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Gene Modulation
DICTIONARY
“AA” leader sequence: Historic nomenclature for siRNA design
guidelines, specifying overhangs to be dTdT or UU. Not part of the
siRNA molecule.
2’-ACE® chemistry: RNA synthesis chemistry proprietary to Thermo
Scientific Dharmacon. The 2’ position of the nucleotide is protected
with an acid labile ACE (2’ acetoxyethoxy) group.
Acrylamide gel electrophoresis: Technique using a polymer gel for
the high resolution separation of small fragments of DNA (10s to
100s of bases).
Adenine: One of the four base groups present in either DNA or RNA.
Abbreviated as “A”.
Adherent cells: Cells that grow as a monolayer attached to the
surface of the culture plate or flask.
Agarose gel electrophoresis: Technique using a polysaccharide gel
for the separation of DNA fragments up to 1Mb in length.
alamarBlue®: A fluorometric assay used for measuring cell viability.
(Available from BioSource Int’l).
Allele: In diploid cells there are two copies of complementary DNA;
when examining a specific nucleotide position or locus on the
DNA each copy has an allele which can be the same as each other
(homozygote) or different (heterozygote).
Allelic discrimination: Multiplexed end point PCR assay that detects
variants of a single DNA sequence (single nucleotide polymorphism)
within a population. Individuals are classified as homozygous (only
one type allele present) or heterozygous (one copy of each allele
present).
Amidite: Synthetic chemical building block for RNA or DNA
synthesis. The natural building block is a nucleotide.
Antisense strand: As part of an siRNA (or processed shRNA), it
represents the strand that is complementary to the target mRNA;
sometimes called the catalytic, targeting, or guide strand.
ATG or AUG: Codon for methionine, the translation initiation codon
or start codon.
Barcode: A unique 60 nucleotide sequence contained within a
shRNAmir construct that can be used to detect a specific construct
from a mixed population. Enables pooled screening with viral RNAi.
Not present in shRNA or SMARTvector constructs.
Base: Component of nucleotides that determine the DNA and RNA
alphabet: dA, dC, dG, dT in DNA, and A, C, G, U in RNA.
Base pair (bp): Unit of length for double-stranded RNA or DNA. It
is sometimes incorrectly used for unit of length for single-stranded
DNA or RNA.
bDNA: Branched DNA is a technique used for quantifying mRNA
level. The bDNA Kit is called QuantiGene® Reagent System and is
available from Panomics, Inc.
Biomarker: A characteristic that is objectively measured as an
indicator of normal cell and pathogenic processes or pharmalogical
responses e.g. cell death, tumorigenesis or chemosensitisation.
Biosafety Level 2: See ‘ BSL-2’ for definition.
BLAST: Basic Local Alignment Search Tool. An algorithm for
comparing primary biological sequence information, such as the
amino-acid sequences of different proteins or the nucleotides of
DNA or RNA sequences.
Branched DNA: See ‘bDNA’ for definition.
BSL-2: Biosafety Level 2. A defined set of standards, practices,
equipment and facilities associated with handling potentially
infectious agents. Applies to most cell culture hoods.
Catalytic strand: Same as the antisense, targeting, or guide strand in
siRNA/miRNA.
cDNA: Complementary DNA. DNA synthesized from a mature
mRNA template in a reaction catalyzed by the enzyme reverse
transcriptase. cDNA is often used to clone eukaryotic genes in
prokaryotes.
Cell Confluency: Density of cells in a culture plate, expressed as %.
Central polypurine tract: See ‘cPPT’ for definition.
Clone: An exact copy of all or part of a macromolecule e.g. DNA.
CMV: A type of promoter from Cytomegalovirus. This is a pol II (“2”)
promoter often used to transcribe long constructs such as naturally
ocurring mRNA or the vector cassette in the case of shRNA/
shRNAmir constructs.
Coding sequence: Section of a gene or mRNA which codes for a
protein.
Codon: In mRNA, a codon is a sequence of three nucleotides which
codes for the incorporation of a specific amino acid into the protein
being produced.
Complementary: Term used with nucleotides, sequence, or strand.
Complementary pairs of nucleotides are G and C, A and U (in RNA),
and A and T (in DNA).
Complementary DNA: See ‘cDNA’ for defintion.
Consensus sequence: A derived sequence inferred from the
alignment and comparison of multiple imperfect sequences.
Control: A reagent or experimental sample intended to confirm the
specificity of results obtained with a test reagent.
Cosuppression: Refers to the specific case of gene silencing in which
RNA from a transgene and a homologous endogenous gene are
suppressed at the same time.
cPPT: Central polypurine tract. Helps translocation of a vector into
the nucleus of non-dividing cells.
Cytosine: One of the four base groups present in either DNA or
RNA. Abbreviated as “C”.
Deoxyribonucleic acid: See ‘DNA’ for definition.
DICER: An enzyme complex which is active in the cytoplasm and
is involved in processing long dsRNA and pre-miRNA into small
interfering RNA and miRNA.
DNA: Deoxyribonucleic acid. Polymers of nucleotides dA, dC, dG
and dT.
DNase: Deoxyribonuclease, a class of endonuclease enzymes which
digest DNA. DNase I is the most common enzyme and digests single
and double-stranded DNA.
DOX: Doxycycline. A derivative of tetracycline, that is often used to
turn on inducible promoters in shRNA/shRNAmir constructs.
Doxycycline: See ‘DOX’ for definition.
Drosha: An enzyme complex involved in processing precursor
shRNA and primary miRNA into hairpin structures. This process
occurs in the nucleus and is followed by DICER processing in the
cytoplasm.
dsRNA: Double-stranded RNA.
Electroporation: A physical method to deliver oligonucleotides into
hard-to-transfect or suspension cells using an electric current.
Endogenous: Naturally present in the cell, e.g. endogenous gene,
mRNA, protein, miRNA.
Endonuclease: An enzyme which digests nucleic acids in the middle
of the sequence e.g. restriction enzymes, DNase I, RNase A.
EST: Expressed Sequence Tag. Partial sequence (500 -800 bp) of a
cDNA with limited supporting information available, typically only a
3’ or 5’ end sequence. Produced by one-shot sequencing of a cloned
mRNA.
Exogenous: Artificially introduced into a cell, e.g. exogenous gene,
mRNA, protein, miRNA.
Exon: Segments of genomic DNA which will be incorporated into
the final mature mRNA. Exons may include coding sequence, 5’
untranslated region or the 3’ untranslated region.
Exonuclease: Enzyme which digests nucleic acids starting at one
end.
Expressed Sequence Tag: See ‘EST’ for definition.
Expression ready: The cDNA or ORF is already cloned into the
expression vector for immediate use in mammalian cells.
Extinction Coefficient, ε, (L/mol•cm): The most quantitative measure
for RNA is Beer’s Law: Absorbance (260 nm) = (ε)(concentration)
(path length in cm), where ε is the molar extinction coefficient
(provided on the siRNA Product Transfer Form supplied with the
order).
FACS: Fluorescent Activated Cell Sorting. A means of measuring
certain physical and biochemical characteristics of cells or particles
as they travel in suspension one by one past a sensing point.
Fluorescence: Light emitted after absorption of light at a lower
wavelength.
Fluorescent Activated Cell Sorting: See ‘FACS’ for definition.
Fluorophore / Fluorochrome: A small molecule or part of a larger
molecule that can fluoresce.
Gag: A lentiviral packaging element that encodes for a structural
precursor protein.
Gateway adapted: A cloning system that enables efficient transfer
of DNA-fragments between plasmids using a proprietary set of
recombination sequences. It has effectively replaced the use of
restriction endonucleases and ligases. This process is patented by
Life Technologies (formerly Invitrogen).
GC Content: Specific for an RNA or DNA sequence. The number of
nucleotides G and C in a sequence, expressed as percent of total
nucleotides. For siRNAs, only one strand needs to be used for
calculating.
Gel: Short for PAGE (PolyAcrylamide Gel Electrophoresis). A method
for assessing size, integrity, and purity of DNA, RNA and protein.
Gene: A DNA sequence that encodes a specific protein. This is a
permanent copy within the cell and (generally) is not susceptible to
degradation.
Gene Ontology: A method of organizing gene products based on
three general principles: molecular function, biological process and
cellular component. These classifications can be used to generate
lists of related gene products, such as kinases (molecular function),
genes involved in apoptosis (biological process), or genes present in
the cell membrane (cellular component).
Genetic marker: Known location on a chromosome that can be used
to identify the region of the DNA by phenotype or polymorphism.
Genome: Total DNA contained within each cell of an organism, e.g.
the human genome contains 6 x 109 base pairs of DNA per cell.
Genotype: Set of alleles that determines the expression of a
particular characteristic or trait (phenotype).
Guanine: One of the four base groups present in either DNA or RNA.
Abbreviated as “G”.
Glycerol Stock: Frozen stock cultures of bacteria or yeast provided in
liquid media.
Guide strand: Same as the antisense, catalytic, or targeting strand in
siRNA/miRNA.
Heat map: A format for displaying microarray analysis data.
Typically green lines indicate decreases in mRNA levels and red
lines indicate increases in mRNA levels.
Helicase: An enzyme function associated with RISC that unwinds the
siRNA into two strands to allow loading of one single strand into the
catalytic site.
Hexadimethrine bromide: See ‘Polybrene’ for definition.
High Performance Liquid Chromatography: See ‘HPLC’ for definition.
High-titer viral particles: Transduction-ready high-titer lentiviral
particle format removes the need to prepare plasmid DNA, package
and then purify each lentivirus preparation before use. High titer is
typically ~ 1 x 10 TU/mL. TU refers to transduction unit/individual
viral particle.
Housekeeping gene: A gene that is expressed in all cell types and
at a constant level during all stages of the cell cycle. Generally used
as a control gene. Recent studies suggest even housekeeping genes
can vary in their expression levels, therefore several housekeeping
genes are often used to normalize data, especially in PCR.
HPLC: High Performance Liquid Chromatography. A method for
assessing integrity, and purity of DNA, RNA and protein (and other
molecules).
Hybridization: The reaction by which complementary strands of
nucleic acid pair and bind together. Imperfect hybrids can also form
but these are much less stable than perfectly matching sequences.
Immortalized cell line: A cell line that has acquired the ability
to proliferate indefinately through either random mutation or
deliberate modification. In contrast to primary cells which are
cultured directly from the subject.
In vitro: Describes biological experiments performed outside of a
whole animal (see in vivo), such as in cultured cells.
In vivo:Describes biological experiments performed in live, whole
laboratory animals.
Insert: The target sequence being cloned within a plasmid clone,
rather than the host vector sequence.
Intercalating dye: Non-specific fluorescent dye which fluoresces
when bound within the minor groove of double-stranded DNA e.g.
SYBR Green.
Interferon response: A cellular immune response which can
ultimately lead to cell death. This reponse can be triggered by long
dsRNA (~> 30 nucleotides) or even high concentrations of siRNAs.
Internal Ribosomal Entry Site: See ‘IRES’ for definition.
IRES: Internal Ribosomal Entry Site. A sequence that allows
translation inititation in the middle of a mRNA sequence, rather than
only at the 5’ end.
Isoforms: Used in “protein isoforms”, which are versions of a
protein with some small differences in their amino acid sequences.
Encoded by mRNA variants.
kb: Abbreviation for kilobase, one thousand bases.
Knockdown: Reduction in a target mRNA or protein level as a result
of RNAi. Expressed as percent of control. Synonym: Silencing.
Knock-out: Technique for deleting, mutating or otherwise
inactivating a gene within an organism.
Lentivirus: A genus of the Retrovirus family. Lentiviruses can deliver
a significant amount of genetic information into the DNA of the host
cell, so are one of the most efficient gene delivery vectors. This class
of virus is able to transduce non-dividing, primary cells.
Library: A molecular biology term that refers to a collection of
molecules that is screened to find the desired one. For example, an
siRNA library is a collection of siRNAs that target different genes,
and is screened to identify which gene affects the biological process
of interest.
Ligase: Enzyme which can join pieces of DNA with compatible ends
together, e.g. T4 DNA ligase.
Ligation: The process of splicing two pieces of DNA together.
Lipid: Jargon for transfection reagents that are composed of cationic
(positively-charged) lipids. Also called a liposome.
LNA: Locked Nucleic Acid. Often referred to as inaccessible RNA,
LNA’s are a modified RNA nucleotide used to increase the sensitivity
and specificity of an RNA sequence. Often used in microarrays,
antisense experiments, as well as by some siRNA and miRNA
inhibitor vendors.
Locked Nucleic Acid: See ‘LNA’ for definition.
Locus (pl. Loci): The location of a gene on a chromosome.
Long terminal repeat: See ‘LTR’ for definition.
LTR: Long terminal repeat. Homologous regions, consisting of
600-900 nucleotides, in the lentiviral vector that are required for
replication, integration, and expression of viral RNA.
MALDI-TOF: Matrix-Assisted Laser Desorption/Ionization-Time
Of Flight mass spectrometry. Method for assessing integrity and
molecular weight of DNA, RNA and protein (and other molecules).
Mass spec: Mass spectrometry. A method for assessing size and
integrity of DNA, RNA and protein (and other molecules).
Medium/Media (pl.): As in “cell culture medium”; a solution used to
grow cells in and contains nutrients necessary for their growth.
microRNA: See ‘miRNA’ for definition.
Minor groove binder (MGB): Naturally occurring antibiotic molecule
that adopts a crescent shape which fits into the minor groove of
DNA. Integration of a MGB into a DNA hybridization probe increases
the Tm of the probe and reduces the length of the required probe.
MIQE: Minimum Information for publication of Quantitative realtime PCR Experiments.
Microarray: A multiplex technology consisting of an arrayed series
of thousands of microscopic spots of DNA oligonucleotides, known
as probes (or reporters). This can be a short section of a gene or
other DNA element that are used to hybridize a cDNA or miRNA
under high-stringency conditions. Probe-target hybridization is
usually detected and quantified by detection of fluorophore.
miRBase: A central repository for miRNA nomenclature, sequence
data annotation and target prediction.
miRNA: Abbreviation for microRNA. Short endogenously expressed
RNA molecules that function as gene expression modulators.
miRNA scaffold: A native non-coding RNA into which sequences
targeting the gene of interest are cloned. This scaffold is readily
processed by the endogenous RNAi machinery, providing
enhancedperformance over other expression cassettes.
Mismatch: Non-complementary nucleotide pairs (in the context of
matching base pairs).
Mods (Modifications): Chemical modifications to the standard A, C,
G, U nucleotides.
MOI: Multiplicity of infection: the ratio of vector transducing
particles to cells.
Molecular Weight (g/mol): Sum of atomic weights of all atoms in a
molecule.
mRNA: Messenger RNA molecule. Transcription product of a
gene that gets translated into a protein. Also called message or
transcript.
Multiplicity of infection: See ‘MOI’ for definition.
NCBI: National Center for Biotechnology Information (http://www.
ncbi.nlm.nih.gov/). Public databases containing information on
DNA, RNA, and protein sequences, function, and publications.
nM (nanomolar): A concentration unit that is defined as nanomole
per liter.
Non-catalytic strand: Same as the sense, passenger, or nontargeting strand in siRNA/miRNA.
Northern Blot: A method for detecting specific mRNAs using radioor chemiluminescent-labeled DNA probes.
Nuclease: Enzyme that degrades nucleic acids; specific enzymes
can be DNA or RNA specific, act on single or double-stranded
sequences or be non-specific.
Nucleofection: A transfection method which enables transfer of
nucleic acids such as DNA, RNA or siRNA into cells. Specifically
relates to transfection via the physical method of electroporation
with the Amaxa Nucleofector system.
Nucleotide (nt): Molecules that consist of a base, a sugar and one or
more phosphates. Naturally present with one of four bases to make
A, C, G, U or T. Also used as unit of length for single-stranded DNA
or RNA.
Off-target: A gene other than the intended target that is also
regulated by the siRNA. When data for multiple genes are displayed
(e.g. from a microarray), it is called the off-target signature of the
siRNA.
Oligonucleotide: Polymer of nucleotides (nt), generally less than 100
nt. Also called an oligo.
Open Reading Frame: See ‘ORF’ for definition.
ORF: Open Reading Frame. The portion of an mRNA that contains
a sequence of bases that could potentially encode a protein. The 5’
untranslated region and 3’ untranslated region are on either side of
this section.
Overhang: Two nucleotides on the 3’-end of an siRNA strand that do
not have complementary nucleotides in the complementary strand.
Packaging: Creation of viral particles that can be used to deliver
and express a specific gene targeting sequence (as an shRNA) into
mammalian cells.
Packaging plasmid: Lentiviral vectors that contain all necessary
elements to efficiently generate active viral particles.
PAGE: Polyacrylamide Gel Electrophoresis. A method for assessing
size, integrity, and purity of DNA, RNA and protein. Sometimes
described as denaturing (to assess size of a single-stranded DNA or
RNA) or non-denaturing (to assess duplexing of two DNA or RNA
strands).
Passenger strand: Same as the sense or non-catalytic strand in
siRNA/miRNA.
PCR: Polymerase Chain Reaction. A method for amplifying specific
DNA or RNA. For RNA, a reverse transcription step before PCR is
necessary; this is termed RT-PCR. When performed as quantitative
assay, also termed quantitative PCR (qPCR) or real-time PCR.
Phenotype: Observable features of cells or organisms, e.g. shape,
size, differentiation state.
Plasmid: Additional piece of circular DNA present in bacteria into
which target DNA can be inserted to be replicated by the host
bacteria, e.g. pBR322 and pUC18.
Pol: A lentiviral packaging element that encodes for a structural
precursor protein.
Polyacrylamide Gel Electrophoresis: See ‘PAGE’ for definition.
Post-transcriptional regulation: Processes occurring after
transcribing the mRNA which affects the amount of protein
produced from a gene. Includes RNA processing efficiency and RNA
stability.
Polybrene: Hexadimethrine bromide. Has been shown to enhance
transduction of mammalian cells by 2-10 fold by binding to the cell
surface and neutralizing surface charge.
Polymerase Chain Reaction: See ‘PCR’ for definition.
Polymerase: Enzyme which uses an existing strand of template
to make a complementary copy by linking individual nucleotides
together, e.g. DNA polymerase used in PCR.
Polymorphism: DNA sequence variations at a specific position or
locus which results in variation within a population. Some diseases
are a direct result of polymorphisms.
Preliminary miRNA: See ‘pre-miRNA’ for definition.
Pre-miRNA: Preliminary miRNA. miRNAs are transcribed as primiRNAs, which are processed in the nucleus by Drosha and Pasha to
hairpin structures of about ~70 nucleotide called pre-miRNAs. These
precursors are exported to the cytoplasm by exportin5, where they
are subsequently processed by the enzyme Dicer to a ~22 nucleotide
mature miRNA.
Primary cells: Cells that are harvested from whole animals and
grown in culture. They generally survive for only a limited time,
unlike immortalized cell lines that can divide infinitely.
Primary miRNA: See ‘Pri-miRNA’ for definition.
Primer: Or oligonucleotide. Short piece of nucleic acid sequence (6 to
50 bases) used to prime DNA synthesis.
Pri-miRNA: Primary miRNA. miRNAs are transcribed as pri-miRNAs,
which are processed in the nucleus by Drosha and Pasha to hairpin
structures of about ~70 nucleotide called pre-miRNAs. These
precursors are exported to the cytoplasm by exportin5, where they
are subsequently processed by the enzyme Dicer to a ~22 nucleotide
mature miRNA.
Probe: Fragment of DNA or RNA that is labeled with a radiolabel or
fluorescent tag which when hybridized to the sequence of interest
allows detection and quantitation.
Promoter: A region of DNA that facilitates the transcription of a
particular gene. Promoters are typically located near the genes they
regulate, on the same strand and upstream (towards the 5’ region of
the sense strand).
Pulse field gel electrophoresis: Technique to size separate very large
fragments of DNA; the voltage is applied alternatively along both
axes (length and width) forcing even large molecules to separate.
qPCR: Quantitative PCR. Based on standard PCR, qPCR enables
both detection and quantification of one or more specific sequences
in a DNA sample.
Quantitative PCR: See ‘qPCR’ for definition.
RefSeq: Curated database at NCBI (see entry for NCBI for details).
This is the mRNA sequence database used by Thermo Scientific
Dharmacon for siRNA designs and Thermo Scientific Open
Biosystems shRNA designs.
Replication incompetent: Lentiviral particles that are incapable of
producing additional viral particles, due to the elimination of wildtype enhancers in the long terminal repeat region.
Restriction enzyme: Class of enzymes, generally from bacteria
which are able to recognize and cut specific sequences in DNA e.g.
ECORI.
Retrovirus: An RNA virus that is replicated in a host cell via the
enzyme reverse transcriptase to produce DNA from its RNA
genome. This class of virus is able to transduce dividing cells only.
Reverse transcriptase: DNA dependant RNA polymerase originally
isolated from retroviruses which produces a copy of DNA
(complementary DNA) from an RNA temperate.
Reverse Transfection Format: See ‘RTF’ for definition.
Ribonuclease: See ‘RNase’ for definition.
Ribonucleic acid: See ‘RNA’ for definition.
RISC: RNA Induced Silencing Complex. Complex of multiple
proteins and siRNA, part of the RNAi pathway.
RNA: Ribonucleic acid. Long polymers of ribonucleotides A, C,
G and U that naturally occurs in cells. This can be coding RNA,
termed mRNA, which is translated into protein. Other types of RNA
includerRNA, tRNA, etc. These have other functions within cells and
do not lead to proteins.
RNA Induced Silencing Complex: See ‘RISC’ for definition.
RNAi: See ‘RNA interference’ for definition.
RNA interference (RNAi): A cellular mechanism by which the
expression of a target gene is reduced due to the presence of siRNA
or miRNA.
RNAi Rescue experiment: Following knockdown of a gene by an
siRNA or shRNA, application of the relevant ORF should recover
expression of the gene. If expression is not retrieved, the phenotype
was most likely due to an off-target effect.
RNase: Ribonuclease. An enzyme responsible for cleaving and
degrading RNA. When associated with RISC it leads to cleavage of
the target mRNA. When part of experimental contamination (bench,
hands, buffers, etc) it can lead to degradation of RNA.
RTF: Reverse Transfection Format, which involves introduction of
siRNA + transfection reagent to cells while the cells are still in a
suspension state prior to adhering to the plate or flask.
S1 nuclease: Enzyme that digests only single-stranded nucleic acids.
Screen: A process for quickly identifying which molecule in an
experimental pathway, process, etc is of interest, using a library of
molecules such as siRNA/miRNA.
Seed region: Nucleotide positions 2 through 7/8 of an miRNA or the
antisense strand of an siRNA. Often called the hexamer, heptamer,
or recognition region.
Self Inactivating: See ‘SIN’ for definition.
Sense strand: When part of an siRNA, it is identical to the target
mRNA region; sometimes called the passenger or non-catalytic
strand.
Sequence: The arrangement of nucleotides in a DNA or RNA
molecule, or amino acids in a protein.
Short hairpin RNA molecule: See ‘shRNA’ for definition.
Short tandem repeat (STR): Pattern of two or more nucleotides
in DNA, repeated directly adjacent to each other. Polymorphisms
occur when the number of repeats differs between individuals;
these variances are used in the forensic analysis to create genetic
profiles of individuals.
shRNA: Short hairpin RNA molecule. Typically used by investigators
trying to develop a stable cell line. The shRNA is cleaved into an
siRNA by Dicer.
shRNAmir: An shRNA construct based on a naturally occurring primicroRNA sequence in which the sequence for the mature miRNA is
removed from the hairpin and replaced with the silencing sequence
of interest.
SIN: Self Inactivating. Self-inactivating lentiviral and retroviral
vectors are constructed by deleting the transcriptional enhancers
or the enhancers and promoter in the U3 region of the 3’ UTR.
After one round of vector replication, these changes are copied into
both the 5’ and the 3’ LTRs producing an inactive provirus that is
replication-incompetent.
Single Nucleotide Polymorphism: See ‘SNP’ for definition.
siRNA: Small interfering RNA. Double-stranded RNA, 19 nucleotide
core sequence, 2 nucleotide overhang on the 3’ end of each strand.
Small interfering RNA: See ‘siRNA’ for definition.
SNP (pronounced “snip”): Single Nucleotide Polymorphism. DNA
sequence variation (mutation) occurring when a single nucleotide
- A, T, C, or G - in the genome differs between members within a
species. SNPs may result in a disease.
Southern blot: Method for detecting specific DNA sequences using
radio or chemiluminescent DNA probes.
Splice variant: Result of alternative processing or splicing of premRNA in eukaryotes by differential inclusion, skipping or exclusion
of exons (and introns) which allows a single gene to code for
multiple proteins.
ssRNA: Single-stranded RNA.
Sticky ends: After digestion of DNA with certain restriction enzymes
the ends left have one strand overhanging the other to form a short
(4 bases) single-stranded segment which can easily anneal to other
complementary ends.
Stringency: The conditions of hybridization; when varied the
salt concentration and temperature may allow the probe to only
hybridize to it’s exact complement (high stringency) or related
sequences (low stringency). Increasing temperature or reducing the
salt concentration increases stringency.
Stop codon: Also known as a termination codon. A nucleotide
triplet within messenger RNA that signals the termination point for
translation.
Suspension cells: Cells that grow without attaching to a surface (see
adherent cells).
Taq polymerase: DNA polymerase from Thermophilus aquaticus;
enzyme is very stable at high temperatures and is able to maintain
activity during the repeated raised temperatures of PCR.
TAT: A lentiviral packaging element required for the efficient
elongation of nascent viral transcripts. Required for packaging GIPZ,
TRIPZ and pLOC.
Tetracycline Response Element: See ‘TRE’ for definition.
Thymine: One of the four base groups present in DNA. Abbreviated
as “T”.
Tm: Melting temperature of an oligonucleotide. A property of G/C
content and thus a measure of stability of two annealed strands.
Transcription: The process of copying DNA to RNA by an enzyme
called RNA polymerase. When done artificially outside of a whole
cell, it is called in vitro transcription (IVT).
Transcription factor: Protein involved in the transcription of genes;
can be tissue-specific or generic.
Transducing Unit: See ‘TU’ for definition.
Transduction: The transfer of viral, bacterial, or both bacterial and
viral DNA from one cell to another using a viral vector.
Transduction Efficiency: Refers to the fraction of cells that
successfully integrate one or more viral genomes during the
transduction process.
Transfection: A method for delivering DNA or RNA into mammalian
cells using a complexing reagent such as cationic lipids.
Transgenic: Organism that carries experimentally introduced
DNA; involves the injection of DNA into a fertilized embryo at the
pronuclear stage which is then incorporated into the genome of the
embryo.
Translation: The process of making protein from an mRNA.
When done artificially outside of a whole cell, it is called in vitro
translation.
TRE: Tetracycline Response Element. Often used in inducible vectors.
TU: Transducing Unit. Unit of measure that refers to the number
of viral particles which can transduce a population of cells and
integrate into the host genome.
Untranslated Region: See ‘UTR’ for definition.
Uridine: One of the four base groups present in RNA. Abbreviated as
“U”.
UTR: Untranslated Region. A portion of an mRNA that contains
important biological signals for gene regulation, present on each
side of the open reading frame.
Variants: As in “mRNA variants”, which are versions of an mRNA
with differences in their nucleotide sequences and may code for
different protein isoforms.
Vector: A vehicle for delivering and expressing an exogenous DNA
sequence in a cell; usually a plasmid or virus.
Vesicular Stomatitis Virus glycoprotein: See ‘VSVg’ for definition.
Viability: As in “cell viability”. A measure of cell health expressed as
percent of control.
Viral Particle: Intact virus capable of transducing cells and
expressing a sequence of interest that target specific genes for
knockdown via the RNAi pathway.
Viral titer: The number of transducing units present in a given
volume (1 mL). Titer can be assessed by a number of methodologies
including antibody and PCR-based methodologies, FACS analysis
and colony formation.
VSVg: Vesicular Stomatitis Virus glycoprotein. An envelope protein
derived from vesicular stomatitis virus. VSVg has been shown
to provide broad tropism so when incorporated into lentiviral
constructs, it enables transduction of a broad range of cell types.
Western Blot: A method for detecting a specific protein in cell
lysates. An antibody is used as a probe to detect the protein of
interest.
Woodchuck Hepatitis Virus Post-Transciptional Regulatory Element:
See ‘WPRE’ for definition.
WPRE: Woodchuck Hepatitis Virus Post-Transciptional Regulatory
Element. Increases transgene expression from a variety of viral
vectors.
Thermo Scientific Gene Modulation DICTIONARY
www.thermoscientific.com/gen
US Literature # 0007506D02U
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