                         SEQUENCE LISTING

<110>  New England Biolabs, Inc.
       McReynolds, Larry
       Jin, Jingmin
 
<120>  Methods and Compositions for Detection and Enrichment of Target 
       Small RNAs

<130>  NEB-294-PCT

<150>  60/983,503
<151>  2007-10-29

<160>  35    

<170>  PatentIn version 3.5

<210>  1
<211>  172
<212>  PRT
<213>  Carnation Italian ringspot virus

<400>  1

Met Glu Arg Ala Ile Gln Gly Asn Asp Thr Arg Glu Gln Ala Asn Gly 
1               5                   10                  15      


Glu Arg Trp Asp Gly Gly Ser Gly Gly Ile Thr Ser Pro Phe Lys Leu 
            20                  25                  30          


Pro Asp Glu Ser Pro Ser Trp Thr Glu Trp Arg Leu Tyr Asn Asp Glu 
        35                  40                  45              


Thr Asn Ser Asn Gln Asp Asn Pro Leu Gly Phe Lys Glu Ser Trp Gly 
    50                  55                  60                  


Phe Gly Lys Val Val Phe Lys Arg Tyr Leu Arg Tyr Asp Arg Thr Glu 
65                  70                  75                  80  


Ala Ser Leu His Arg Val Leu Gly Ser Trp Thr Gly Asp Ser Val Asn 
                85                  90                  95      


Tyr Ala Ala Ser Arg Phe Leu Gly Ala Asn Gln Val Gly Cys Thr Tyr 
            100                 105                 110         


Ser Ile Arg Phe Arg Gly Val Ser Val Thr Ile Ser Gly Gly Ser Arg 
        115                 120                 125             


Thr Leu Gln His Leu Cys Glu Met Ala Ile Arg Ser Lys Gln Glu Leu 
    130                 135                 140                 


Leu Gln Leu Thr Pro Val Glu Val Glu Ser Asn Val Ser Arg Gly Cys 
145                 150                 155                 160 


Pro Glu Gly Ile Glu Thr Phe Lys Lys Glu Ser Glu 
                165                 170         


<210>  2
<211>  22
<212>  RNA
<213>  unknown

<220>
<223>  completely synthetic

<400>  2
aacaccauug ucacacucca ua                                                22


<210>  3
<211>  80
<212>  RNA
<213>  Homo sapiens

<400>  3
ugggaugagg uaguagguug uauaguuuua gggucacacc caccacuggg agauaacuau       60

acaaucuacu gucuuuccua                                                   80


<210>  4
<211>  21
<212>  RNA
<213>  unknown

<220>
<223>  synthetic oligonucleotide

<400>  4
cguacgcgga auacuucgau u                                                 21


<210>  5
<211>  21
<212>  RNA
<213>  unknown

<220>
<223>  synthetic oligonucleotide

<400>  5
ucgaaguauu ccgcguacgu u                                                 21


<210>  6
<211>  17
<212>  RNA
<213>  unknown

<220>
<223>  synthetic oligonucleotide

<400>  6
cucaaccagc cacugcu                                                      17


<210>  7
<211>  17
<212>  RNA
<213>  unknown

<220>
<223>  synthetic oligonucleotide

<400>  7
caguggcugg uugagau                                                      17


<210>  8
<211>  25
<212>  RNA
<213>  unknown

<220>
<223>  synthetic oligonucleotide

<400>  8
cguacgcgga auacuucgaa auguu                                             25


<210>  9
<211>  25
<212>  RNA
<213>  unknown

<220>
<223>  synthetic oligonucleotide

<400>  9
cauuucgaag uauuccgcgu acguu                                             25


<210>  10
<211>  21
<212>  RNA
<213>  unknown

<220>
<223>  synthetic oligonucleotide

<400>  10
cguacgcgga auacuucgau u                                                 21


<210>  11
<211>  21
<212>  RNA
<213>  unknown

<220>
<223>  synthetic oligonucleotide

<400>  11
ucgaaguauu ccgcguacgu u                                                 21


<210>  12
<211>  21
<212>  RNA
<213>  unknown

<220>
<223>  synthetic oligonucleotide

<400>  12
cguacgcgga auacuucgau u                                                 21


<210>  13
<211>  19
<212>  RNA
<213>  unknown

<220>
<223>  synthetic oligonucleotide

<400>  13
cguacgcgga auacuucga                                                    19


<210>  14
<211>  19
<212>  RNA
<213>  unknown

<220>
<223>  synthetic oligonucleotide

<400>  14
cguacgcgga auacuucga                                                    19


<210>  15
<211>  21
<212>  RNA
<213>  unknown

<220>
<223>  synthetic oligonucleotide

<400>  15
acguacgcgg aauacuucga u                                                 21


<210>  16
<211>  21
<212>  RNA
<213>  unknown

<220>
<223>  synthetic oligonucleotide

<400>  16
cguacgcgga auacuucgau u                                                 21


<210>  17
<211>  21
<212>  DNA
<213>  unknown

<220>
<223>  synthetic oligonucleotide

<400>  17
tcgaagtatt ccgcgtacgt t                                                 21


<210>  18
<211>  21
<212>  DNA
<213>  unknown

<220>
<223>  synthetic oligonucleotide

<400>  18
cgtacgcgga atacttcgat t                                                 21


<210>  19
<211>  21
<212>  DNA
<213>  unknown

<220>
<223>  synthetic oligonucleotide

<400>  19
tcgaagtatt ccgcgtacgt t                                                 21


<210>  20
<211>  21
<212>  RNA
<213>  unknown

<220>
<223>  synthetic oligonucleotide

<400>  20
cguacgcgga auacuucgau u                                                 21


<210>  21
<211>  21
<212>  DNA
<213>  unknown

<220>
<223>  synthetic oligonucleotide


<220>
<221>  misc_feature
<222>  (7)..(7)
<223>  This position contains FAM covalently linked to thymadine; FAM is
       5-[(N-(3'-diphenylphosphinyl-4'-methoxycarbonyl)phenylcarbonyl)am
       inoacetamido]fluorescein

<400>  21
ucgaagtauu ccgcguacgu u                                                 21


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

<220>
<223>  synthetic oligonucleotide

<400>  22
cguacgcgga auacuucgau u                                                 21


<210>  23
<211>  22
<212>  RNA
<213>  Caenorhabditis elegans

<400>  23
ugagguagua gguuguauag uu                                                22


<210>  24
<211>  22
<212>  RNA
<213>  Caenorhabditis elegans

<400>  24
cuaugcaauu uucuaccuua cc                                                22


<210>  25
<211>  21
<212>  RNA
<213>  Gallus gallus

<400>  25
agagguagug gguugcauag u                                                 21


<210>  26
<211>  21
<212>  RNA
<213>  Gallus gallus

<400>  26
uauacaaccu gcugccuuuc u                                                 21


<210>  27
<211>  21
<212>  RNA
<213>  Caenorhabditis elegans

<400>  27
ugacuagaga cacauucagc u                                                 21


<210>  28
<211>  22
<212>  RNA
<213>  Caenorhabditis elegans

<400>  28
cuggaugugc ucguuaguca ua                                                22


<210>  29
<211>  22
<212>  RNA
<213>  unknown

<220>
<223>  synthetic

<400>  29
uggaguguga caaugguguu ug                                                22


<210>  30
<211>  22
<212>  DNA
<213>  unknown

<220>
<223>  synthetic


<220>
<221>  misc_feature
<222>  (6)..(6)
<223>  This position contains FAM covalently linked to thymadine; FAM is
       5-[(N-(3'-diphenylphosphinyl-4'-methoxycarbonyl)phenylcarbonyl)am
       inoacetamido]fluorescein

<400>  30
aacactauug ucacacucca ua                                                22


<210>  31
<211>  21
<212>  RNA
<213>  unknown

<220>
<223>  synthetic

<400>  31
ucgaaguauu ccgcguacgu u                                                 21


<210>  32
<211>  1881
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  combination synthetic and Carnation Italian ringstpot virus


<220>
<221>  CDS
<222>  (1)..(1878)

<220>
<221>  1184CDS
<222>  (1)..(1698)

<400>  32
atg aaa act gaa gaa ggt aaa ctg gta atc tgg att aac ggc gat aaa         48
Met Lys Thr Glu Glu Gly Lys Leu Val Ile Trp Ile Asn Gly Asp Lys           
1               5                   10                  15                

ggc tat aac ggt ctc gct gaa gtc ggt aag aaa ttc gag aaa gat acc         96
Gly Tyr Asn Gly Leu Ala Glu Val Gly Lys Lys Phe Glu Lys Asp Thr           
            20                  25                  30                    

gga att aaa gtc acc gtt gag cat ccg gat aaa ctg gaa gag aaa ttc        144
Gly Ile Lys Val Thr Val Glu His Pro Asp Lys Leu Glu Glu Lys Phe           
        35                  40                  45                        

cca cag gtt gcg gca act ggc gat ggc cct gac att atc ttc tgg gca        192
Pro Gln Val Ala Ala Thr Gly Asp Gly Pro Asp Ile Ile Phe Trp Ala           
    50                  55                  60                            

cac gac cgc ttt ggt ggc tac gct caa tct ggc ctg ttg gct gaa atc        240
His Asp Arg Phe Gly Gly Tyr Ala Gln Ser Gly Leu Leu Ala Glu Ile           
65                  70                  75                  80            

acc ccg gac aaa gcg ttc cag gac aag ctg tat ccg ttt acc tgg gat        288
Thr Pro Asp Lys Ala Phe Gln Asp Lys Leu Tyr Pro Phe Thr Trp Asp           
                85                  90                  95                

gcc gta cgt tac aac ggc aag ctg att gct tac ccg atc gct gtt gaa        336
Ala Val Arg Tyr Asn Gly Lys Leu Ile Ala Tyr Pro Ile Ala Val Glu           
            100                 105                 110                   

gcg tta tcg ctg att tat aac aaa gat ctg ctg ccg aac ccg cca aaa        384
Ala Leu Ser Leu Ile Tyr Asn Lys Asp Leu Leu Pro Asn Pro Pro Lys           
        115                 120                 125                       

acc tgg gaa gag atc ccg gcg ctg gat aaa gaa ctg aaa gcg aaa ggt        432
Thr Trp Glu Glu Ile Pro Ala Leu Asp Lys Glu Leu Lys Ala Lys Gly           
    130                 135                 140                           

aag agc gcg ctg atg ttc aac ctg caa gaa ccg tac ttc acc tgg ccg        480
Lys Ser Ala Leu Met Phe Asn Leu Gln Glu Pro Tyr Phe Thr Trp Pro           
145                 150                 155                 160           

ctg att gct gct gac ggg ggt tat gcg ttc aag tat gaa aac ggc aag        528
Leu Ile Ala Ala Asp Gly Gly Tyr Ala Phe Lys Tyr Glu Asn Gly Lys           
                165                 170                 175               

tac gac att aaa gac gtg ggc gtg gat aac gct ggc gcg aaa gcg ggt        576
Tyr Asp Ile Lys Asp Val Gly Val Asp Asn Ala Gly Ala Lys Ala Gly           
            180                 185                 190                   

ctg acc ttc ctg gtt gac ctg att aaa aac aaa cac atg aat gca gac        624
Leu Thr Phe Leu Val Asp Leu Ile Lys Asn Lys His Met Asn Ala Asp           
        195                 200                 205                       

acc gat tac tcc atc gca gaa gct gcc ttt aat aaa ggc gaa aca gcg        672
Thr Asp Tyr Ser Ile Ala Glu Ala Ala Phe Asn Lys Gly Glu Thr Ala           
    210                 215                 220                           

atg acc atc aac ggc ccg tgg gca tgg tcc aac atc gac acc agc aaa        720
Met Thr Ile Asn Gly Pro Trp Ala Trp Ser Asn Ile Asp Thr Ser Lys           
225                 230                 235                 240           

gtg aat tat ggt gta acg gta ctg ccg acc ttc aag ggt caa cca tcc        768
Val Asn Tyr Gly Val Thr Val Leu Pro Thr Phe Lys Gly Gln Pro Ser           
                245                 250                 255               

aaa ccg ttc gtt ggc gtg ctg agc gca ggt att aac gcc gcc agt ccg        816
Lys Pro Phe Val Gly Val Leu Ser Ala Gly Ile Asn Ala Ala Ser Pro           
            260                 265                 270                   

aac aaa gag ctg gca aaa gag ttc ctc gaa aac tat ctg ctg act gat        864
Asn Lys Glu Leu Ala Lys Glu Phe Leu Glu Asn Tyr Leu Leu Thr Asp           
        275                 280                 285                       

gaa ggt ctg gaa gcg gtt aat aaa gac aaa ccg ctg ggt gcc gta gcg        912
Glu Gly Leu Glu Ala Val Asn Lys Asp Lys Pro Leu Gly Ala Val Ala           
    290                 295                 300                           

ctg aag tct tac gag gaa gag ttg gcg aaa gat cca cgt att gcc gcc        960
Leu Lys Ser Tyr Glu Glu Glu Leu Ala Lys Asp Pro Arg Ile Ala Ala           
305                 310                 315                 320           

act atg gaa aac gcc cag aaa ggt gaa atc atg ccg aac atc ccg cag       1008
Thr Met Glu Asn Ala Gln Lys Gly Glu Ile Met Pro Asn Ile Pro Gln           
                325                 330                 335               

atg tcc gct ttc tgg tat gcc gtg cgt act gcg gtg atc aac gcc gcc       1056
Met Ser Ala Phe Trp Tyr Ala Val Arg Thr Ala Val Ile Asn Ala Ala           
            340                 345                 350                   

agc ggt cgt cag act gtc gat gaa gcc ctg aaa gac gcg cag act aat       1104
Ser Gly Arg Gln Thr Val Asp Glu Ala Leu Lys Asp Ala Gln Thr Asn           
        355                 360                 365                       

tcg agc tcg aac aac aac aac aat aac aat aac aac aac ctc ggg ccg       1152
Ser Ser Ser Asn Asn Asn Asn Asn Asn Asn Asn Asn Asn Leu Gly Pro           
    370                 375                 380                           

ggt gcg gca cac tac gta gaa ttc gga tcc atg gaa cga gct ata caa       1200
Gly Ala Ala His Tyr Val Glu Phe Gly Ser Met Glu Arg Ala Ile Gln           
385                 390                 395                 400           

gga aac gac act agg gaa caa gct aac ggt gaa cgt tgg gat gga gga       1248
Gly Asn Asp Thr Arg Glu Gln Ala Asn Gly Glu Arg Trp Asp Gly Gly           
                405                 410                 415               

tca gga ggt atc act tct ccc ttc aaa ctt cct gac gaa agt ccg agt       1296
Ser Gly Gly Ile Thr Ser Pro Phe Lys Leu Pro Asp Glu Ser Pro Ser           
            420                 425                 430                   

tgg act gag tgg cgg cta tat aac gat gag acg aat tcg aat caa gat       1344
Trp Thr Glu Trp Arg Leu Tyr Asn Asp Glu Thr Asn Ser Asn Gln Asp           
        435                 440                 445                       

aat ccc ctt ggt ttc aag gaa agc tgg ggt ttc ggg aaa gtt gta ttt       1392
Asn Pro Leu Gly Phe Lys Glu Ser Trp Gly Phe Gly Lys Val Val Phe           
    450                 455                 460                           

aag aga tat ctc aga tac gac agg acg gaa gct tca ctg cac aga gtc       1440
Lys Arg Tyr Leu Arg Tyr Asp Arg Thr Glu Ala Ser Leu His Arg Val           
465                 470                 475                 480           

ctt gga tct tgg acg gga gat tcg gtt aac tat gca gca tct cga ttt       1488
Leu Gly Ser Trp Thr Gly Asp Ser Val Asn Tyr Ala Ala Ser Arg Phe           
                485                 490                 495               

ctc ggt gcc aac cag gtc gga tgt acc tat agt att cgg ttt cga gga       1536
Leu Gly Ala Asn Gln Val Gly Cys Thr Tyr Ser Ile Arg Phe Arg Gly           
            500                 505                 510                   

gtt agt gtc acc att tct gga ggg tcg aga act ctt cag cat ctc tgt       1584
Val Ser Val Thr Ile Ser Gly Gly Ser Arg Thr Leu Gln His Leu Cys           
        515                 520                 525                       

gag atg gca att cgg tct aag caa gaa ctg tta cag ctt acc cca gtc       1632
Glu Met Ala Ile Arg Ser Lys Gln Glu Leu Leu Gln Leu Thr Pro Val           
    530                 535                 540                           

gaa gtg gaa agt aat gta tca aga gga tgc cct gaa ggt att gaa acc       1680
Glu Val Glu Ser Asn Val Ser Arg Gly Cys Pro Glu Gly Ile Glu Thr           
545                 550                 555                 560           

ttc aag aaa gaa agc gag gga tcc tct aga gtc gac ctg cag acg aca       1728
Phe Lys Lys Glu Ser Glu Gly Ser Ser Arg Val Asp Leu Gln Thr Thr           
                565                 570                 575               

aat cct ggt gta tcc gct tgg cag gtc aac aca gct tat act gcg gga       1776
Asn Pro Gly Val Ser Ala Trp Gln Val Asn Thr Ala Tyr Thr Ala Gly           
            580                 585                 590                   

caa ttg gtc aca tat aac ggc aag acg tat aaa tgt ttg cag ccc cac       1824
Gln Leu Val Thr Tyr Asn Gly Lys Thr Tyr Lys Cys Leu Gln Pro His           
        595                 600                 605                       

acc tcc ttg gca gga tgg gaa cca tcc aac gtt cct gcc ttg tgg cag       1872
Thr Ser Leu Ala Gly Trp Glu Pro Ser Asn Val Pro Ala Leu Trp Gln           
    610                 615                 620                           

ctt caa tga                                                           1881
Leu Gln                                                                   
625                                                                       


<210>  33
<211>  626
<212>  PRT
<213>  Artificial Sequence

<220>
<223>  Synthetic Construct

<400>  33

Met Lys Thr Glu Glu Gly Lys Leu Val Ile Trp Ile Asn Gly Asp Lys 
1               5                   10                  15      


Gly Tyr Asn Gly Leu Ala Glu Val Gly Lys Lys Phe Glu Lys Asp Thr 
            20                  25                  30          


Gly Ile Lys Val Thr Val Glu His Pro Asp Lys Leu Glu Glu Lys Phe 
        35                  40                  45              


Pro Gln Val Ala Ala Thr Gly Asp Gly Pro Asp Ile Ile Phe Trp Ala 
    50                  55                  60                  


His Asp Arg Phe Gly Gly Tyr Ala Gln Ser Gly Leu Leu Ala Glu Ile 
65                  70                  75                  80  


Thr Pro Asp Lys Ala Phe Gln Asp Lys Leu Tyr Pro Phe Thr Trp Asp 
                85                  90                  95      


Ala Val Arg Tyr Asn Gly Lys Leu Ile Ala Tyr Pro Ile Ala Val Glu 
            100                 105                 110         


Ala Leu Ser Leu Ile Tyr Asn Lys Asp Leu Leu Pro Asn Pro Pro Lys 
        115                 120                 125             


Thr Trp Glu Glu Ile Pro Ala Leu Asp Lys Glu Leu Lys Ala Lys Gly 
    130                 135                 140                 


Lys Ser Ala Leu Met Phe Asn Leu Gln Glu Pro Tyr Phe Thr Trp Pro 
145                 150                 155                 160 


Leu Ile Ala Ala Asp Gly Gly Tyr Ala Phe Lys Tyr Glu Asn Gly Lys 
                165                 170                 175     


Tyr Asp Ile Lys Asp Val Gly Val Asp Asn Ala Gly Ala Lys Ala Gly 
            180                 185                 190         


Leu Thr Phe Leu Val Asp Leu Ile Lys Asn Lys His Met Asn Ala Asp 
        195                 200                 205             


Thr Asp Tyr Ser Ile Ala Glu Ala Ala Phe Asn Lys Gly Glu Thr Ala 
    210                 215                 220                 


Met Thr Ile Asn Gly Pro Trp Ala Trp Ser Asn Ile Asp Thr Ser Lys 
225                 230                 235                 240 


Val Asn Tyr Gly Val Thr Val Leu Pro Thr Phe Lys Gly Gln Pro Ser 
                245                 250                 255     


Lys Pro Phe Val Gly Val Leu Ser Ala Gly Ile Asn Ala Ala Ser Pro 
            260                 265                 270         


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


Glu Gly Leu Glu Ala Val Asn Lys Asp Lys Pro Leu Gly Ala Val Ala 
    290                 295                 300                 


Leu Lys Ser Tyr Glu Glu Glu Leu Ala Lys Asp Pro Arg Ile Ala Ala 
305                 310                 315                 320 


Thr Met Glu Asn Ala Gln Lys Gly Glu Ile Met Pro Asn Ile Pro Gln 
                325                 330                 335     


Met Ser Ala Phe Trp Tyr Ala Val Arg Thr Ala Val Ile Asn Ala Ala 
            340                 345                 350         


Ser Gly Arg Gln Thr Val Asp Glu Ala Leu Lys Asp Ala Gln Thr Asn 
        355                 360                 365             


Ser Ser Ser Asn Asn Asn Asn Asn Asn Asn Asn Asn Asn Leu Gly Pro 
    370                 375                 380                 


Gly Ala Ala His Tyr Val Glu Phe Gly Ser Met Glu Arg Ala Ile Gln 
385                 390                 395                 400 


Gly Asn Asp Thr Arg Glu Gln Ala Asn Gly Glu Arg Trp Asp Gly Gly 
                405                 410                 415     


Ser Gly Gly Ile Thr Ser Pro Phe Lys Leu Pro Asp Glu Ser Pro Ser 
            420                 425                 430         


Trp Thr Glu Trp Arg Leu Tyr Asn Asp Glu Thr Asn Ser Asn Gln Asp 
        435                 440                 445             


Asn Pro Leu Gly Phe Lys Glu Ser Trp Gly Phe Gly Lys Val Val Phe 
    450                 455                 460                 


Lys Arg Tyr Leu Arg Tyr Asp Arg Thr Glu Ala Ser Leu His Arg Val 
465                 470                 475                 480 


Leu Gly Ser Trp Thr Gly Asp Ser Val Asn Tyr Ala Ala Ser Arg Phe 
                485                 490                 495     


Leu Gly Ala Asn Gln Val Gly Cys Thr Tyr Ser Ile Arg Phe Arg Gly 
            500                 505                 510         


Val Ser Val Thr Ile Ser Gly Gly Ser Arg Thr Leu Gln His Leu Cys 
        515                 520                 525             


Glu Met Ala Ile Arg Ser Lys Gln Glu Leu Leu Gln Leu Thr Pro Val 
    530                 535                 540                 


Glu Val Glu Ser Asn Val Ser Arg Gly Cys Pro Glu Gly Ile Glu Thr 
545                 550                 555                 560 


Phe Lys Lys Glu Ser Glu Gly Ser Ser Arg Val Asp Leu Gln Thr Thr 
                565                 570                 575     


Asn Pro Gly Val Ser Ala Trp Gln Val Asn Thr Ala Tyr Thr Ala Gly 
            580                 585                 590         


Gln Leu Val Thr Tyr Asn Gly Lys Thr Tyr Lys Cys Leu Gln Pro His 
        595                 600                 605             


Thr Ser Leu Ala Gly Trp Glu Pro Ser Asn Val Pro Ala Leu Trp Gln 
    610                 615                 620                 


Leu Gln 
625     


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

<220>
<223>  primer

<400>  34
gactctgcag acgacaaatc ctggtgtatc cgct                                   34


<210>  35
<211>  37
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  primer

<400>  35
taggaagctt tcattgaagc tgccacaagg caggaac                                37


