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37 Cards in this Set
- Front
- Back
Gel Mobility shift assay
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To check whether a protein will bind to a nucleic acid
Only need fragments Bound DNA with protein will move slower on the gel |
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Co-precipitation
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Protein-protein interaction
If antibody is available for YFP, it can be used to precipitate YFP via column Epitope tag is available if an antibody is not present |
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DNas foot printing
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-For DNA-protein interactions
-To determine where the protein interacts with nucleic acid -Bound protein will hinder the digestion of DNA at binding sites -DNA is end-labeled at one strand of DNA |
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Cross-linking
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-Protein-protein interactions
-Irreversible reaction -Inhibit enzyme activity -e.g. glutaraldehyde reacts with primary amines to form an imine bond linking the protein to the glutaraldehyde |
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SMRT
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Single molecule real time
-Example of 3rd (next) generation sequencing -Base corporation release fluoresce close to the polymerase. -Detect dNTP incorporation into single molecules based on fluorescence. |
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Pyrosequencing or sequencing by synthesis (454 sequencing)
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-2nd generation sequencing
-Pely on coupled reaction to detect polymerization -Release PPi to ATP, which in turn provides the energy for the luciferase to emit light |
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Primer extension
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Using R.T. to extend a short primer to the 5' end of the RNA
Use this for "transcript mapping" |
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In situ hybridization
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To locate genes on chromosomes or to detect expression in tissues
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Northern blot
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RNA on the membrane
Don't denature; RNA in NaOH RNA- RNA is chemically unstable i basic solutions |
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Eukaryotic vector
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Used for protein production expression
Allow post-transcriptional modifications Fold properly |
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Shuttle vector
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Allow cloning and modification steps to be done in bacteria
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Phagemid
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Example- pBluescript
Replicate like a plasmid |
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ORC
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Origin replication complex
DNA-binding complex that binds in all eukaryotes to origin of replication Directs DNA replication |
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qRT-PCR
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Quantitative reverse transcription PCR
qPCR Called qRT-PCR if the template is cDNA Requires specialized thermocycles to monitor eg. SYBR green dye-intercalates btwn bases of dsDNA and fluoresces, so amt fluorescence indicated amt of product |
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DNA A
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DNA/RNA hybrid or dsRNA; 11bp/turn
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DNA B
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Standard for of DNA; 10.5 bp/turn
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DNA Z
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dsDNA; left-handed and found in high [salt]
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AFLP
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Amplified fragment length polumorphism
-PCR based -Use R.E. to digest gDNA. Ligase adapters to sticky ends of restriction fragments. Use primers complementary to adapter sequence. -Restriction fragment is selecteded to be amplified. -Amplified fragments are visualized on PAGE |
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His tag
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His 6 (H6)
-Used to express YFP -Make mRNA with YFP+EK+H6. Then translate and becomes protein with H6 tag along with different proteins. Then elute proteins in a column that has nickel or antibody for H6. -Proteins with H6 tagged will be separated. Use EK to separate YFP and H6. |
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Ontology
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Conceptualization of categories and/ or relationships between anything
Means a controlled vocabulary describing biochemical, cellular, or biological roles for every sequences. |
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Polylinker
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aka Multiple cloning site (MCS)
Short segment of DNA that contains several continuous restriction sites, at which you place your insert |
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RRM
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RNA recognition motif
Protein domain that consists of 4-beta sheets Recognize sugar-phosphate backbone, intercalates with bases Sequence specific |
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Isoschizomer
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Restriction enzymes from different organisms with the same recognition sequence
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ChIP
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Chromatin immunoprecipitation
To investigate protein-DNA interactions; aimed at determining whether specific proteins are associated with specific genomic regions |
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Cosmid
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(Cos sequence + plasmid)
A hybrid plasmid that contains lambda phage cos sequences; they can be useful to build genetic libraries, especially involving large inserts |
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Zn motif
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DNA-protein interactions with cysteines on B-sheets and histidines on A-helix (which binds DNA), stabilized by zinc ion.
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Telomerase
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Adds DNA sequence repeats to the 3' end of DNA to prevent loss of important DNA from chromosome ends (because with each replication, the telomere regions are shortened.)
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TdT
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Terminal deoxynucleotidyl transferase
Used in 5' RACE: adds non-template nucleotides to the 3" end of the DNA Can make blunt ends sticky |
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RACE
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Rapid amplification of cDNA ends
Identify unknown sequence of RNA |
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Laz z(alpha)
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The lacZ gene encodes for the alpha subunit of B-galactosidase which serves as the associations/assembly domain
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HDAC
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Histone deacetylase
Enzymes that remove acetyl groups on the lysine amino acids of histones to allow DNA to wrap more tightly |
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Paralog
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Two or more different genes in the same species which are so similar in their nucleotide sequences that they are assumed to have originated following the duplication of a single ancestral gene
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E-value
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Expected value
Is a parameter that describes the number of hits one can "expect" to see by chance when searching a database of a particular size. (eg. BLAST: basic local alignment search tool used for comparing primary sequences of proteins or DNA) |
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Southern blot
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A complementary DNA hybridization prode is used to detect specific DNA sequence;
from the blot you can determine which cells incorporated the gene of interest |
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Nick translation
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Moving a nick in a phosphodiester bind around
-nick=a break in one strand -5'->3' exonuclease (DNA pol) -Tagging tecchnique takes out nick so radioactively tagger dNTPs can be inserted and moves the nick down to the 3' end |
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Intercalate
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Inclusion between bases or other molecules (eg Ethidium Bromide in between bases of DNA double helix)
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Tm
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Temperature at which there is 50% ssDNA and 50% dsDNA
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