Molecular Biology Working with DNA Working with DNA
TopicsTopics
Genomic vs. Vector DNAGenomic vs. Vector DNA Purifying plasmid DNAPurifying plasmid DNA Restriction enzymesRestriction enzymes Restriction maps Restriction maps
DNADNA
GenomicGenomic Prokaryote vs. eukaryoteProkaryote vs. eukaryote Circular or linearCircular or linear One or more chromosomes One or more chromosomes
Extra-genomicExtra-genomic VectorsVectors PlasmidsPlasmids
Vectors Vs PlasmidsVectors Vs Plasmids
Vector: Vector: DNA vehicle that allows the cloning, DNA vehicle that allows the cloning,
maintenance and amplification of a maintenance and amplification of a DNA sequenceDNA sequence
PlasmidsPlasmids VirusVirus ChromosomesChromosomes
All plasmids are vectorsAll plasmids are vectors Not all vectors are plasmids Not all vectors are plasmids
PlasmidsPlasmids
Small circular DNA molecules Small circular DNA molecules maintained and amplified in maintained and amplified in eukaryotic or prokaryotic cellseukaryotic or prokaryotic cells Amplification in bacteriaAmplification in bacteria
Used as vector for cloning or Used as vector for cloning or expression of DNA of interestexpression of DNA of interest
Characteristics of plasmid vectorsCharacteristics of plasmid vectors
Restriction sites for Restriction sites for cloningcloning
Origin of replication Origin of replication (Ori)(Ori)
Selection markerSelection marker Genes conferring Genes conferring
resistance to antibioticsresistance to antibiotics
DNA IsolationDNA Isolation
GoalsGoals Isolation of DNA of interestIsolation of DNA of interest
Chromosomal or plasmid?Chromosomal or plasmid? Eliminate other componentsEliminate other components
Chromosomal or plasmid DNA?Chromosomal or plasmid DNA? ProteinsProteins RNARNA ChemicalsChemicals
Salts, detergents, etc.Salts, detergents, etc.
DNA isolation DNA isolation (cont’d)(cont’d)
Cell lysisCell lysis Cell wall and membraneCell wall and membrane
EnzymaticEnzymatic ChemicalChemical MechanicalMechanical
Isolation of DNA of interestIsolation of DNA of interest Differential sedimentationDifferential sedimentation ChromatographyChromatography
Removing other componentsRemoving other components EnzymaticEnzymatic Differential sedimentationDifferential sedimentation ChromatographyChromatography
Solutions UsedSolutions Used
Sol. I – Resuspension bufferSol. I – Resuspension buffer Tris HCl – Buffer that protects nucleic Tris HCl – Buffer that protects nucleic
acids acids EDTA - Chelates Mg++, prevents EDTA - Chelates Mg++, prevents
nucleases from working nucleases from working Sol. II – Lysis solutionSol. II – Lysis solution
NaOH - ^pH lyses cells, denatures DNA NaOH - ^pH lyses cells, denatures DNA SDS – Dissolves membranes, denatures SDS – Dissolves membranes, denatures
and binds proteins and binds proteins
Solutions Used Solutions Used (Cont’d)(Cont’d)
Sol. III- Potassium acetateSol. III- Potassium acetate Renaturation of DNARenaturation of DNA Precipitates SDSPrecipitates SDS Precipitates genomic DNA and proteinsPrecipitates genomic DNA and proteins
Isopropanol / Ethanol Isopropanol / Ethanol Precipitates nucleic acids (plasmid and ?) Precipitates nucleic acids (plasmid and ?) Salts remain soluble Salts remain soluble
TE-RNase - Tris & EDTA again; RNase??TE-RNase - Tris & EDTA again; RNase??
Quantification of DNAQuantification of DNA
Determining Conc. of DNADetermining Conc. of DNA A260 of 1.0 = 50µg/mL or 50ng/µLA260 of 1.0 = 50µg/mL or 50ng/µL
Determining Amount of DNADetermining Amount of DNA 1mL of a solution with an A260 of 1.0 contains 50µg DNA1mL of a solution with an A260 of 1.0 contains 50µg DNA 1µL of a solution with an A260 of 1.0 contains 50ng DNA1µL of a solution with an A260 of 1.0 contains 50ng DNA
Do not forget to account for the DILUTION FACTORDo not forget to account for the DILUTION FACTOR
Restriction enzymes Restriction enzymes
EndonucleaseEndonuclease Cleaves internal phosphodiester Cleaves internal phosphodiester
linkages.linkages. Recognize specific double stranded Recognize specific double stranded
DNA sequencesDNA sequences Different endonucleases recognize Different endonucleases recognize
different sequencesdifferent sequences Recognize Recognize palindrome sequencespalindrome sequences
PalindromesPalindromes
The same sequence is read in the The same sequence is read in the 5’ » 3’ direction on both strands5’ » 3’ direction on both strands
5’-GGATCC-3’3’-CCTAGG-5’
The same phosphodiester linkages The same phosphodiester linkages are cleaved on both strands!are cleaved on both strands!
5’-G
3’-C C T A G
G A T C C-3’
G-5’
Different ends are Different ends are generatedgenerated
5’-G
3’-C C T
G A
A G
T C C-3’
G-5’Blunt ends
Different ends are Different ends are generatedgenerated
5’ overhangs5’-G
3’-C C T A G
G A T C C-3’
G-5’
Different ends are Different ends are generatedgenerated
3’ overhangs3’-C
5’-G G A T C C-3’
C T A G G-5’
Compatibility of endsCompatibility of ends
Overhangs
P-CTAGHOGATC-P
OH
Compatible
P-CTAGOGATC-P
O
Annealing
Compatibility of endsCompatibility of ends
Overhangs
P-TCCAHOGATC-P
OH
Incompatible
P-TCCAHO
GATC-POH
Annealing
Restriction mapsRestriction maps
Determining the positions of Determining the positions of restriction enzyme sitesrestriction enzyme sites Linear DNA mapsLinear DNA maps Circular DNA maps (plasmids)Circular DNA maps (plasmids) Maps of inserts within vectorsMaps of inserts within vectors
ApproachApproach
1.1. Determine whether the DNA has Determine whether the DNA has digesteddigested
2.2. Is the digestion complete or Is the digestion complete or partial?partial?
3.3. How many cuts?How many cuts?
4.4. Determine the relative positionsDetermine the relative positions
1.1. Is the DNA digested?Is the DNA digested?
Compare to the Compare to the undigested controlundigested control Which samples were Which samples were
not digested?not digested? 1 and 41 and 4
Which samples were Which samples were digested?digested?
2 and 32 and 3
Ladder
Control
1 2 3 4
2.2. Is the digestion complete?Is the digestion complete?
Complete digestionComplete digestion All the DNA molecules are cleaved at all All the DNA molecules are cleaved at all
the possible sitesthe possible sites Partial digestionPartial digestion
A fraction of the molecules are not A fraction of the molecules are not digesteddigested
Partial undigestedPartial undigested A fraction of the molecules were digested, A fraction of the molecules were digested,
but not at all the possible sitesbut not at all the possible sites Partial digestionPartial digestion
Is the digestion complete Is the digestion complete or partial?or partial?
Compare to Compare to controlcontrol
Verify the Verify the intensity of the intensity of the bandsbands
Verify the sizesVerify the sizes
Ladder
Control
1 2 3 4
3.3. How many cuts?How many cuts?
Number of sitesNumber of sites Circular DNA = number of bandsCircular DNA = number of bands Linear DNA = Number of bands – 1Linear DNA = Number of bands – 1
4.4. Determine the relative Determine the relative positionspositions
The fragment sizes represent the distances The fragment sizes represent the distances between the sitesbetween the sites
Linear DNA mapsLinear DNA maps
Enzyme Fragments (Kb)
HindIII 3 and 4
SalI 2 and 5
HindIII + SalI 2 and 3
3.0 4.0 HindIII
7.0
HindIII + SalI2.0 2.03.0
Circular DNA maps (plasmids)Circular DNA maps (plasmids)
Enzyme Fragments (Kb)
BamHI 2, 3 and 5
HindIII 1 and 9
BamHI + HindIII 1, 1.5, 2, 2.5 and 3
10.0
7.0
10.0
1.0
9.0 3.0 2.0
1.0
1.5
2.5
ApproachApproach
1.1. Determine the total sizeDetermine the total size
2.2. Determine size of the insertDetermine size of the insert Total size – size of vectorTotal size – size of vector
3.3. Determine the insertion site within the Determine the insertion site within the MCSMCS
4.4. Determine which enzymes cut wihin Determine which enzymes cut wihin the insertthe insert
5.5. Relative mapping in relation to the sites Relative mapping in relation to the sites at known positionsat known positions
Insertion mapsInsertion maps
Enzyme Fragments
BamHI 7.7Kb
EcoRI 1.0, 3.0, 3.7Kb
PstI 2.0 and 5.7
XbaI 2.7 and 5.0
1.1. Total sizeTotal size• 7.7Kb7.7Kb
2.2. Insert sizeInsert size• 7.7 – 2.7 = 5.0Kb7.7 – 2.7 = 5.0Kb
3.3. Insertion siteInsertion site• Generates 2 Generates 2
fragments of which fragments of which one is the size of the one is the size of the vectorvector
• XbaIXbaI
Insertion mapsInsertion maps
Enzyme
FragmentsTotal cuts
Sites in vector
Sites in insert
BamHI 7.7Kb 1 1 0
EcoRI 1.0, 3.0, 3.7Kb 3 1 2
PstI 2.0 and 5.7 2 1 1
XbaI 2.7 and 5.0 2 Insertion site
0
Sites to map