                         SEQUENCE LISTING

<110>  Didenko Vladimir
 
<120>  FLUORESCENCE DETECTION OF DNA BREAKS USING MOLECULAR OSCILLATORS

<130>  44111-P004WO Baylor College of Medicine

<140>  PCT/US08/69558
<141>  2008-09-26

<150> US 60/948,617
<151> 2007-07-09

<160>  6     

<170>  PatentIn version 3.5

<210>  1
<211>  38
<212>  DNA
<213>  Artificial Sequence

<220>  
<223>  Synthesized by Integrated DNA Technologies (IDT, Coralville, IA)

<220>  
<221>  misc_feature
<222>  (12)..(12)
<223>  'n' is fluorescein-dT, a modified thymidine wherein a fluorescein
       tag is attached to the 5-position of the thymidine ring by a 
       CH=CHC(=O)NH(CH2)6NHC(=O) spacer

<220>  
<221>  misc_feature
<222>  (31)..(31)
<223>  'n' is rhodamine-dT, a modified thymidine wherein a rhodamine tag
       is attached to the 5-position of the thymidine ring by a 
       CH=CHC(=O)NH(CH2)6NHC(=O) spacer

<400>  1
aagggacctg cngcaggtcc cttaacgcat natgcgtt                               38

<210>  2
<211>  314
<212>  PRT
<213>  Vaccinia virus

<400>  2

Met Arg Ala Leu Phe Tyr Lys Asp Gly Lys Leu Phe Thr Asp Asn Asn 
1               5                   10                  15      


Phe Leu Asn Pro Val Ser Asp Asp Asn Pro Ala Tyr Glu Val Leu Gln 
            20                  25                  30          


His Val Lys Ile Pro Thr His Leu Thr Asp Val Val Val Tyr Glu Gln 
        35                  40                  45              


Thr Trp Glu Glu Ala Leu Thr Arg Leu Ile Phe Val Gly Ser Asp Ser 
    50                  55                  60                  


Lys Gly Arg Arg Gln Tyr Phe Tyr Gly Lys Met His Val Gln Asn Arg 
65                  70                  75                  80  


Asn Ala Lys Arg Asp Arg Ile Phe Val Arg Val Tyr Asn Val Met Lys 
                85                  90                  95      


Arg Ile Asn Cys Phe Ile Asn Lys Asn Ile Lys Lys Ser Ser Thr Asp 
            100                 105                 110         


Ser Asn Tyr Gln Leu Ala Val Phe Met Leu Met Glu Thr Met Phe Phe 
        115                 120                 125             


Ile Arg Phe Gly Lys Met Lys Tyr Leu Lys Glu Asn Glu Thr Val Gly 
    130                 135                 140                 


Leu Leu Thr Leu Lys Asn Lys His Ile Glu Ile Ser Pro Asp Glu Ile 
145                 150                 155                 160 


Val Ile Lys Phe Val Gly Lys Asp Lys Val Ser His Glu Phe Val Val 
                165                 170                 175     


His Lys Ser Asn Arg Leu Tyr Lys Pro Leu Leu Lys Leu Thr Asp Asp 
            180                 185                 190         


Ser Ser Pro Glu Glu Phe Leu Phe Asn Lys Leu Ser Glu Arg Lys Val 
        195                 200                 205             


Tyr Glu Cys Ile Lys Gln Phe Gly Ile Arg Ile Lys Asp Leu Arg Thr 
    210                 215                 220                 


Tyr Gly Val Asn Tyr Thr Phe Leu Tyr Asn Phe Trp Thr Asn Val Lys 
225                 230                 235                 240 


Ser Ile Ser Pro Leu Pro Ser Pro Lys Lys Leu Ile Ala Leu Thr Ile 
                245                 250                 255     


Lys Gln Thr Ala Glu Val Val Gly His Thr Pro Ser Ile Ser Lys Arg 
            260                 265                 270         


Ala Tyr Met Ala Thr Thr Ile Leu Glu Met Val Lys Asp Lys Asn Phe 
        275                 280                 285             


Leu Asp Val Val Ser Lys Thr Thr Phe Asp Glu Phe Leu Ser Ile Val 
    290                 295                 300                 


Val Asp His Val Lys Ser Ser Thr Asp Gly 
305                 310                 


<210>  3
<211>  21
<212>  DNA
<213>  Artificial Sequence

<220>  
<223>  Synthesized by Integrated DNA Technologies (IDT, Coralville, IA)

<220>  
<223>  Oligonucleotide

<400>  3
gcgctagacc tggtctagcg c                                                 21

<210>  4
<211>  34
<212>  DNA
<213>  Artificial Sequence

<220>  
<223>  Synthesized by Integrated DNA Technologies (IDT, Coralville, IA)

<220>  
<221>  misc_feature
<222>  (1)..(1)
<223>  'n' is 6-carboxyfluorescein (FAM) functionalized adenosine.  The 
       attachment point is the 5' phospate group through a (CH2)6NHC(=O)
       spacer to the fluorescein tag.

<220>  
<221>  misc_feature
<222>  (34)..(34)
<223>  'n' is a thymidine modified with a BHQ-1 (TM) quencher attached 
       through the 3'-phosphate group.

<400>  4
nagggacctc tgaggtccct tacgcattat gcgn                                   34

<210>  5
<211>  29
<212>  DNA
<213>  Artificial Sequence

<220>  
<223>  Synthesized by Integrated DNA Technologies (IDT, Coralville, IA)

<220>  
<221>  misc_feature
<222>  (9)..(9)
<223>  'n' is a fluorescein-dT (iFluorT), a modified thymidine wherein 
       an internal fluorescein tag is attached to the 5-position of the 
       thymidine ring by CH=CHC(=O)NH(CH2)6NHC(=O) spacer.

<220>  
<221>  misc_feature
<222>  (24)..(24)
<223>  'n' is a TAMRA NHS-modified thymidine, wherein the internal TAMRA
       tag is attached to the 5-position of the thymidine ring by a 
       CH=CHC(=O)NH(CH2)6NHC(=O) spacer.

<400>  5
aagggactna gtcccttacg attnatcgt                                         29

<210>  6
<211>  38
<212>  DNA
<213>  Artificial Sequence

<220>  
<223>  Synthesized by Integrated DNA Technologies (IDT, Coralville, IA)

<220>  
<221>  misc_feature
<222>  (6)..(6)
<223>  'n' is a TAMRA NHS modified thymidine, wherein the internal TAMRA
       tag is attached to the 5-position of the thymidine ring by a 
       CH=CHC(=O)NH(CH2)6NHC(=O) spacer.

<220>  
<221>  misc_feature
<222>  (37)..(37)
<223>  'n' is a fluorescein-dT (iFluorT), a modified thymidine wherein 
       an internal fluorescein tag is attached to the 5-position of the 
       thymidine ring by CH=CHC(=O)NH(CH2)6NHC(=O) spacer.


<400>  6
aagggncctg ctgcaggacc cttaacgcat tatgcgnt                               38


