Streptavidin sepharose was purchased from GE Healthcare (High Performance; ligand:
streptavidin; matrix: highly cross-linked agarose, 6%; average particle size: 34 μm;
binding capacity: >300 nmol biotin/ml medium). Hemin and 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulphonic acid) (ABTS) were purchased from Sigma-Aldrich.
Detection without signal amplification
10 µL streptavidin sepharose suspension was spun down and the supernatant was carefully removed. The residual was washed two times with 60µL 1x binding buffer before 5 µL immobilized primer 2 (10 µM, 50 pmol) and 5 µL 1x binding buffer were added. After 10 min the suspension was spun down and the supernatant was removed. The residual was washed with 60 µL 1x binding buffer and two times with 60 µL 1 x buffer 2.
1.2 µL template 5A/T (10 µM, 12 pmol), 1.5 µL 10x buffer 2 and 9 µL H2O were added.
After 5 min 0.3 µL KF (exo-) (5 U/µL, 1.5 U) and 3 µL G4-modified dNTP (100 µM, 300 pmol) were added and the reaction was incubated 1 h at 30°C. The suspension was spun down and the supernatant was removed. The residual was washed with 60 µL 1x buffer 2 and three times with 60 µL 1x 40K buffer.
Materials and Methods 87
5 µL 1x 40K buffer, 1.5 µL hemin (10 µM, 15 pmol), 3 µL ABTS (10 mM, 30 nmol) and 1.8 µL H2O2 (10 mM, 18 nmol) were added. For absorbance measurement a NanoDrop ND-1000 Spectrometer (ThermoScientific) was used. Pictures were taken by an iPhone4S (Apple).
Detection with signal amplification
10 µL streptavidin sepharose suspension was spun down and the supernatant was carefully removed. The residual was washed two times with 60µL 1 x binding buffer before 5 µL immobilized primer 2 (10 µM, 50 pmol) and 5 µL 1x binding buffer were added. After 10 min the suspension was spun down and the supernatant was removed.
The residual was washed with 60 µL 1 x binding buffer and two times with 60 µL 1x buffer 2.
1.2 µL template 5A/B (10 µM, 12 pmol), 1.5 µL 10 x buffer 2 and 9 µL H2O were added.
After 5 min 0.3 µL KF- (5 U/µL, 1.5 U) and 3 µL ODN-modified dNTP (100 µM, 300 pmol) were added and the reaction was incubated 1 h at 30°C. The suspension was spun down and the supernatant was removed. The residual was washed three times with 60 µL 1x buffer 2.
For signal amplification 1.2 µL circ. RCA template (10 µM, 12 pmol), 1.5 µL 10x buffer 2, 1.5 µL dNTPs (1 mM, 1.5 nmol), 10.6 µL H2O and 0.2 µL KF- (5 U/µL, 1.0 U) were added.
The reaction mixture was incubated 1 h at 30°C. The residual was washed three times with 60 µL 1x buffer 2.
15 µL DNAzyme-tagged complementary strand (0.1 nmol) in 1x buffer 2 was added and incubated for 15 min. The residual was washed with 60 µL 1x buffer 2and three times with 60 µL 1x 40K buffer.
5 µL 1x 40K buffer, 1.5 µL hemin (10 µM, 15 pmol), 3 µL ABTS (10 mM, 30 nmol) and 1.8 µL H2O2 (10 mM, 18 nmol) were added. Pictures were taken by an iPhone4S (Apple). For absorbance measurement a NanoDrop ND-1000 Spectrometer (ThermoScientific) was used.
88 Materials and Methods
89
7 Abbreviations
ABTS 2,2’-azino-bis(3-ethylbenzothiozoline-6-sulfonic acid)
Ac acetyl
ACN acetonitrile
AIDS Acquired Immune Deficiency Syndrome APS ammonium peroxodisulfate
ATP adenosine triphosphates
B nucleobase
dATP 2’-deoxyadenosine triphosphate dCTP 2’-deoxycytidine triphosphate
dNTP deoxynucleotide triphosphate
dsDNA double stranded deoxyribonucleic acid dTTP thymidine triphosphate
e.g. exempli gratia (for example) EDTA ethylenediamine tetraacetic acid
EE ethyl acetate
90 Abbreviations
ESI electron spray ionization exo- exonuclease-deficient
FPLC fast performance liquid chromatography
h hour
HIV human immunodeficiency virus HPLC high pressure liquid chromatography HR high resolution
MPLC middle pressure liquid chromatography
MS mass spectrometry
NADH Nicotinamide adenine dinucleotide NMR nucleic magnetic resonance
nt nucleotides
ODN oligodeoxynucleotide
PAGE polyacrylamide gel electrophoresis PCR polymerase chain reaction
RP-MPLC reversed phase middle pressure chromatography
s singlet
sec second
Abbreviations 91
ssDNA single stranded DNA STV streptavidin
SELEX systematic enrichment of ligands by exponential amplification SNP single nucleotide polymorphism
t triplet
Taq Thermus aquaticus
TEAA triethylammonium acetate TEAB triethylammonium bicarbonate TEMED N,N,N’,N’-tetramethylethylenediamine TFA trifluoroacetic acid
TLC thin layer chromatography
tNTP α-L-threofuranosyl nucleoside triphosphate TOF time of flight
UV ultraviolet
VIS visual light
92 Abbreviations
93
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