬ ‭by‬ ‭●‬ ‭Spatula,‬
‭emitting‬ ‭high‬ ‭levels‬ ‭of‬ ‭UV‬ ‭radiation‬ ‭through‬ ‭the‬ ‭viewing‬ ‭●‬ ‭Baker’s cup,‬
‭s urface.‬ ‭●‬ ‭Graduated conical tubes,‬
‭Gel electrophoresis chamber:‬ ‭●‬ ‭Freezer boxes,‬
‭●‬ ‭used‬ ‭to‬ ‭isolated‬ ‭DNA‬ ‭or‬ ‭protein‬ ‭fragments‬‭by‬‭s ize‬‭in‬‭a‬‭gel‬ ‭●‬ ‭Ice buckets‬
‭m ade‬‭of‬‭agarose‬‭or‬‭polyacrylamide‬‭by‬‭the‬‭help‬‭of‬‭an‬‭electric‬
‭charge‬ ‭REAGENTS‬
‭Spectrophotometer:‬ ‭LIST OF REAGENTS USED FOR MOLECULAR LABORATORY :‬
‭●‬ ‭m easures‬ ‭light‬ ‭intensity‬ ‭as‬ ‭a‬ ‭function‬ ‭of‬ ‭a‬ ‭wavelength‬ ‭to‬ ‭Tris-base‬ ‭Glacial acetic acid‬
‭m easure‬ ‭the‬ ‭concentration‬ ‭of‬ ‭a‬ ‭compound‬ ‭in‬ ‭aqueous‬ ‭NaCl (salt)‬ ‭Proteinase K‬
‭s olution‬ ‭MgCl2‬ ‭Restriction enzymes‬
‭Microcentrifuge:‬ ‭EDTA powder‬ ‭HCl NaOH‬
‭●‬ ‭used‬ ‭for‬ ‭s pinning‬ ‭s amples‬ ‭at‬ ‭high-speed‬ ‭that‬ ‭allows‬ ‭Gel loading dye‬ ‭Boric acid‬
‭s eparation‬ ‭of‬‭s olutions‬‭based‬‭on‬‭density‬‭s uch‬‭as‬‭enabling‬ ‭Molecular weight markers‬ ‭Sodium acetate‬
‭the pelleting of nucleic acids or proteins from solutions‬ ‭Absolute ethanol‬ ‭PCR kit‬
‭Microcentrifuge tubes:‬ ‭Nuclease free water‬ ‭ELSIA kit‬
‭●‬ ‭s pecially‬ ‭engineered‬ ‭test‬ ‭tubes‬ ‭that‬ ‭can‬ ‭resist‬ ‭high‬ ‭Distilled water‬ ‭DNA isolation kit‬
‭gravitational force‬
‭Refrigerated centrifuge:‬
‭STORAGE OF BUFFER AND SOLUTION‬
‭●‬ ‭used‬ ‭for‬ ‭s amples‬ ‭that‬ ‭need‬ ‭a‬ ‭consistent‬ ‭range‬ ‭of‬ ‭ROOM TEMPERATURE‬ ‭4C‬
‭temperature‬
‭●‬ ‭Detergent‬ ‭●‬ ‭Bacterial culture‬
‭Vortex mixer:‬
‭●‬ ‭Ethanol‬ ‭●‬ ‭PCR products‬
‭●‬ ‭used‬ ‭for‬ ‭m ixing‬ ‭laboratory‬ ‭s amples,‬ ‭for‬ ‭agitation‬ ‭and‬ ‭●‬ ‭Buffers‬ ‭●‬ ‭DNA samples‬
‭encourage‬‭reactions‬‭or‬‭homogenization‬‭with‬‭high‬‭degree‬‭of‬ ‭●‬ ‭Concentrated solution‬ ‭●‬ ‭Media‬
‭precision‬ ‭●‬ ‭Acid and bases‬ ‭●‬ ‭Serum‬
‭Shaker:‬ ‭●‬ ‭Buffer‬
‭●‬ ‭used‬ ‭to‬‭m ix‬‭or‬‭agitate‬‭s olutions,‬‭often‬‭prior‬‭to‬‭placement‬‭in‬ ‭-20C‬ ‭-70C‬
‭the centrifuge‬ ‭●‬ ‭Enzymes‬ ‭●‬ ‭Bacterial culture‬
‭Analytical Balance:‬ ‭●‬ ‭RNA samples‬ ‭●‬ ‭Lipids‬
‭●‬ ‭designed for accurate measurement of mass‬ ‭●‬ ‭Always‬ ‭refer‬ ‭to‬ ‭the‬ ‭MSDS‬ ‭of‬ ‭each‬ ‭reagent‬ ‭to‬ ‭know‬ ‭its‬
‭Dry bath or water bath:‬ ‭composition‬ ‭and‬ ‭properties‬ ‭on‬ ‭how‬ ‭to‬ ‭proper‬ ‭handle‬
‭●‬ ‭used to heat sample appropriate for their incubation period‬ ‭especially when spilled and if for disposal.‬
‭pH meter:‬
‭●‬ ‭an‬‭electric‬‭devise‬‭used‬‭to‬‭m easure‬‭hydrogen‬‭ion‬‭activity‬‭of‬‭a‬
‭s olution‬
‭Biosafety cabinet:‬
‭●‬ ‭primary device used for containing infectious microorganism‬
‭●‬ ‭ utomated‬ ‭m ethod‬ ‭usually‬ ‭uses‬ ‭m agnetic‬ ‭bead‬ ‭extraction‬
A
‭m ethods‬
‭LABORATORY PROTOCOL‬ ‭Performance of Molecular Tests‬
‭●‬ ‭Check‬ ‭all‬ ‭the‬ ‭parameters‬ ‭that‬ ‭s hould‬ ‭be‬ ‭within‬ ‭the‬
‭PREANALYTICAL STANDARDS‬ ‭acceptable limits‬
‭Reduction of Identification errors‬ ‭●‬ ‭Confidence‬ ‭intervals‬‭(CIs)‬‭is‬‭used‬‭to‬‭determine‬‭the‬‭assays‬
‭●‬ ‭Patient and specimen compatibility‬ ‭performance‬

‭●‬ ‭ pecimen‬ ‭identification:‬ ‭checking‬ ‭of‬ ‭label,‬ ‭fixative‬ ‭used,‬


S ‭ OSTANALYTICAL PHASE‬
P
‭transport date and time‬ ‭Molecular Diagnostic Report‬
‭Sample Receipt and Handling‬ ‭●‬ ‭Should convey accurate information‬
‭●‬ ‭Accession‬‭numbers:‬‭this‬‭is‬‭to‬‭ensure‬‭the‬‭proper‬‭handling‬ ‭○‬ ‭Patient identification‬
‭of‬‭every‬‭sample‬‭in‬‭accordance‬‭w ith‬‭the‬‭ISO15189‬‭and‬‭ISO‬ ‭○‬ ‭Reporting style and content‬
‭9001 guide‬ ‭■‬ ‭One page of single screen reports is preferred‬
‭■‬ ‭Name‬ ‭of‬‭individual‬‭taking‬‭responsibility‬‭of‬‭the‬‭tesT‬
‭●‬ ‭ pecimen‬ ‭should‬ ‭be‬ ‭handled‬ ‭properly‬ ‭based‬ ‭on‬ ‭their‬
S ‭and contact details is important‬
‭required standard operating procedure‬ ‭■‬ ‭There‬ ‭s hould‬ ‭be‬ ‭s pell‬ ‭checkers‬ ‭to‬ ‭prevent‬
‭○‬ ‭Tissue‬‭biopsy‬‭s ample:‬‭can‬‭be‬‭received‬‭in‬‭either‬‭fixed‬‭or‬ ‭typographical errors‬
‭fresh sample‬ ‭○‬ ‭Interpretation‬
‭○‬ ‭Tissue‬ ‭blocks‬ ‭and‬ ‭s lides:‬ ‭s tored‬ ‭in‬ ‭■‬ ‭It‬ ‭m ust‬ ‭be‬ ‭reported‬ ‭correctly‬ ‭and‬ ‭interpretation‬
‭temperature-controlled environment‬ ‭s hould be provided‬
‭○‬ ‭Blood‬ ‭s ample:‬ ‭received‬ ‭in‬ ‭the‬ ‭required‬ ‭anticoagulant‬ ‭■‬ ‭Genotyping‬ ‭results‬ ‭s hould‬ ‭be‬ ‭given‬ ‭according‬ ‭to‬
‭and discarded within few days‬ ‭Human‬ ‭Genome‬‭Variation‬‭Society‬‭nomenclature‬‭at‬
‭●‬ ‭Minimization of cross-contamination‬ ‭the DNA level‬
‭○‬ ‭Replace‬ ‭the‬ ‭knife‬ ‭blades‬ ‭regularly‬ ‭especially‬‭for‬‭FFPE‬
‭block‬
‭REPORT INFORMATION‬
‭○‬ ‭The‬ ‭use‬ ‭of‬ ‭water‬ ‭baths‬ ‭to‬ ‭s tretch‬ ‭s ection‬ ‭can‬ ‭be‬
‭avoided‬ ‭by‬ ‭using‬ ‭a‬ ‭droplet‬ ‭of‬ ‭PCR-‬ ‭quality‬ ‭water‬ ‭on‬ ‭ egistration‬
R ‭number,‬ ‭age,‬
‭Patient Identification‬
‭glass slides‬ ‭gender, ordering physician‬
‭○‬ ‭Collection‬ ‭time‬ ‭and‬ ‭date‬ ‭s hould‬ ‭be‬ ‭indicated‬ ‭in‬ ‭the‬ ‭Formalin-fixed‬ ‭paraffin‬
‭Specimen Type‬
‭s pecimen‬ ‭embedded, fresh, frozen‬
‭○‬ ‭Specimen‬ ‭processing‬ ‭s hould‬ ‭be‬ ‭done‬ ‭within‬ ‭30‬ ‭Pathological Diagnosis‬ ‭Name of disease‬
‭m inutes‬ ‭Specimen‬ ‭number,‬ ‭block‬
‭Tissue sample Identification‬
‭●‬ ‭Specimen Requirements‬ ‭number‬
‭○‬ ‭Criteria‬ ‭s hould‬ ‭be‬ ‭m ade‬ ‭for‬ ‭FFPE,‬ ‭fresh‬ ‭tissue,‬ I‭mportant dates‬ ‭Date on reception or report‬
‭blood/bone‬ ‭m arrow,‬ ‭cell-free‬ ‭DNA‬ ‭for‬ ‭s pecimen‬ ‭NGS Method‬ ‭Molecular method used‬
‭acceptance‬ ‭that‬ ‭includes‬ ‭both‬ ‭quality‬ ‭and‬ ‭quantity‬ ‭of‬ ‭Interpretation‬
‭s pecimen‬
‭○‬ ‭Storage of DNA and RNA‬
‭Sample results form:‬
‭■‬ ‭Extracted DNA and RNA sample: -20C or lower‬
‭■‬ ‭PCR products: -20C or lower‬
‭■‬ ‭Sequencing libraries sample: -20C or lower‬
‭●‬ ‭Choice of analytical methods‬
‭○‬ ‭Considers‬‭the‬‭volume,‬‭diagnostic‬‭yield‬‭and‬‭feasibility‬‭of‬
‭performing‬‭the‬‭test‬‭in‬‭the‬‭laboratory‬‭s ettings‬‭that‬‭is‬‭cost‬
‭effective to consumers‬
‭○‬ ‭Factors‬ ‭determining‬ ‭the‬‭feasibility‬‭includes‬‭the‬‭training‬
‭required,‬‭turn‬‭around‬‭time‬‭of‬‭the‬‭test‬‭to‬‭perform‬‭and‬‭the‬
‭purpose of the test‬

‭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

‭M olecular Biology & Diagnostics‬ ‭M AKATAK‬ ‭3‬


‭pH‬ ‭●‬ ‭ igh‬ ‭pressure‬ ‭liquid‬ ‭chromatography‬‭(HPLC)‬‭–‬‭purification‬
H
‭ ‬ ‭Low pH –acid solution (pH <7)‬
● ‭of‬ ‭m any‬ ‭m olecules‬ ‭within‬ ‭a‬ ‭s hort‬ ‭time‬ ‭(carbohydrates,‬
‭●‬ ‭High pH –basic solution (pH >7)‬ ‭lipids, proteins, nucleic acids)‬
‭BIOLOGICAL SAFETY CABINET‬
‭●‬ ‭Primary containment of microorganisms‬ ‭‬
● ‭ ATP, dCTP, dGTP, and dTTP‬
d
‭●‬ ‭Acts as barriers‬ ‭●‬ ‭RUTH ELLEN ALONZO10:47 AM‬
‭●‬ ‭Minimize the risk of airborne infections‬ ‭●‬ ‭deoxyadenosine‬ ‭triphosphate‬ ‭(dATP),‬ ‭deoxythymidine‬
‭●‬ ‭Primary‬ ‭purpose‬ ‭protect‬ ‭the‬ ‭laboratory‬ ‭personnel‬ ‭and‬ ‭the‬ ‭triphosphate‬ ‭(dTTP),‬ ‭deoxycytidine‬ ‭triphosphate‬ ‭(dCTP),‬
‭environment from pathogenic microogranisms‬ ‭deoxyguanosine triphosphate (dGTP)‬
‭●‬ ‭With HEPA and ULPA filters‬
‭●‬ ‭Have different classes: Class I, II, and III BSC’s‬
‭FUME HOODS‬
‭●‬ ‭Used‬‭to‬‭contain‬‭hazardous‬‭gases,‬‭vapors,‬‭m ists,‬‭aerosols,‬
‭and paraticulates‬
‭SPECTROPHOTOMETER/SPECTROMETER‬
‭●‬ ‭Produces‬‭light‬‭of‬‭desired‬‭wavelength‬‭and‬‭it‬‭passes‬‭through‬
‭your‬‭s ample‬‭and‬‭reaches‬‭the‬‭photometer‬‭that‬‭m easures‬‭its‬
‭intensity‬
‭●‬ ‭Reports the value as amount of light absorbed (ABS)‬
‭●‬ ‭Uses:‬
‭○‬ ‭Measure‬ ‭growth‬ ‭of‬ ‭m icroorganisms‬ ‭like‬ ‭bacteria‬ ‭and‬
‭yeast or other cells grown in suspension‬
‭○‬ ‭Find concentration of proteins or nucleic acids‬
‭○‬ ‭Detect contaminants‬
‭ELECTROPHORESIS APPARATUS‬
‭●‬ ‭Separate‬ ‭DNA,‬ ‭RNA,‬‭and‬‭protein‬‭m olecules‬‭based‬‭on‬‭their‬
‭s ize and electrical charge‬
‭●‬ ‭Gel matrix to sieve into pieces according to sizes‬
‭●‬ ‭Components of the apparatus:‬
‭○‬ ‭Gel box, wells, comb‬
‭○‬ ‭Electrodes‬ ‭–‬ ‭provide‬ ‭current,‬ ‭positive‬ ‭and‬ ‭negative‬
‭electrodes‬
‭○‬ ‭DNA‬ ‭binding‬ ‭dye‬ ‭–‬ ‭to‬ ‭visualize‬ ‭DNA/RNA‬ ‭or‬ ‭protein‬
‭bands separated by gel electrophoresis‬
‭GEL ELECTROPHORESIS CHAMBER‬
‭●‬ ‭Used‬ ‭to‬ ‭isolate‬ ‭DNA‬ ‭or‬ ‭Protein‬ ‭fragments‬ ‭by‬ ‭s ize‬ ‭in‬ ‭a‬‭gel‬
‭m ade of agarose (DNA/RNA) or Polyacrylamide (proteins)‬
‭●‬ ‭The‬ ‭electrophoresis‬ ‭chamber‬ ‭has‬ ‭a‬ ‭electrical‬ ‭charge‬
‭running‬ ‭through‬ ‭it‬ ‭with‬ ‭the‬ ‭help‬ ‭of‬ ‭a‬ ‭power‬‭s ource‬‭to‬‭carry‬
‭DNA and protein through the gel‬
‭GEL DOCUMENTATION SYSTEM‬
‭●‬ ‭Aka gel doc, gel image system or gel imager‬
‭●‬ ‭Visualize gel images‬
‭●‬ ‭Document nucleic acids and protein in gels‬
‭●‬ ‭UV light and camera/image capturing‬
‭POLYMERASE CHAIN REACTION (PCR) MACHINES‬
‭●‬ ‭Aka Thermal cyclers or Thermocyclers‬
‭●‬ ‭Amplify DNA; highly specialized instruments‬
‭●‬ ‭Regulates temperature of the reaction‬
‭●‬ ‭3 step reaction:‬
‭○‬ ‭Denaturation‬
‭○‬ ‭Annealing‬
‭○‬ ‭Extension‬
‭●‬ ‭Application of PCR:‬
‭○‬ ‭Genotyping,‬ ‭Cloning,‬ ‭Mutation‬ ‭detection,‬ ‭Sequencing,‬
‭Microarrays, Forensics, Paternity testing‬
‭CHROMATOGRAPHY EQUIPMENT‬
‭●‬ ‭Qualitative and quantitative analysis‬
‭●‬ ‭Column‬ ‭chromatography‬ ‭–most‬ ‭common‬ ‭for‬ ‭protein‬
‭purification‬
‭●‬ ‭Gas chromatography –simple, highly sensitive‬
‭M olecular Biology & Diagnostics‬ ‭M AKATAK‬ ‭4‬
‭BASIC LABORATORY SKILLS‬ ‭enzyme mix required volume‬
‭https://www.youtube.com/watch?v=DJVNI1fgCN4‬ ‭EXAMPLE:‬
‭PIPETTING EXERCISES‬ ‭●‬ ‭There‬‭are‬‭53‬‭s amples‬‭to‬‭be‬‭tested‬‭and‬‭you‬‭need‬‭to‬‭prepare‬
‭●‬ ‭MICROPIPETTE:‬‭plunger‬‭is‬‭depressed‬‭by‬‭the‬‭thumb‬‭and‬‭as‬ ‭for‬‭a‬‭m aster‬‭m ix‬‭using‬‭BGI‬‭test‬‭kit.‬‭There‬‭are‬‭3‬‭controls‬‭you‬
‭it‬ ‭is‬ ‭released,‬ ‭liquid‬ ‭is‬ ‭drawn‬ ‭into‬ ‭a‬‭disposable‬‭plastic‬‭tip;‬ ‭need‬ ‭to‬ ‭use‬ ‭and‬ ‭to‬ ‭possible‬ ‭pipetting‬ ‭error‬ ‭is‬ ‭drop‬ ‭into‬‭2.‬
‭when the plunger is pressed again, the liquid is dispensed.‬ ‭What is the total volume of master mix you need to prepare?‬
‭PARTS OF THE MICROPIPETTE‬ ‭●‬ ‭Get the overall total (N).‬
‭●‬ ‭Plunger button‬ ‭●‬ ‭N = samples + control + error = 53 + 3 + 2‬
‭●‬ ‭Volume adjustment‬ ‭●‬ ‭N = 58‬
‭●‬ ‭Tip ejector button‬
‭●‬ ‭Tip cone/attachment‬ ‭‬
● ‭ equired volume for reaction mix = RM x N‬
R
‭PROPER HANDLING OF MICROPIPETTE‬ ‭●‬ ‭= 18.5 uL x 58‬
‭●‬ ‭= 1073 uL‬
‭●‬ ‭Make‬ ‭s ure‬ ‭it‬ ‭is‬ ‭placed‬ ‭in‬ ‭the‬ ‭right‬ ‭amount‬‭of‬‭volume‬‭to‬‭be‬
‭●‬ ‭Required volume for enzyme mix = EM x N‬
‭dispensed‬
‭●‬ ‭= 1.5 uL x 58‬
‭●‬ ‭Add‬ ‭the‬ ‭appropriate‬ ‭disposable‬ ‭pipette‬ ‭tip‬ ‭and‬ ‭press‬ ‭the‬
‭●‬ ‭= 87 uL‬
‭plunger on its first stop‬
‭●‬ ‭TOTAL MASTER MIX = required volume for RM + EM‬
‭●‬ ‭Insert‬ ‭the‬ ‭tip‬ ‭into‬ ‭the‬ ‭s olution‬ ‭to‬ ‭be‬ ‭transferred‬ ‭and‬‭s lowly‬
‭●‬ ‭= 1073 uL + 87 uL‬
‭aspirate‬
‭●‬ ‭TOTAL MASTER MIX = 1,160 uL‬
‭●‬ ‭Move‬ ‭the‬ ‭pipette‬ ‭tip‬ ‭and‬ ‭dispense‬ ‭to‬ ‭the‬ ‭desired‬ ‭tube‬ ‭by‬
‭pressing the plunger pass the first stop then to second stop‬
‭●‬ ‭ ou‬ ‭will‬ ‭now‬ ‭aspirate‬ ‭1,073‬ ‭uL‬ ‭of‬ ‭RM‬ ‭and‬ ‭87‬ ‭uL‬ ‭EM‬ ‭in‬ ‭a‬
Y
‭●‬ ‭Eject the disposable tip‬
‭s ingle tube and mix.‬
‭COMMON ERRORS IN HANDLING PIPETTES‬
‭●‬ ‭After‬‭m ixing,‬‭aspirate‬‭20‬‭uL‬‭of‬‭your‬‭m aster‬‭m ix‬‭and‬‭dispense‬
‭●‬ ‭Using uncalibrated micropipettes‬ ‭to 53 micropipette tubes.‬
‭●‬ ‭Using contaminated solution or contaminated tips‬
‭●‬ ‭Aspirating too quickly‬
‭PH METER‬
‭●‬ ‭Pipetting an angle can cause volume variation‬
‭●‬ ‭ easure‬ ‭the‬ ‭hydrogen‬ ‭ion‬ ‭activity‬ ‭in‬ ‭a‬ ‭s olution‬ ‭indicating‬
M
‭REAGENT PREPARATION‬ ‭acidity of alkalinity‬
‭MASTER MIX‬ ‭●‬ ‭pH‬ ‭of‬ ‭a‬ ‭s olution‬ ‭is‬ ‭the‬ ‭m ost‬ ‭commonly‬ ‭performed‬
‭●‬ ‭Premixed‬‭concentrated‬‭s olution‬‭that‬‭has‬‭all‬‭the‬‭components‬ ‭m easurement in the molecular laboratory‬
‭for‬ ‭a‬ ‭real‬ ‭time‬ ‭PCR‬ ‭reaction‬ ‭which‬ ‭includes‬ ‭DNA‬ ‭●‬ ‭Buffer‬‭s olution‬‭pH‬‭7.0‬‭(+/-‬‭0.02)‬‭is‬‭used‬‭as‬‭a‬‭s tandard‬‭buffer‬
‭polymerase, dNTPs, MgCl2 and buffer‬ ‭in molecular laboratory‬
‭MASTER MIX PREPARATION‬ ‭●‬ ‭It is mainly used as a calibration buffer for pH meters‬
‭●‬ ‭PCR‬ ‭Reagent‬ ‭Preparation‬ ‭involves‬ ‭the‬ ‭creation‬ ‭of‬ ‭“master‬ ‭●‬ ‭A‬ ‭buffer‬ ‭s olution‬ ‭is‬‭one‬‭which‬‭resists‬‭changes‬‭in‬‭pH‬‭when‬
‭m ix”‬ ‭s mall quantities of an acid or an alkali are added to it‬
‭●‬ ‭In BGI test kit, the master mix consists of the reagents:‬ ‭●‬ ‭It‬ ‭functions‬ ‭by‬ ‭m easuring‬ ‭the‬ ‭voltage‬ ‭developed‬ ‭between‬
‭●‬ ‭Reaction mix‬ ‭two‬ ‭electrodes‬ ‭immersed‬ ‭in‬ ‭the‬ ‭s ample‬‭and‬‭compare‬‭that‬
‭●‬ ‭Probe‬ ‭value‬ ‭to‬ ‭a‬ ‭calibration‬ ‭derived‬ ‭from‬‭the‬‭s ame‬‭electrode‬‭pair‬
‭●‬ ‭Primers‬ ‭and known standards‬
‭●‬ ‭Free nucleotides (dNTPs)‬ ‭●‬ ‭These‬ ‭s tandard‬ ‭buffer‬ ‭s olutions‬ ‭m ust‬ ‭be‬ ‭accurate‬ ‭and‬
‭●‬ ‭Enzyme mix‬ ‭reliable and are used for pH meter calibration‬
‭●‬ ‭Taq‬ ‭polymerase‬ ‭–‬ ‭a‬ ‭thermostable‬ ‭DNA‬ ‭polymerase‬ ‭PARTS OF THE pH METER‬
‭(Thermus aquaticus)‬ ‭●‬ ‭Display screen‬
‭●‬ ‭Reverse transcriptase‬ ‭●‬ ‭Selection keys‬
‭HOW TO COMPUTE FOR THE MASTER MIX?‬ ‭●‬ ‭Electrode holder‬
‭1.‬ ‭Check‬ ‭the‬ ‭package‬ ‭insert‬ ‭and‬ ‭look‬ ‭for‬ ‭the‬ ‭protocol‬ ‭●‬ ‭Probe‬
‭requirement.‬ ‭CALIBRATING PH METER‬
‭○‬ ‭Reaction mix should be 18.5 uL per well (RM)‬ ‭●‬ ‭TWO-POINT CALIBRATION‬
‭○‬ ‭Enzyme mix should be 1.5 uL per well (EM)‬ ‭○‬ ‭When using acidic solution, use a buffer that is acidic‬
‭○‬ ‭RM + EM = 20 uL per well‬ ‭○‬ ‭When using basic solution, use a buffer that is basic‬
‭2.‬ ‭Categorize‬ ‭w hat‬ ‭you‬ ‭need‬ ‭for‬ ‭the‬ ‭test‬ ‭and‬ ‭the‬ ‭possible‬ ‭PROCEDURE‬
‭errors that may occur during pipetting.‬ ‭1.‬ ‭Rinse the electrode with distilled water.‬
‭○‬ ‭Total number of samples to be tested‬ ‭2.‬ ‭Place‬ ‭the‬ ‭electrode‬ ‭in‬ ‭a‬ ‭neutral‬ ‭buffer‬ ‭with‬ ‭pH‬ ‭7.00‬
‭○‬ ‭Total number of controls to be used‬ ‭s olution.‬
‭○‬ ‭Total number of pipetting errors‬ ‭3.‬ ‭Wait‬‭for‬‭the‬‭m eter‬‭to‬‭s tabilize‬‭and‬‭adjust‬‭the‬‭m eter‬‭until‬‭it‬
‭○‬ ‭Overall total = N‬ ‭reads a pH of 7.00.‬
‭3.‬ ‭Get the required volume of the RM & EM.‬ ‭4.‬ ‭Remove‬‭the‬‭electrode‬‭from‬‭the‬‭s olution‬‭and‬‭rinse‬‭it‬‭with‬
‭○‬ ‭Required volume of reaction mix = N x RM‬ ‭distilled water.‬
‭○‬ ‭Required volume of enzyme mix = N x EM‬ ‭5.‬ ‭Place‬ ‭the‬ ‭electrode‬ ‭in‬ ‭the‬ ‭s econd‬ ‭buffer‬ ‭that‬ ‭is‬ ‭either‬
‭4.‬ ‭Get the total volume of your master mix.‬ ‭acidic or alkaline.‬
‭○‬ ‭Master‬ ‭m ix‬ ‭(uL)‬ ‭=‬ ‭reaction‬ ‭m ix‬ ‭required‬ ‭volume‬ ‭+‬ ‭6.‬ ‭Wait‬‭for‬‭a‬‭m oment‬‭to‬‭s tabilize‬‭then‬‭adjust‬‭the‬‭m eter‬‭until‬
‭M olecular Biology & Diagnostics‬ ‭M AKATAK‬ ‭5‬
‭it‬ ‭displays‬ ‭the‬ ‭s ame‬ ‭pH‬ ‭as‬ ‭the‬‭buffer‬‭you‬‭have‬‭used‬‭to‬
c‭ alibrate.‬
‭ .‬ ‭Re-place‬ ‭the‬ ‭electrode‬ ‭in‬ ‭the‬ ‭pH‬ ‭7.00‬ ‭buffer‬‭s olution.‬‭If‬
7
‭the‬ ‭reading‬ ‭does‬ ‭not‬ ‭return‬ ‭to‬ ‭7.00pH‬ ‭then‬ ‭repeat‬ ‭the‬
‭calibration procedure using both buffers.‬

‭M olecular Biology & Diagnostics‬ ‭M AKATAK‬ ‭6‬


‭ISOLATION TECHNIQUES‬
‭https://www.youtube.com/watch?v=matNxUzRwUU‬ ‭B. DIFFERENTIAL EXTRACTION‬
‭DNA ISOLATION‬ ‭●‬ ‭Specimen: sperm, epithelial cell, blood‬
‭●‬ ‭DNA‬‭can‬‭be‬‭isolated‬‭from‬‭two‬‭different‬‭types‬‭of‬‭cells‬‭without‬
‭SPECIMEN FOR DNA ISOLATION AND ITS YIELD‬
‭m ixing their contents‬
‭DNA YIELD (‬‭w ithout‬ ‭●‬ ‭Modified‬‭technique‬‭for‬‭s elective‬‭isolation‬‭of‬‭DNA‬‭for‬‭profiling‬
‭DNA YIELD (‬‭w ith‬‭amplification)‬
‭amplification)‬ ‭in cases of sexual assaults‬
‭0.5ml serum or‬ ‭Procedure‬
‭1 ml blood‬ ‭10-50ug‬ ‭0.3-3ug‬
‭plasma‬ ‭1.‬ ‭Epithelial‬ ‭cells‬ ‭are‬ ‭s electively‬ ‭lysed‬ ‭by‬ ‭the‬ ‭addition‬ ‭of‬
‭0.5cm dried‬ ‭SDS and Proteinase K‬
‭1ml buffy coat‬ ‭50-200ug‬ ‭0.04-0.7ug‬
‭blood‬ ‭2.‬ ‭Centrifugation‬ ‭is‬ ‭used‬ ‭to‬ ‭s electively‬ ‭pellet‬ ‭any‬ ‭intact‬
‭1ml bone‬ ‭s perm cells‬
‭100-500ug‬ ‭1ml saliva‬ ‭5-15 ug‬
‭m arrow‬ ‭3.‬ ‭The‬ ‭s upernatant‬ ‭with‬ ‭both‬ ‭m ale‬ ‭and‬ ‭female‬ ‭epithelial‬
‭107 cultured‬ ‭500mg bone or‬ ‭cells can be removed to a separate tube‬
‭30-70 ug‬ ‭30-50ug‬
‭cells‬ ‭teeth‬ ‭4.‬ ‭In‬‭the‬‭first‬‭tube,‬‭the‬‭isolated‬‭s perm‬‭cells‬‭are‬‭lysed‬‭by‬‭the‬
‭1mg solid‬ ‭1 pc hair‬ ‭addition‬ ‭of‬ ‭SDS,‬ ‭proteinase‬ ‭K‬ ‭and‬ ‭dithiothreitol‬ ‭to‬
‭1-10ug‬ ‭0.1-0.2ug‬ ‭release‬‭the‬‭s perm‬‭cell‬‭and‬‭on‬‭the‬‭s econd‬‭tube,‬‭the‬‭lysed‬
‭tissue‬ ‭follicles‬
‭0.5ml bacterial‬ ‭epithelial cells are kept‬
‭10-35 ug‬ ‭1mg feces‬ ‭2-100pg‬ ‭5.‬ ‭Purify‬‭both‬‭tubes‬‭by‬‭either‬‭organic‬‭or‬‭non-organic‬‭m ethod‬
‭culture‬
‭1mg feces‬ ‭2-228ug‬ ‭and transfer to a new set of tubes‬

‭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

‭B. INORGANIC ISOLATION METHODS‬


‭●‬ ‭Also known as the salting out method‬
‭●‬ ‭Uses‬ ‭low‬ ‭pH,‬ ‭high‬ ‭s alt‬ ‭condition‬ ‭to‬ ‭precipitate‬ ‭proteins‬
‭leaving DNA in the solution‬
‭●‬ ‭DNA‬‭can‬‭also‬‭be‬‭precipitated‬‭by‬‭using‬‭isopropanol‬‭pelleted‬
‭and resuspend in TE buffer‬

‭C. SOLID PHASE ISOLATION‬


‭●‬ ‭More rapid and comparable effective DNA extraction‬
‭●‬ ‭Can‬ ‭be‬ ‭performed‬ ‭using‬ ‭s olid‬ ‭m atrices‬ ‭to‬ ‭bind‬ ‭and‬ ‭wash‬
‭DNA‬
‭●‬ ‭Uses silica-based products such as diatomaceous earth‬
‭●‬ ‭Ideal for the viral and bacterial DNA isolation‬

‭ 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

‭B. SPIN COLUMN METHOD‬


‭●‬ ‭Alternative‬ ‭m ethod‬ ‭to‬ ‭guanidium‬ ‭m ethod;‬ ‭faster‬ ‭and‬ ‭less‬
‭toxic‬
‭●‬ ‭Samples should be homogenized before isolation‬

‭C. POLY(A) ISOLATION‬


‭●‬ ‭Poly(A)‬ ‭is‬ ‭the‬ ‭template‬ ‭for‬ ‭protein‬ ‭translation‬ ‭and‬ ‭m ost‬
‭m RNA carry this‬
‭●‬ ‭1-2% of total RNA is made up of mRNA‬
‭●‬ ‭Separated by affinity chromatography on oligo(dT) cellulose‬

‭M olecular Biology & Diagnostics‬ ‭M AKATAK‬ ‭8‬

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