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MBv1 GCGTGG/3IAbRQSp/ GTGCCAAGGAAGATCGACATCCAGATAGGTTA/iSpC3/iCy3/CACGC Version 1 pre 3-2017 comp2-CO-M-9-beacon-cy3-IAbRQ Complement is 21 bases long iSpC3/ The C3 Spacer phosphoramidite can be incorporated internally or at the 5'-end of the oligo https://sg.idtdna.com/site/Catalog/Modifications/Product/1056 TM CO-M-9-beacon-cy3-IAbRQ Int Cy3 iCy3/ Inspired by Yao 2003 3’-ACCTAATTCTAACGACGCACC-5’ ||| | |||| || ||| || || ||| | GTGCCAAGGAAGATCGACATCCAGATAGGTTA/iSpC3/iCy3/CACGCTGGATTAAGATTGCTGCGTGG/3IAbRQSp/ 3’-ACCTAATTCTAACGACGCACC-5’ 3IAbRQSp /iCy3/ MW 506.6 ABS 550 EM 564 https://sg.idtdna.com/pages/support/technical-vault/reading-room/quick-reference/allmodifications https://sg.idtdna.com/site/Catalog/Modifications/Product/2349 Although unclear from IDT site, 2 separate chats with IDT support confirm that Cy3 is optimally quenched by 3IAbRQSp MBv1 5’-TAACCTATCAGGATGTCGATCTTCCTTGGCAC-3’ comp-co-01L-tailyaobeacon GTGCCAAGGAAGATCGACATCCAGATAGGTTA/iSpC3/iCy3/CACGC This is tail sequence intended to mimic dna origami. Same in both MB versions. GCGTGG/3IAbRQSp/TAACCTATCAGGATGTCGATCTTCCTTGGCAC |||| ||| || ||| | | ||| |||| ||| | ||| | ||| GCGTGG/3IAbRQSp/ GTGCCAAGGAAGATCGACATCCAGATAGGTTA/iSpC3/iCy3/CACGC Version 1 pre 3-2017 Monitoring Molecular Beacon DNA Probe Hybridization at the Single-Molecule Level Gang Yao, Xiaohong Fang, Hiroaki Yokota,Toshio Yanagida, and Weihong Tan 2003 The MB sequence was 5’-biotin TTT TTT TTT T (dC-C6-NH-TMR)-C ACG CTG GAT TAA GAT TGC TGC GTG G-(DABCYL)-3’. cDNA was 5’- CCA CGC AGC AAT CTT AAT CCA-3’. 10um MBv2 5-TATATGCCGGC-3 5-GCCGGCA/IATTO647NN/ATAT-3 Version 2 post 3-2017 Our stem sequence is not identical to that in ref. Check 5’ to 3’ polarity. I think we did this to avoid multiple-Gs next to fluors. comp-to-v2-MBeacon 5’ CCAGTGAAACATACAGCACCAAC 3’ 5’ CCAGTGAAACATACAGCACCAAC 3’ 5’ GTGCCAAGGAAGATCGACATCCAGATAGGTTA/iSpC3//iCy3/TATATGCCGGCGTTGGTGCTGTATGTTTCACTGGGCCGGCA/IATTO647NN/ATAT 3’ 5’-TAACCTATCAGGATGTCGATCTTCCTTGGCAC-3’ Inspired by: Spectroscopic investigation of a FRET molecular beacon containing two fluorophores for probing DNA/RNA sequences Steffen Jockusch, Angel A. Mart´ı, Nicholas J. Turro, Zengmin Li, Xiaoxu Li, Jingyue Ju, Nathan Stevens and Daniel L. Akins IDT name is Oligo1 - our name is v2-Mbeacon-CO-M-9-cy3-ATTO647 5’ 3’ ‘The loop sequence was selected based on our interest to study sensorin mRNA in neurons. We selected as a target the 271–293 region of sensorin mRNA, which is present in the sensory neurons of the mollusk Aplysia Californica.’ comp-to-v2-MBeacon CCA GTG AAA CAT ACA GCA CCA AC idt name is Oligo1 - our name is v2-Mbeacon-CO-M-9-cy3-ATTO647 GTGCCAAGGAAGATCGACATCCAGATAGGTTA/iSpC3//iCy3/TATATGCCGGCGTTGGTGCTGTATGTTTCACTGGGCCGGCA/IATTO647NN/ATAT MBv2 IDT name is Oligo1 - our name is v2-Mbeacon-CO-M-9-cy3-ATTO647 GTGCCAAGGAAGATCGACATCCAGATAGGTTA/iSpC3/iCy3/TATATGCCGGC Version 2 post 3-2017 -idt recommendations TAACCTATCAGGATGTCGATCTTCCTTGGCAC |||| ||| || ||| | | ||| |||| ||| | ||| | ||| GCCGGCA/IATTO647NN/ATAT 23 BASE TARGET for V2 comp-to-v2-MBeacon 5’CCAGTGAAACATACAGCACCAAC3’ IDT ATTO/Cy strand GTGCCAAGGAAGATCGACATCCAGATAGGTTA/iSpC3//iCy3/TATATGCCGGCGTTGGTGCTGTATGTTTCACTGGGCCGGCA/IATTO647NN/ATAT 23 BASE LOOP 5’CCAGTGAAACATACAGCACCAAC3’ Loop: 3’ GGTCACTTTGTATGTCGTGGTTG 5’ Loop: 5’ GTTGGTGCTGTATGTTTCACTGG 3’ 5’ 3’ comp-to-v2-MBeacon CCA GTG AAA CAT ACA GCA CCA AC idt name is Oligo1 - our name is v2-Mbeacon-CO-M-9-cy3-ATTO647 GTGCCAAGGAAGATCGACATCCAGATAGGTTA/iSpC3//iCy3/TATATGCCGGCGTTGGTGCTGTATGTTTCACTGGGCCGGCA/IATTO647NN/ATAT MBv2 IDT name is Oligo1 - our name is v2-Mbeacon-CO-M-9-cy3-ATTO647 GTGCCAAGGAAGATCGACATCCAGATAGGTTA/iSpC3/iCy3/TATATGCCGGC Version 2 post 3-2017 -idt recommendations TAACCTATCAGGATGTCGATCTTCCTTGGCAC |||| ||| || ||| | | ||| |||| ||| | ||| | ||| GCCGGCA/IATTO647NN/ATAT 23 BASE TARGET for V2 comp-to-v2-MBeacon 5’CCAGTGAAACATACAGCACCAAC3’ IDT ATTO/Cy strand GTGCCAAGGAAGATCGACATCCAGATAGGTTA/iSpC3//iCy3/TATATGCCGGCGTTGGTGCTGTATGTTTCACTGGGCCGGCA/IATTO647NN/ATAT 5’CCAGTGAAACATACAGCACCAAC3’ One sequence with one more base on each end 5’-CCCAGTGAAACATACAGCACCAACG-3’ 23 BASE LOOP One with two more bases on each end and One with three more bases on each end 5’CCAGTGAAACATACAGCACCAAC3’ 5’-GCCCAGTGAAACATACAGCACCAACGC-3’ 5’-GGCCCAGTGAAACATACAGCACCAACGCC-3’ extended by one on one side only 5’-CCAGTGAAACATACAGCACCAACG-3’ Loop: 3’ GGTCACTTTGTATGTCGTGGTTG 5’ extended by two on one side only 5’-CCAGTGAAACATACAGCACCAACGC-3’ Loop: 5’ GTTGGTGCTGTATGTTTCACTGG 3’ 5’ 3’ Extended by three on one side only 5’-CCAGTGAAACATACAGCACCAACGCC-3’ extended by 4 on one side only 5’-CCAGTGAAACATACAGCACCAACGCCG-3’ MBv2 comp-to-v2-MBeacon CCA GTG AAA CAT ACA GCA CCA AC idt name is Oligo1 - our name is v2-Mbeacon-CO-M-9-cy3-ATTO647 GTGCCAAGGAAGATCGACATCCAGATAGGTTA/iSpC3//iCy3/TATATGCCGGCGTTGGTGCTGTATGTTTCACTGGGCCGGCA/IATTO647NN/ATAT 23 BASE TARGET for V2 comp-to-v2-MBeacon 5’CCAGTGAAACATACAGCACCAAC3’ IDT ATTO/Cy strand GTGCCAAGGAAGATCGACATCCAGATAGGTTA/iSpC3//iCy3/TATATGCCGGCGTTGGTGCTGTATGTTTCACTGGGCCGGCA/IATTO647NN/ATAT 5’-CCAGTGAAACATACAGCACCAACGCCG-3’ 5’-CCAGTGAAACATACAGCACCAACGCC-3’ 5’-CCAGTGAAACATACAGCACCAACGC-3’ 5’-CCAGTGAAACATACAGCACCAACG-3’ 5’-GGCCCAGTGAAACATACAGCACCAACGCC-3’ 5’-GCCCAGTGAAACATACAGCACCAACGC-3’ 5’-CCCAGTGAAACATACAGCACCAACG-3’ One sequence with one more base on each end 5’-CCCAGTGAAACATACAGCACCAACG-3’ One with two more bases on each end and One with three more bases on each end 5’-GCCCAGTGAAACATACAGCACCAACGC-3’ 5’-GGCCCAGTGAAACATACAGCACCAACGCC-3’ extended by one on one side only 5’-CCAGTGAAACATACAGCACCAACG-3’ extended by two on one side only 5’-CCAGTGAAACATACAGCACCAACGC-3’ Extended by three on one side only 5’-CCAGTGAAACATACAGCACCAACGCC-3’ extended by 4 on one side only 5’-CCAGTGAAACATACAGCACCAACGCCG-3’ below ordered 3-23-2017 comp-to-v2-Mbeacon+1-3'and5' comp-to-v2-Mbeacon+2-3'and5' comp-to-v2-Mbeacon+3-3'and5' comp-to-v2-Mbeacon+1-3' comp-to-v2-Mbeacon+2-3' comp-to-v2-Mbeacon+3-3' comp-to-v2-Mbeacon+4-3' CCCAGTGAAACATACAGCACCAACG GCCCAGTGAAACATACAGCACCAACGC GGCCCAGTGAAACATACAGCACCAACGCC CCAGTGAAACATACAGCACCAACG CCAGTGAAACATACAGCACCAACGC CCAGTGAAACATACAGCACCAACGCC CCAGTGAAACATACAGCACCAACGCCG
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