                         SEQUENCE LISTING

<110>  University of Iowa Research Foundation
       McCaffrey, Anton P.
       Cradick, Thomas J.
 
<120>  ZINC-FINGER NUCLEASE AND RNA INTERFERENCE MEDIATED INACTIVATION 
       OF VIRAL GENOMES

<130>  79880-365458

<150>  60/908,240
<151>  2007-03-27

<160>  28    

<170>  PatentIn version 3.3

<210>  1
<211>  7
<212>  PRT
<213>  Artificial

<220>
<223>  Linker

<400>  1

Pro Lys Lys Lys Arg Lys Val 
1               5           


<210>  2
<211>  5
<212>  PRT
<213>  Artificial

<220>
<223>  Linker

<400>  2

Asp Gly Gly Gly Ser 
1               5   


<210>  3
<211>  5
<212>  PRT
<213>  Artificial

<220>
<223>  Linker

<400>  3

Thr Gly Glu Lys Pro 
1               5   


<210>  4
<211>  9
<212>  PRT
<213>  Artificial

<220>
<223>  Linker

<400>  4

Leu Arg Gln Lys Asp Gly Glu Arg Pro 
1               5                   


<210>  5
<211>  4
<212>  PRT
<213>  Artificial

<220>
<223>  Linker

<400>  5

Gly Gly Arg Arg 
1               


<210>  6
<211>  8
<212>  PRT
<213>  Artificial

<220>
<223>  Linker

<400>  6

Gly Gly Arg Arg Gly Gly Gly Ser 
1               5               


<210>  7
<211>  9
<212>  PRT
<213>  Artificial

<220>
<223>  Linker

<400>  7

Leu Arg Gln Arg Asp Gly Glu Arg Pro 
1               5                   


<210>  8
<211>  12
<212>  PRT
<213>  Artificial

<220>
<223>  Linker

<400>  8

Leu Arg Gln Lys Asp Gly Gly Gly Ser Glu Arg Pro 
1               5                   10          


<210>  9
<211>  22
<212>  RNA
<213>  Artificial

<220>
<223>  RNAi trigger

<400>  9
ugaaguaugc cucaaggucg gu                                              22


<210>  10
<211>  22
<212>  RNA
<213>  Artificial

<220>
<223>  RNAi trigger

<400>  10
ugacauugcu gagaguccaa ga                                              22


<210>  11
<211>  22
<212>  RNA
<213>  Artificial

<220>
<223>  RNAi trigger

<400>  11
uacauagagg uuccuugagc ag                                              22


<210>  12
<211>  22
<212>  RNA
<213>  Artificial

<220>
<223>  RNAi trigger

<400>  12
uuacuguucc ugaacuggag cc                                              22


<210>  13
<211>  22
<212>  RNA
<213>  Artificial

<220>
<223>  RNAi trigger

<400>  13
ucuauaacug uuucucuucc aa                                              22


<210>  14
<211>  22
<212>  RNA
<213>  Artificial

<220>
<223>  RNAi trigger

<400>  14
uguaguaugc ccugagccug ag                                              22


<210>  15
<211>  22
<212>  RNA
<213>  Artificial

<220>
<223>  RNAi trigger

<400>  15
uaguguugac auaacugacu ac                                              22


<210>  16
<211>  22
<212>  RNA
<213>  Artificial

<220>
<223>  RNAi trigger

<400>  16
uacaaaggca ucaacgcagg au                                              22


<210>  17
<211>  22
<212>  RNA
<213>  Artificial

<220>
<223>  RNAi trigger

<400>  17
uaacugacua cuaggucucu ag                                              22


<210>  18
<211>  22
<212>  RNA
<213>  Artificial

<220>
<223>  RNAi trigger

<400>  18
uacuaggucu cuagacgcug ga                                              22


<210>  19
<211>  22
<212>  RNA
<213>  Artificial

<220>
<223>  RNAi trigger

<400>  19
uagagugugu aaauaguguc ua                                              22


<210>  20
<211>  22
<212>  RNA
<213>  Artificial

<220>
<223>  RNAi trigger

<400>  20
uuugguggaa gguuguggaa uu                                              22


<210>  21
<211>  22
<212>  RNA
<213>  Artificial

<220>
<223>  RNAi trigger

<400>  21
uuggugagug auuggagguu gg                                              22


<210>  22
<211>  22
<212>  RNA
<213>  Artificial

<220>
<223>  RNAi trigger

<400>  22
ugauagucca gaagaaccaa ca                                              22


<210>  23
<211>  22
<212>  RNA
<213>  Artificial

<220>
<223>  RNAi trigger

<400>  23
ugauuaacua gauguucugg au                                              22


<210>  24
<211>  30
<212>  DNA
<213>  Artificial

<220>
<223>  Binding site


<220>
<221>  misc_feature
<222>  (1)..(2)
<223>  n is a, c, g, or t

<220>
<221>  misc_feature
<222>  (3)..(3)
<223>  Y=C or T

<220>
<221>  misc_feature
<222>  (4)..(5)
<223>  n is a, c, g, or t

<220>
<221>  misc_feature
<222>  (6)..(6)
<223>  Y=C or T

<220>
<221>  misc_feature
<222>  (7)..(8)
<223>  n is a, c, g, or t

<220>
<221>  misc_feature
<222>  (9)..(9)
<223>  Y=C or T

<220>
<221>  misc_feature
<222>  (10)..(11)
<223>  n is a, c, g, or t

<220>
<221>  misc_feature
<222>  (12)..(12)
<223>  Y=C or T

<220>
<221>  misc_feature
<222>  (13)..(18)
<223>  n is a, c, g, or t

<220>
<221>  misc_feature
<222>  (19)..(19)
<223>  R=G or A

<220>
<221>  misc_feature
<222>  (20)..(21)
<223>  n is a, c, g, or t

<220>
<221>  misc_feature
<222>  (22)..(22)
<223>  R=G or A

<220>
<221>  misc_feature
<222>  (23)..(24)
<223>  n is a, c, g, or t

<220>
<221>  misc_feature
<222>  (25)..(25)
<223>  R=G or A

<220>
<221>  misc_feature
<222>  (26)..(27)
<223>  n is a, c, g, or t

<220>
<221>  misc_feature
<222>  (28)..(28)
<223>  R=G or A

<220>
<221>  misc_feature
<222>  (29)..(30)
<223>  n is a, c, g, or t

<400>  24
nnynnynnyn nynnnnnnrn nrnnrnnrnn                                      30


<210>  25
<211>  110
<212>  PRT
<213>  Artificial

<220>
<223>  Backbone sequence


<220>
<221>  misc_feature
<222>  (17)..(22)
<223>  Xaa can be any naturally occurring amino acid

<220>
<221>  misc_feature
<222>  (44)..(50)
<223>  Xaa can be any naturally occurring amino acid

<220>
<221>  misc_feature
<222>  (73)..(78)
<223>  Xaa can be any naturally occurring amino acid

<220>
<221>  misc_feature
<222>  (100)..(105)
<223>  Xaa can be any naturally occurring amino acid

<400>  25

Met Ala Glu Arg Pro Phe Gln Cys Arg Ile Cys Met Arg Asn Phe Ser 
1               5                   10                  15      


Xaa Xaa Xaa Xaa Xaa Xaa His Ile Arg Thr His Thr Gly Glu Lys Pro 
            20                  25                  30          


Phe Ala Cys Asp Ile Cys Gly Arg Lys Phe Ala Xaa Xaa Xaa Xaa Xaa 
        35                  40                  45              


Xaa Xaa His Thr Lys Ile His Thr Gly Ser Gln Lys Pro Phe Gln Cys 
    50                  55                  60                  


Arg Ile Cys Met Arg Asn Phe Ser Xaa Xaa Xaa Xaa Xaa Xaa His Ile 
65                  70                  75                  80  


Arg Thr His Thr Gly Glu Lys Pro Phe Ala Cys Asp Ile Cys Gly Arg 
                85                  90                  95      


Lys Phe Ala Xaa Xaa Xaa Xaa Xaa Xaa His Gln Arg Thr His 
            100                 105                 110 


<210>  26
<211>  113
<212>  PRT
<213>  Artificial

<220>
<223>  Alternate binding residue (SEQ ID NO: 25)

<400>  26

Met Ala Glu Arg Pro Phe Gln Cys Arg Ile Cys Met Arg Asn Phe Ser 
1               5                   10                  15      


Arg Ser Asp Asp Leu Ser Arg His Ile Arg Thr His Thr Gly Glu Lys 
            20                  25                  30          


Pro Phe Ala Cys Asp Ile Cys Gly Arg Lys Phe Ala Gln Ser Ser Ala 
        35                  40                  45              


Leu Thr Arg His Thr Lys Ile His Thr Gly Ser Gln Lys Pro Phe Gln 
    50                  55                  60                  


Cys Arg Ile Cys Met Arg Asn Phe Ser Arg Ser Asp His Leu Thr Arg 
65                  70                  75                  80  


His Ile Arg Thr His Thr Gly Glu Lys Pro Phe Ala Cys Asp Ile Cys 
                85                  90                  95      


Gly Arg Lys Phe Ala Arg Ser Asp Ser Leu Thr Arg His Gln Arg Thr 
            100                 105                 110         


His 
    


<210>  27
<211>  113
<212>  PRT
<213>  Artificial

<220>
<223>  Alternate binding residue (SEQ ID NO: 25)

<400>  27

Met Ala Glu Arg Pro Phe Gln Cys Arg Ile Cys Met Arg Asn Phe Ser 
1               5                   10                  15      


Gln Ser Gly Asp Leu Thr Thr His Ile Arg Thr His Thr Gly Glu Lys 
            20                  25                  30          


Pro Phe Ala Cys Asp Ile Cys Gly Arg Lys Phe Ala Arg Ser Asp His 
        35                  40                  45              


Leu Thr Thr His Thr Lys Ile His Thr Gly Ser Gln Lys Pro Phe Gln 
    50                  55                  60                  


Cys Arg Ile Cys Met Arg Asn Phe Ser Gln Ser Ser Asp Leu Thr Arg 
65                  70                  75                  80  


His Ile Arg Thr His Thr Gly Glu Lys Pro Phe Ala Cys Asp Ile Cys 
                85                  90                  95      


Gly Arg Lys Phe Ala Arg Ser Asp His Leu Ser Arg His Gln Arg Thr 
            100                 105                 110         


His 
    


<210>  28
<211>  113
<212>  PRT
<213>  Artificial

<220>
<223>  Alternate binding residue (SEQ ID NO: 25)

<400>  28

Met Ala Glu Arg Pro Phe Gln Cys Arg Ile Cys Met Arg Asn Phe Ser 
1               5                   10                  15      


Arg Ser Asp His Leu Thr Gln His Ile Arg Thr His Thr Gly Glu Lys 
            20                  25                  30          


Pro Phe Ala Cys Asp Ile Cys Gly Arg Lys Phe Ala Arg Ser Asp Thr 
        35                  40                  45              


Leu Thr Thr His Thr Lys Ile His Thr Gly Ser Gln Lys Pro Phe Gln 
    50                  55                  60                  


Cys Arg Ile Cys Met Arg Asn Phe Ser Arg Ser Asp Asp Leu Thr Thr 
65                  70                  75                  80  


His Ile Arg Thr His Thr Gly Glu Lys Pro Phe Ala Cys Asp Ile Cys 
                85                  90                  95      


Gly Arg Lys Phe Ala Arg Ser Asp His Leu Ser Arg His Gln Arg Thr 
            100                 105                 110         


His 
    


