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Appendix 1: Abbreviations
A
Ac2O
ACD
ACE
ADAR
ADP
Ago-2
Amp
Ampr
AntP
APS
asRNA
ATCC
ATP
attB
BCA
BDGP
BGH
BLAST
C
C. elegans
ccdB
CDC
cDNA
CIP
CmR
CMV
CPG
CPP
Cppt
Cre
CTD
Dcr-1

adenine/adenosine
acetic anhydride
active cell death
[bis(2-acetoxyethoxy)methyl orthoester]
adenosine deaminase that acts on dsRNA
adenosine diphosphate
Argonaute-like protein 2
ampicillin
ampicillin resistance
peptide derived from the Antennapedia protein
ammonium persulfate
antisense RNA
American Type Culture Collection
adenosine triphosphate
recombination site
bicinchonic acid
Berkeley Drosophila Genome Project
bovine growth hormone (gene)
basic local alignment search tool
cytosine/cytidine
Caenorhabditis elegans
blasticidin resitance gene
Centers for Disease Control
copy DNA
calf intestinal phosphatase
chloramphenicol resistance (gene)
cytomegalovirus
controlled pore glass
cell penetrating peptide
central polypurine tract
site that causes recombination
C-terminal domain
Dicer-1 phenotype (C. elegans)

RNA Interference in Practice: Principles, Basics, and Methods for Gene Silencing
in C. elegans, Drosophila, and Mammals. Ute Schepers
Copyright # 2005 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim
ISBN: 3-527-31020-7

248

Appendix 1: Abbreviations

DCR-1/2
DDM1
DEAD-box
DEC
DEPC
DexH/DEAH
DMEM
DMF
DMSO
DMT
DNase
DOD
DRSC
d-siRNA
dsOligo
dsRDB
DSRM
dsRNA
dT
DTT
dUTP
E. coli
E3L
EB
ECL
EDTA
EGFP
EGTA
eIF2C1/2
eIF2a
EMBL
endAenv
EPRIL
EURIT
ERS
ESC
esiRNA
EST
FACS
FCS
fed
FITC
FLAP
FPMP

Dicer 1/2 (Drosophila)


chromatin remodeling complex in Arabidopsis
Asp-Glu-Ala-Asp motif
1-(3-dimethylaminopropyl)-3-ethylcarbodiimide hydrochloride
diethylpyrocarbonate
RNA helicase domain
Dulbeccos modified medium
dimethylformamide
dimethylsulfoxide
dimethoxytrityl
deoxyribonuclease
[bis(trimethylsiloxy)cyclododecyloxysilyl ether]
Drosophila RNAi Screening Center
Dicer generated siRNA
double stranded oligonucleotide
double stranded RNA binding domain
double stranded RNA binding motif
double stranded RNA
deoxythymidine
dithiothreitol
deoxyuridine triphosphate
Escherichia coli
double stranded RNA binding protein of vaccinia
elution buffer from Qiagen
enhanced chemiluminescence
ethylenediamine tetraacetate
enhanced green fluorescent protein
ethyleneglycol tetraacetic acid
translation initiation factor 2 C1/2
translation initiation factor 2 alpha
European Molecular Biology Laboratory
endonuclease deficient strain
HIV gene encoding an envelope protein
enzymatic production of RNAi library
European Union for RNA Interference Technology
end-restriction site
embryonic stem cell
endoribonuclease-prepared siRNA
expressed sequence tag
fluorescence assisted cell sorting
fetal calf serum
RNAi defective mutant in C. elegans when fed with dsRNA
fluoresceine isothiocyanate
human 5-lipoxygenase activating protein
[1-(2-fluorophenyl)-4-methoxypiperidin-4-yl]

Appendix 1: Abbreviations

G
GAL4
GAPDH
GFP
Glac
globin IVS
GSMP
GST
H1
H1/2
HBS
HDV
HEPES
HGMP
Hi5
HIV
HRE
HRP
HSC
HSV
hsp
Hz
ID
IFN-a
int
IPRS
IPTG
I-SceI
ISG
JAK
K3L
kan
L14
lacI
lacUV5
lacZ
LB
let-7
let-858
LexGAD
lhRNA
lin-4
LL
loxP

guanine/guanosine
yeast transactivator
glyceraldehyde-3-phosphate dehydrogenase
green fluorescent protein
glacial
the second intron (beta IVS-II) of the human beta-globin gene
5-desoxy-5-thioguanoside-monophosphorothioate
glutathione-S-transferase
human promoter region
homology regions
HEPES buffered saline
hepatitis delta virus
2-[4-(2-hydroxyethyl)-1piperazino-ethane sulfonic acid
MRC bioinformatics resource center
insect cells from Trichoplusia ni
human immunodeficiency virus
hormone response element
horseradish peroxidase
hematopoietic stem cell
human stomatitis virus
heat shock protein
Hertz
identity
interferon a
bacteriophage lambda gene with nicking and closing activity
inversion point restriction site
isopropyl-1-thio-b-D-galactoside
mitochondrial endonuclease that recognizes and cuts an 18-bp
restriction site
interferon stimulated gene
Janus kinase
double-stranded RNA binding protein of vaccinia
kanamycin
larvae stages of C. elegans
lactose operon repressor
constitutive promoter region in the lac operon
gene encoding b-galactosidase
Luria Bertani (culture medium)
lethal-7 phenotype in C. elegans
ubiquitously expressed C. elegans gene
LexA protein transactivator
long hairpin RNA
lineage abnormal 4 phenotype in C. elegans
LexGAD response element
locus of crossover P1

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250

Appendix 1: Abbreviations

LTR
m 7G
M9
MAGIC
MAZ
MCS
MDCK cells
F
MEM
MET1
mir-23
miRNA
MOI
MRC
mRNA
MTD
mut-7
myo-2
myo-3
N
N. crassa
N3
NCBI
NEB
Neor
NIH
Ni-NTA
NLS
NMD
N-Me-Imid
NMR
nt
OAS
OD
ORF
P1,2,3
PAGE
PAZ domain
PB
PBS
PCD
pCMV
PCR
pDNA
PE

long terminal repeat


7-methylguanosine
minimal culture medium
mating assisted genetically integrated cloning
RNA polymerase pausing site
multiple cloning site
Madin-Darby canine kidney cells
Farad (unit of electrical capacitance)
minimal essential medium
methyltransferase 1
micro RNA 23
micro RNA
multiplicity of infection
Medical Research Council (UK)
messenger RNA
modification of common transfer RNA-derived
mutant phenotype in C. elegans
C. elegans gene expressed in pharyngeal muscle
C. elegans gene expressed in body wall muscle
any nucleotide
Neurospora crassa
buffer from Qiagen
National Center for Bioinformatics (USA)
New England Biolabs
neomycin resistance (gene)
National Institutes of Health (USA)
nickel-nitrilotriacetic acid
nuclear localization signal
nonsense mediated RNA decay
N-methylimidazole
nuclear magnetic resonance
nucleotide
2-5-oligoadenylate synthase
optical density
open reading frame
buffers from Qiagen
polyacrylamide gel electrophoresis
domain conserved in PIWI, Argonaute, Zwille (Drosophila)
buffer from Qiagen
phosphate buffered saline
programmed cell death
CMV promoter
polymerase chain reaction
plasmid DNA
buffer from Qiagen

Appendix 1: Abbreviations

PEI
P-element
pepsiRNA
pfu
PGK-Puro
PI
Pi
PKR
Pol II
Pol III
pol
pre-miRNA
pri-miRNA
psiRNA
PTD
PTGS
puro
PVDF
C
QDE-1
R2D2
RDE-1
RDE-4
RdRp
recAre-hDicer
REV
RISC
RISC*
RNAi
RNase III
RNP
rNTP
r.p.m.
RPMI
rps-5/28
RRE
RRF-1/2/3
rrf-3
rRNA
RS
RSV
RT
RT-PCR
RZPD

polyethyleneimine
Drosophila transposon
peptide coupled siRNA
plaque forming units
phosphoglycerate kinase promoter-puromycin resistance
propidium iodide
pyrophosphate
protein kinase R
RNA polymerase II
RNA polymerase III
HIV gene encoding a polymerase gene
precursor miRNA
primary transcript of miRNA
plasmid based siRNA
protein transduction domain
post transcriptional gene silencing
puromycin
polyvinylidene fluoride
Psi element (HIV packaging sequence)
quelling deficient phenotype in Neurospora crassa
tandem dsRNA binding domain (R2)-Dicer-2 (D2) complex
RNAi deficient-1 phenotype in C. elegans
RNAi deficient-4 phenotype in C. elegans
RNA dependent (directed) RNA polymerase
recombinase deficiency in E. coli
recombinant-human Dicer
HIV gene
RNA induced silencing complex
activated RNA induced silencing complex
RNA interference
ribonuclease type III
ribonucleotide protein complex
ribonucleotide triphosphate
revolutions per minute
media formulation
C. elegans gene expressed in multiple tissues
Rev response element
RdRp deficient phenotype in C. elegans
putative RNA-directed RNA polymerase in C. elegans
ribosomal RNA
restriction site
Rous sarcoma virus
room temperature
reverse transcription-PCR
Deutsches Resourcenzentrum fr Genomforschung

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252

Appendix 1: Abbreviations

S2
S2Na2
SARS
sbCD
SDS
Sf9
sgs2/sde2
SH2
shRNA
sid
Sil
SIN-LTR
siRNA
snb-1
SOS
SPEED
sRNA
SSearch
ssRNA
STAT
stRNA
SURE II
T
T/A cloning
T5
T7 promoter
T7/T3/Sp6
TAE
TAT
TATA
TAT-NLS
TB
TBDMS
TBE
TBS-T
TCA
TE
TEAHF
TEMED
tet
tetO
tetR

Schneider cells, Drosophila cells


disodium-2-carbamoyl-2-cyanoethylene-1,1dithiolate trihydrate
severe acute respiratory syndrome
E. coli exonuclease
sodium dodecyl sulphate
insect cells from Spodoptera frugiperda
PTGS deficient mutant of C. elegans
Src homology domain
short hairpin RNA
systemic RNAi defective mutants of C. elegans
silyl
self inactivating -LTR
small (short) interfering RNA
C. elegans maternal gene
repair system in E. coli
small interfering RNA production by enzymatic engineering
of DNA
sense RNA
Smith-Waterman algorithm
single stranded RNA
signal transducer and activator of transcription
small temporal RNA
E. coli strain
thymine/thymidine
cloning with single 3-T overhangs into a vector with
5-A overhangs
Pol III termination signal
recognition sequence for T7 RNA polymerase
RNA polymerases (from bacteriophages)
tris-acetate-EDTA buffer
HIV protein
promoter element
fusion peptide from TAT peptide and nuclear localization
sequence
terrific broth culture medium
tert-butyldimethylsilyl
tris-borate-EDTA buffer
tris buffered saline plus Tween 20
trichloroethane
tris-EDTA buffer
triethylammonium fluoride
N,N,N,N-tetramethylene diamine
tetracycline
tetracycline operon
tetracycline repressor

Appendix 1: Abbreviations

TGS
TOM
TRE
Tris
tRNA
TRz
tTA
TU
Tudor SN
Tyk2
u
U
U6
UAS
unc-119
unc-22
UTR
uvrC
VA RNA
Vif
vit-2
VSV
VSVG
WRE
WPRE
WT
x-gal
XYT
zeor

transcriptional gene silencing


[(triisopropylsilyl)oxy]methyl group
tTA response element
trishydroxymethylaminomethane
transfer RNA
trimming ribozyme
tetracycline controlled transactivator
transducing units
Tudor staphylococcal nuclease
Janus family tyrosine kinase
unit
uracil/uridine
gene/promoter element in mice
upstream activation sequence
C. elegans gene expressed in neurons
C. elegans gene expressed in adults
untranslated region
UV repair system
two virus-associated RNA
viral infectivity factor of HIV
C. elegans gene expressed in intestine
vesicular stomatitis virus
vesicular stomatitis virus glycoprotein
Woodchuck hepatitis B virus RNA regulatory element
Woodchuck hepatitis virus posttranscriptional regulatory element
wild type
5-chloro-4-bromo-3-indolyl-b-D-galactoside
culture medium formulation
Zeocin resistance

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