                         SEQUENCE LISTING

<110>  ENCODIA, INC.
       GUNDERSON, Kevin L.
       MURANAKA, Norihito
 
<120>  METHODS FOR STABLE COMPLEX FORMATION AND RELATED KITS

<130>  4614-2002140

<150>  62/958,176
<151>  2020-01-07

<160>  50    

<170>  PatentIn version 3.5

<210>  1
<211>  20
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  P5 primer

<400>  1
aatgatacgg cgaccaccga                                                   20


<210>  2
<211>  24
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  P7 primer

<400>  2
caagcagaag acggcatacg agat                                              24


<210>  3
<211>  20
<212>  PRT
<213>  Artificial Sequence

<220>
<223>  FA-PA

<400>  3

Phe Ala Gly Val Ala Met Pro Gly Ala Glu Asp Asp Val Val Gly Ser 
1               5                   10                  15      


Gly Ser Gly Lys 
            20  


<210>  4
<211>  20
<212>  PRT
<213>  Artificial Sequence

<220>
<223>  AFA-PA

<400>  4

Ala Phe Ala Gly Val Ala Met Pro Gly Ala Glu Asp Asp Val Val Gly 
1               5                   10                  15      


Ser Gly Ser Lys 
            20  


<210>  5
<211>  19
<212>  PRT
<213>  Artificial Sequence

<220>
<223>  AA-PA

<400>  5

Ala Ala Gly Val Ala Met Pro Gly Ala Glu Asp Asp Val Val Gly Ser 
1               5                   10                  15      


Gly Ser Lys 
            


<210>  6
<211>  103
<212>  PRT
<213>  Agrobacterium tumefaciens


<220>
<221>  MISC_FEATURE
<222>  (1)..(103)
<223>  Scaffold for binder selection 1

<400>  6

Met Ser Asp Ser Pro Val Asp Leu Lys Pro Lys Pro Lys Val Lys Pro 
1               5                   10                  15      


Lys Leu Glu Arg Pro Lys Leu Tyr Lys Val Met Leu Leu Asn Asp Asp 
            20                  25                  30          


Tyr Thr Pro Arg Glu Phe Val Thr Val Val Leu Lys Ala Val Phe Arg 
        35                  40                  45              


Met Ser Glu Asp Thr Gly Arg Arg Val Met Met Thr Ala His Arg Phe 
    50                  55                  60                  


Gly Ser Ala Val Val Val Val Cys Glu Arg Asp Ile Ala Glu Thr Lys 
65                  70                  75                  80  


Ala Lys Glu Ala Thr Asp Leu Gly Lys Glu Ala Gly Phe Pro Leu Met 
                85                  90                  95      


Phe Thr Thr Glu Pro Glu Glu 
            100             


<210>  7
<211>  164
<212>  PRT
<213>  Homo sapiens


<220>
<221>  MISC_FEATURE
<222>  (1)..(164)
<223>  Scaffold for binder selection 2

<400>  7

Gln Val Ser Val Gln Pro Asn Phe Gln Gln Asp Lys Phe Leu Gly Arg 
1               5                   10                  15      


Trp Phe Ser Ala Gly Leu Ala Ser Asn Ser Ser Trp Leu Arg Glu Lys 
            20                  25                  30          


Lys Ala Ala Leu Ser Met Ala Lys Ser Val Val Ala Pro Ala Thr Asp 
        35                  40                  45              


Gly Gly Leu Asn Leu Thr Ser Thr Phe Leu Arg Lys Asn Gln Cys Glu 
    50                  55                  60                  


Thr Arg Thr Met Leu Leu Gln Pro Ala Gly Ser Leu Gly Ser Tyr Ser 
65                  70                  75                  80  


Tyr Arg Ser Pro His Phe Gly Ser Thr Tyr Ser Val Ser Val Val Glu 
                85                  90                  95      


Thr Asp Tyr Asp Gln Tyr Ala Leu Leu Tyr Ser Gln Gly Ser Lys Gly 
            100                 105                 110         


Pro Gly Glu Asp Phe Arg Met Ala Thr Leu Tyr Ser Arg Thr Gln Thr 
        115                 120                 125             


Pro Arg Ala Glu Leu Lys Glu Lys Phe Thr Ala Phe Ser Lys Ala Gln 
    130                 135                 140                 


Gly Phe Thr Glu Asp Thr Ile Val Phe Leu Pro Gln Thr Asp Lys Cys 
145                 150                 155                 160 


Met Thr Glu Gln 
                


<210>  8
<211>  5
<212>  PRT
<213>  Artificial Sequence

<220>
<223>  Bait peptide for binder selection 1


<220>
<221>  MISC_FEATURE
<222>  (1)..(1)
<223>  N-terminal pyrazole methaniminated

<220>
<221>  MISC_FEATURE
<222>  (2)..(2)
<223>  Xaa is any natural amino acid

<220>
<221>  MISC_FEATURE
<222>  (4)..(5)
<223>  an internal nine atom polyethylene glycol spacer

<220>
<221>  MISC_FEATURE
<222>  (5)..(5)
<223>  C-terminal biotinylated

<400>  8

Phe Xaa Gly Gly Lys 
1               5   


<210>  9
<211>  174
<212>  PRT
<213>  Homo sapiens


<220>
<221>  MISC_FEATURE
<222>  (1)..(174)
<223>  Scaffold for binder selection 3

<400>  9

Gly Pro Val Pro Thr Pro Pro Asp Asn Ile Gln Val Gln Glu Asn Phe 
1               5                   10                  15      


Asn Ile Ser Arg Ile Tyr Gly Lys Trp Tyr Asn Leu Ala Ile Gly Ser 
            20                  25                  30          


Thr Ser Pro Trp Leu Lys Lys Ile Met Asp Arg Met Thr Val Ser Thr 
        35                  40                  45              


Leu Val Leu Gly Glu Gly Ala Thr Glu Ala Glu Ile Ser Met Thr Ser 
    50                  55                  60                  


Thr Arg Trp Arg Lys Gly Val Cys Glu Glu Thr Ser Gly Ala Tyr Glu 
65                  70                  75                  80  


Lys Thr Asp Thr Asp Gly Lys Phe Leu Tyr His Lys Ser Lys Trp Asn 
                85                  90                  95      


Ile Thr Met Glu Ser Tyr Val Val His Thr Asn Tyr Asp Glu Tyr Ala 
            100                 105                 110         


Ile Phe Leu Thr Lys Lys Phe Ser Arg His His Gly Pro Thr Ile Thr 
        115                 120                 125             


Ala Lys Leu Tyr Gly Arg Ala Pro Gln Leu Arg Glu Thr Leu Leu Gln 
    130                 135                 140                 


Asp Phe Arg Val Val Ala Gln Gly Val Gly Ile Pro Glu Asp Ser Ile 
145                 150                 155                 160 


Phe Thr Met Ala Asp Arg Gly Glu Cys Val Pro Gly Glu Gln 
                165                 170                 


<210>  10
<211>  5
<212>  PRT
<213>  Artificial Sequence

<220>
<223>  Bait peptide for binder selection 2


<220>
<221>  MISC_FEATURE
<222>  (1)..(1)
<223>  N-terminal pyrazole methaniminated

<220>
<221>  MISC_FEATURE
<222>  (2)..(2)
<223>  Xaa is any natural amino acid

<220>
<221>  MISC_FEATURE
<222>  (4)..(5)
<223>  An internal nine atom polyethylene glycol spacer

<220>
<221>  MISC_FEATURE
<222>  (5)..(5)
<223>  C-terminal biotinylated

<400>  10

Leu Xaa Gly Gly Lys 
1               5   


<210>  11
<211>  46
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  amRT_Cs2 oligonucleotide


<220>
<221>  misc_feature
<222>  (21)..(30)
<223>  n is a, c, g, or t

<400>  11
ttcgtagtcc gcgacactag nnnnnnnnnn gttaatggac tgagtg                      46


<210>  12
<211>  46
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  amRT_Cs4 oligonucleotide


<220>
<221>  misc_feature
<222>  (21)..(30)
<223>  n is a, c, g, or t

<400>  12
ttcgtagtcc gcgacactag nnnnnnnnnn cagtaccgac tgagtg                      46


<210>  13
<211>  46
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  amRT_Cs5 oligonucleotide


<220>
<221>  misc_feature
<222>  (21)..(30)
<223>  n is a, c, g, or t

<400>  13
ttcgtagtcc gcgacactag nnnnnnnnnn gttggttaac tgagtg                      46


<210>  14
<211>  46
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  amRT_Cs1 oligonucleotide


<220>
<221>  misc_feature
<222>  (21)..(30)
<223>  n is a, c, g, or t

<400>  14
ttcgtagtcc gcgacactag nnnnnnnnnn ttaagtcgac tgagtg                      46


<210>  15
<211>  25
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  coding tag oligonucleotide

<400>  15
cactcagtca gactattcac tcagt                                             25


<210>  16
<211>  20
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  am-PL1 oligonucleotide

<400>  16
catagactag tagccggaac                                                   20


<210>  17
<211>  20
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  am-PL2oligonucleotide

<400>  17
tcgacgtaat gacaccgctc                                                   20


<210>  18
<211>  45
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  CT_PL1_S6 adaptor molecule


<220>
<221>  misc_feature
<222>  (20)..(21)
<223>  an internal six atom polyethylene glycol spacer

<400>  18
gttccggcta ctagtctatg cactcagttt ttcctgtcac tcagt                       45


<210>  19
<211>  45
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  CT_PL2_S6 adaptor molecule


<220>
<221>  misc_feature
<222>  (20)..(21)
<223>  an internal six atom polyethylene glycol spacer

<400>  19
gagcggtgtc attacgtcga cactcagttt ttcctgtcac tcagt                       45


<210>  20
<211>  20
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  coding tag barcode sequence 1

<400>  20
tggtagagcc acaaacagcc                                                   20


<210>  21
<211>  20
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  coding tag barcode sequence 2

<400>  21
ggtacaagca acgatctcca                                                   20


<210>  22
<211>  20
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  coding tag barcode sequence 3

<400>  22
ggaccatctg aatcatgcgc                                                   20


<210>  23
<211>  20
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  coding tag barcode sequence 4

<400>  23
ggatgacacg aactcacgac                                                   20


<210>  24
<211>  20
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  coding tag barcode sequence 5

<400>  24
ggcgatcaca gacattaacc                                                   20


<210>  25
<211>  20
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  coding tag barcode sequence 6

<400>  25
cacagccgat aattgcagac                                                   20


<210>  26
<211>  20
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  coding tag barcode sequence 7

<400>  26
ggtacagaca ctgcgacaac                                                   20


<210>  27
<211>  20
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  coding tag barcode sequence 8

<400>  27
gtggcaattc gtcgcaatac                                                   20


<210>  28
<211>  20
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  coding tag barcode sequence 9

<400>  28
gggtcatcac ggctcatcat                                                   20


<210>  29
<211>  20
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  coding tag barcode sequence 10

<400>  29
gccagatgtc aacacagcta                                                   20


<210>  30
<211>  20
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  coding tag barcode sequence 11

<400>  30
ccgccaaaca aatgtgtgca                                                   20


<210>  31
<211>  20
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  coding tag barcode sequence 12

<400>  31
atacacgctc ggaagactgc                                                   20


<210>  32
<211>  20
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  coding tag barcode sequence 13

<400>  32
atgatgaccg cactgactgg                                                   20


<210>  33
<211>  20
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  coding tag barcode sequence 14

<400>  33
ggacagcaga tccacctaag                                                   20


<210>  34
<211>  20
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  coding tag barcode sequence 15

<400>  34
cctgtgagag aagcagacac                                                   20


<210>  35
<211>  20
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  coding tag barcode sequence 16

<400>  35
ccgacagatc aaggcagtta                                                   20


<210>  36
<211>  20
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  coding tag barcode sequence 17

<400>  36
aatcgcagcc aagtgagtga                                                   20


<210>  37
<211>  20
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  coding tag barcode sequence 18

<400>  37
atagatgacg caccacggtc                                                   20


<210>  38
<211>  20
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  coding tag barcode sequence 19

<400>  38
agacacgaca cactggctta                                                   20


<210>  39
<211>  20
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  coding tag barcode sequence 20

<400>  39
aggagacgcc acatcgtatc                                                   20


<210>  40
<211>  41
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  adaptor molecule 1


<220>
<221>  misc_feature
<222>  (20)..(21)
<223>  an internal three carbon spacer

<220>
<221>  misc_feature
<222>  (41)..(40)
<223>  a 3'-terminal three carbon spacer

<400>  40
ggctgtttgt ggctctacca ggtaagagcg actgtagtgt g                           41


<210>  41
<211>  41
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  adaptor molecule 2


<220>
<221>  misc_feature
<222>  (20)..(21)
<223>  an internal three-carbon spacer

<220>
<221>  misc_feature
<222>  (41)..(41)
<223>  a 3'-terminal three-carbon spacer

<400>  41
tggagatcgt tgcttgtacc ggtaagagcc gatgtagtgt g                           41


<210>  42
<211>  41
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  adaptor molecule 3


<220>
<221>  misc_feature
<222>  (20)..(21)
<223>  an internal three-carbon spacer

<220>
<221>  misc_feature
<222>  (41)..(41)
<223>  a 3'-terminal three-carbon spacer

<400>  42
ggctgtttgt ggctctacca agagatggca cgtggtaaga g                           41


<210>  43
<211>  41
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  adaptor molecule 4


<220>
<221>  misc_feature
<222>  (20)..(21)
<223>  an internal three-carbon spacer

<220>
<221>  misc_feature
<222>  (41)..(41)
<223>  a 3'-terminal three-carbon spacer

<400>  43
tggagatcgt tgcttgtacc agagatggtg cgtggtaaga g                           41


<210>  44
<211>  52
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Capping oligonucleotide


<220>
<221>  misc_feature
<222>  (52)..(52)
<223>  a 3'-terminal three-carbon spacer

<400>  44
gactggagtt cagacgtgtg ctcttccgat ctttctactc ttctcactca gt               52


<210>  45
<211>  13
<212>  PRT
<213>  Artificial Sequence

<220>
<223>  target peptide 1

<400>  45

Phe Ser Gly Val Ala Arg Gly Asp Val Arg Gly Gly Lys 
1               5                   10              


<210>  46
<211>  13
<212>  PRT
<213>  Artificial Sequence

<220>
<223>  target peptide 2

<400>  46

Phe Leu Ala Glu Ile Arg Gly Asp Val Arg Gly Gly Lys 
1               5                   10              


<210>  47
<211>  21
<212>  PRT
<213>  Artificial Sequence

<220>
<223>  target peptide 3

<400>  47

Leu Ala Gly Glu Leu Ala Gly Glu Leu Ala Gly Glu Ile Arg Gly Asp 
1               5                   10                  15      


Val Arg Gly Gly Lys 
            20      


<210>  48
<211>  28
<212>  PRT
<213>  Artificial Sequence

<220>
<223>  target peptide 4


<220>
<221>  MISC_FEATURE
<222>  (1)..(1)
<223>  N-terminal dimethylated

<400>  48

Ala Glu Ser Ala Glu Ser Ala Ser Arg Phe Ser Gly Val Ala Met Pro 
1               5                   10                  15      


Gly Ala Glu Asp Asp Val Val Gly Ser Gly Ser Lys 
            20                  25              


<210>  49
<211>  18
<212>  PRT
<213>  Artificial Sequence

<220>
<223>  target peptide 5

<400>  49

Leu Ala Glu Ser Ala Phe Ser Gly Val Ala Arg Gly Asp Val Arg Gly 
1               5                   10                  15      


Gly Lys 
        


<210>  50
<211>  12
<212>  PRT
<213>  Artificial Sequence

<220>
<223>  target peptide 6

<400>  50

Ser Gly Val Ala Arg Gly Asp Val Arg Gly Gly Lys 
1               5                   10          


