4Plants cells contain three distinct sets of DNA: nuclear, plastidic, mitochondrial
5The cell interior is separated from its surrounding environment by a phospholipid bilayer: the plasma membranePhospholipids of the plasma membrane are amphipathic, containing both a polar (hydrophilic) head and a nonpolar (hydrophobic) tail.
6Plant cells are enclosed within a rigid extracellular polysaccharide matrix: the cell wall Cellulose microfibrils, the main constituent of plant cell walls, as viewed through an electron microscope
7Nucleic Acid Extraction Requirements 1. Disruption of cell wall and membranes to liberate cellular components.2. Inactivation of DNA- and RNA-degrading enzymes (DNases, RNases).3. Separation of nucleic acids from other cellular components.• Extraction/Precipitation method• Adsorption Chromatography method
8Getting Prepared: Creating a Nuclease-Free Environment Living organisms produce several enzymes designed to degrade DNA and RNA molecules. There are several things you can do to minimize the risk of exposing your samples to external DNases and RNases.• Autoclave solutions. This is usually sufficient for getting rid of DNases,and most RNases as well.• Treat solutions with 0.1% DEPC. DEPC inactivates nucleases by covalentlymodifying the His residues in proteins. Generally considered unnecessaryfor DNA extraction. Not compatible with solutions containing Tris or HEPES.• Have a dedicated set of pipettors or use aerosol barrier tips.• Wear gloves. You should be doing this anyway forsafety reasons, but skin cells also produce RNase7,a potent RNA-degrading enzyme.• Bake glass, metal, or ceramic equipment at high temp.
10Extraction/Precipitation Method Step 1: Disruption of cell walls by grindingStep 1+2: mechanical disruption and homogenization in extraction bufferGrind sample into a fine powder to shear cell walls and membranesStep 2: Lysis of cells in extraction bufferA homogenizer allows cells to be mechanically disrupted within the extraction bufferMix thoroughly with extraction buffer to dissolve cell membranes and inhibit nuclease activityCrude lysate
11(phospholipid bilayer) DetergentsChaotropic saltsMetal chelatorsSaltsReducing agentsCTABPVPExtraction/Precipitation MethodPurposes of the Extraction Buffer1. Dissolve cellular membranes2. Inactivation of DNase and RNase3. Assist in the removal of contaminantsUse of Detergents to Lyse Cells: Like Dissolves LikeMixed micelleDetergent moleculesPlasma membrane(phospholipid bilayer)+SDS
12Extraction/Precipitation Method Step 3: Organic extractionMix thoroughly with an equal volume of organic solventAqueousCentrifugeCollect aqueous phasee.g. phenol, chloroform, or phenol:chloroformInterphaseOrganicPerform additional extractions for increased purityCrude lysate containing nucleic acids and other cell constituentsThe aqueous phase contains water-soluble molecules, including nucleic acids. Proteins and lipids become trapped in the organic phase, and are thus separated away. Insoluble plant debris become trapped in the interphase between the two layers
13Extraction/Precipitation Method Step 4: Nucleic Acid PrecipitationBeforeAfterAfterSupernatant70% EtOHCentrifugeWashCentrifugePelletDissolve pellet (H2O, TE, etc.)• Pellet down nucleic acids.• Wash pellet with 70% ethanol to removeresidual salts and other contaminants.• Discard ethanol and allow pellet to dry.• Pellet down nucleic acids.• Wash pellet with 70% ethanol to removeresidual salts and other contaminants.• Pellet down nucleic acids.Add alcohol and salt to precipitate nucleic acids from the aqueous fraction
14Overview of the Adsorption Chromatography Method Adsorption: the binding of molecules or particles to a surface
15Nucleic acids within a crude lysate are bound to a silica surface Basic PrincipleNucleic acids within a crude lysate are bound to a silica surfaceThe silica surface is washed with a solution that keeps nucleic acids bound, but removes all other substancesThe silica surface is washed with a solution unfavorable to nucleic acid binding. The solution, containing purified DNA and/or RNA, is recovered.
16Adsorption Chromatography Method Step 1: Prepare crude lysateStep 2: Adsorb to silica surfaceApply to columnCentrifugeNucleic acidsSilica-gel membraneExtraction Buffer composition favors DNA and RNA adsorption to silica:• Low pH• High ionic strength• Chaotropic saltFlow through(discard)Nucleic acids bind to the membrane, while contaminants pass through the column.Surface silanol groups are weakly acidic, and will repel nucleic acids at near neutral or high pH due to their negative charge
18Using Nucleases to Remove Unwanted DNA or RNA Add DNase+ DNase (protein)Add RNase+ RNase (protein)Depending on when nuclease treatment is performed, it may be necessary to repeat purification steps for protein removal (e.g. phenol/chloroform extraction).
19Assessing the Quality and Yield of Nucleic Acids
20Nucleic Acid Analysis via UV Spectrophotometry DNA Absorption SpectraBy measuring the amount of light absorbed by your sample at specific wavelengths, it is possible to estimate the concentration of DNA and RNA. Nucleic acids have an absorption peak at ~260nm.[dsDNA] ≈ A260 x (50 µg/mL)[ssDNA] ≈ A260 x (33 µg/mL)[ssRNA] ≈ A260 x (40 µg/mL)
21How pure is your sample?The A260/A280 ratio is ~1.8 for dsDNA, and ~2.0 for ssRNA. Ratios lower than 1.7 usually indicate significant protein contamination.The A260/A230 ratio of DNA and RNA should be roughly equal to its A260/A280 ratio (and therefore ≥ 1.8). Lower ratios may indicate contamination by organic compounds (e.g. phenol, alcohol, or carbohydrates).Turbidity can lead to erroneous readings due to light interference. Nucleic acids do not absorb light at the 320 nm wavelength. Thus, one can correct for the effects of turbidity by subtracting the A320 from readings at A230, A260 and A280.
22Checking for Degradation: DNA genomicDNARunning your sample through an agarose gel is a common method for examining the extent of DNA degradation. Good quality DNA should migrate as a high molecular weight band, with little or no evidence of smearing.RNA(degraded)
23Checking for Degradation: RNA Ribosomal RNA (rRNA) makes up more than 80% of total RNA samples. Total RNA preps should display two prominent bands after gel electrophoresis. These correspond to the 25S and 18S rRNAs, which are 3.4 kb and 1.9 kb in Arabidopsis (respectively).Good quality RNA will have:No evidence of smearing25S/18S ratio between25S18S
24Today’s Lab Objectives: Use the RNeasy Extraction Kit to isolate total RNA from Arabidopsis thaliana.Determine RNA yield