5.3 Diels Alder based ligation
5.3.8 Diels Alder reactions on DNA
5.3.8.1 Labelling of ODN DA1 with N-methylmaleimide (MMI)
In 10µl overall reaction volume ODN DA1 (5µM) was combined with MMI (1µl, 100 mM in methanol) leading to a final concentration of 10 mM MMI in 10 % methanol in water.
After 1 h at r.t. the reaction was analyzed by ESI-MS.
MS-ESIcalculated for [M-H]− 6557.3, found 6556.1.
5.3.8.2 Labelling of ODN DA1 with maleimide linked fluorescein (66)
In 1 ml overall reaction volume ODN DA1 (10µM) was combined with maleimide linked fluorescein 66 (8µl or 100µl, 5 mM in DMSO) leading to a final concentration of either 40µM or 0.5 mM of 66 in 0.8 % or 10 % DMSO in sodium phosphate buffer (10 mM, pH 7.0) at r.t. 100µl were subjected to HPLC (gradient water - acetonitrile, 0-5 min 5-35 %, 5-10 min 5-35-39 %, 10-15 min 39-75 % acetonitrile) from time to time to monitor the reaction. With 40µM of 66 after 24 h 23 % of labelled DNA were detected, employing 0.5 mM of 66 after 24 h 56 % were labelled. The extent of labelling was quantified by HPLC peak integration at 260 nm. Conversion was determined using the ratio of labelled and unlabelled DNA. The product peak was identified by comparing the extinction ratio at 260 nm and 500 nm of the UV/VIS spectrum recorded by the pda-detector to be consistent with calculated results.
5.3.8.3 Labelling of 420mer PCR product with maleimide linked fluorescein (66) The PCR reaction product as obtained after PCR as described in 5.3.2.2 (10µl) was in-cubated with maleimide linked fluorescein 66 (1µl, 5 mM in DMSO) for 20 min at 0◦C.
After addition of agarose load solution (2µl) samples were analyzed by agarose gel elec-trophoresis.
Abbreviations
AA amino acid
APS ammonium peroxodisulfate ATP adenosine triphosphate Boc tert.-butyloxycarbonyl
bp base pairs
br broad
CDI carbonyl diimidazole conc. concentrated
CuAAC copper catalyzed azide alkyne cycloaddition
d doublet
DA Diels Alder cycloaddition dA 2’-deoxyadenosine
dATP 2’-deoxyadenosine triphosphate DEAE diethylaminoethyl
dG 2’-deoxyguanosine DIPEA diisopropylethylamine DMAP 4-dimethylaminopyridine DMF N,N-dimethyl formamide DMTr 4,4’-dimethoxytrityl DNA deoxyribonucleic acid
dNTP deoxynucleotide triphosphate DPPA diphenoxyl phosphoryl azide
dsDNA double stranded deoxyribonucleic acid dT 2’-deoxythymidine
dTTP thymidine triphosphate
EDC 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide EDTA ethylenediamine tetraacetic acid
ESI electron spray ionization ESI-IT ESI ion trap
EVE ethyl vinyl ether
FITC fluorescein isothiocyanate
HPLC high pressure liquid chromatography HR high resolution
IdU 5-iodo-2’deoxyuridine
ind. indole
LG leaving group
LNA locked nucleic acid
m multiplet
MMI N-methyl maleimide
MOM methoxymethyl
MPLC middle pressure liquid chromatography MS mass spectrometry
NMR nucleic magnetic resonance
nt nucleotides
ODN oligodeoxynucleotide
PAGE polyacrylamide gel electrophoresis PAMAM polyamidoamine
PCR polymerase chain reaction PNK polynucleotide kinase
PPTS pyridiniumpara-toluenesulfonate
q quartet
qn quintet
r.t. room temperature
RP reverse phase
s singlet
sat. saturated
STV streptavidin
t triplet
TBE Tris, borat, EDTA buffer
TBTA tris-(benzyltriazolyl-methyl)amine TDA-1 tris[2-(2-methoxyethoxy)ethyl]amine TEAA triethylammonium acetate
TEAB triethylammonium bicarbonate TEMED N,N,N’,N’-tetramethylethylenediamine TFA trifluoroacetic acid
TIPS triisopropylsilyl
TLC thin layer chromatography
TMEDA N,N,N’,N’-tetramethylethylendiamine TMS trimethylsilyl
UV ultraviolet
VIS visual light
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