Scientific Reports

Table 1 Oligonucleotides used for RCA and in in situ PLA.

From: Compaction of rolling circle amplification products increases signal integrity and signal-to-noise ratio

Oligonucleotide	Description	Vendor	DNA sequence
A	Detection oligo Texas Red	Integrated DNA Technology	5' – CAGTGAATGCGAGTCCGTCTZZZZ – 3'
B	Compaction oligo	Integrated DNA Technology	5' – AGAGAGTAGTACAGCAGCCGTAAAAGAGAGTAGTACAGCAGCCGTZZZ^b – 3'
C^a	Long circularization oligo	Integrated DNA Technology	5' – CTATTAGCGTCCAGTGAATGCGAGTCCGTCTA AGAGAGTAGTACAGCAGCCGTCAAGAGTGTCTA – 3'
D^a	Short circularization oligo	Integrated DNA Technology	5' – GTTCTGTCATATTTAAGCGTCTTAA – 3'
E	Biotinylated RCA template	Eurogentech	5' – biotin-AAAAAAAAAATATGACAGAACTAGACACTCTT – 3'
F^a	Long circularization oligo for Cy3	Integrated DNA Technology	5' – CTATTAGCGTCAAGAGAGTAGTACAGCAGCCGTATCAGTG AATGCGAGTCCGTCTAACTAGTGCTGGATGATCGTCCAAGAGT GTCTA – 3'
G^a	Long circularization oligo for FITC and Cy5	Integrated DNA Technology	5' – CTATTAGCGTCAAGAGAGTAGTACAGCAGCCGTATCAGTG AATGCGAGTCCGTCTAAAGCGATCTGCGAGACCGTATAAGAGT GTCTA – 3'
H	Ligation template	Biomers	5' – GACGCTAATAGTTAAGACGCTTZZZ^b – 3'
I	Detection oligo Cy3	Integrated DNA Technology	5' – Cy3-CTAGTGCTGGATGATCGTCCZZZZ^b – 3'
J	Detection oligo FITC	Integrated DNA Technology	5' – FITC-AGCGATCTGCGAGACCGTATZZZZ^b– 3'
K^a	Padlock probe	Integrated DNA Technology	5' – GTTCTGTCATACAGTGAATGCGAGTCCGTCTAA GAGAGTAGTACAGCAGCCGTCAAGAGTGTCTA – 3'
L	Detection oligo Alexa 488	Integrated DNA Technology	5' – Alexa488-AAAAAACAGTGAATGCGAGTCCGTCTZZZZ^b – 3'
M	Ligation template	Integrated DNA Technology	5' – biotin-CTCTCTCTCTCTCTCTCTCTGTTCACGCTCACCGT GCCCAGTGAGCGAGGACTGCAGCGTAGACG – 3'
N^a	Padlock probe	Integrated DNA Technology	5' – CACTGGGCACGGTGAGTGTATGCAGCTCCTC AGTAATAGTGTCTTACAAATCAGTCATACGAGCGCCGCTGCA GTCCTCGCT – 3'
O	Ligation template	Integrated DNA Technology	5' – GACGCTAATAGTAGACACTCTT – 3'
P	Detection oligo Cy5	Integrated DNA Technology	5' – Cy5-AGCGATCTGCGAGACCGTATZZZZ^b – 3'
Q	Detection oligo Alexa 642	Integrated DNA Technology	5'– Alexa642-AGCGATCTGCGAGACCGTATZZZ^b – 3´

^aThe oligonucleotide was phosphorylated at a concentration of 2.5 mM prior to use in a buffer containing 1 mM ATP (Thermo Scientific), 1x Reaction buffer A (Thermo Scientific) and 1 U/μl T4 Polynucleotide Kinase (EK0031; Thermo Scientific) for 30 min at 37 °C. The kinase was then heat inactivated at 65 °C for 15 min.
^bZ represents 2’O-methyl-RNA Uracil.

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