                         SEQUENCE LISTING

<110>  The Regents of the University of California
       Cherf, Gerald Maxwell
       Lieberman, Kate R
       Lam, Christopher Evan
       Doody, Michael
       Akeson, Mark A
 
<120>  Control of DNA Movement in a Nanopore at One Nucleotide Precision
        by a Processive Enzyme

<130>  UCSC2011-156 WO

<150>  61/402,903
<151>  2010-09-07

<150>  61/574,237
<151>  2011-07-30

<150>  61/574,238
<151>  2011-07-30

<150>  61/574,236
<151>  2011-07-30

<150>  61/574,240
<151>  2011-07-30

<150>  61/574,239
<151>  2011-07-30

<150>  61/574,235
<151>  2011-07-30

<150>  61/574,233
<151>  2011-07-30

<160>  28    

<170>  PatentIn version 3.5

<210>  1
<211>  885
<212>  DNA
<213>  Staphylococcus aureus

<400>  1
atggcagatt ctgatattaa tattaaaacc ggtactacag atattggaag caatactaca       60

gtaaaaacag gtgatttagt cacttatgat aaagaaaatg gcatgcacaa aaaagtattt      120

tatagtttta tcgatgataa aaatcacaat aaaaaactgc tagttattag aacaaaaggt      180

accattgctg gtcaatatag agtttatagc gaagaaggtg ctaacaaaag tggtttagcc      240

tggccttcag cctttaaggt acagttgcaa ctacctgata atgaagtagc tcaaatatct      300

gattactatc caagaaattc gattgataca aaaaactata tgagtacttt aacttatgga      360

ttcaacggta atgttactgg tgatgataca ggaaaaattg gcggccttat tggtgcaaat      420

gtttcgattg gtcatacact gaactatgtt caacctgatt tcaaaacaat tttagagagc      480

ccaactgata aaaaagtagg ctggaaagtg atatttaaca atatggtgaa tcaaaattgg      540

ggaccatacg atcgagattc ttggaacccg gtatatggca atcaactttt catgaaaact      600

agaaatggtt ctatgaaagc agcagataac ttccttgatc ctaacaaagc aagttctcta      660

ttatcttcag ggttttcacc agacttcgct acagttatta ctatggatag aaaagcatcc      720

aaacaacaaa caaatataga tgtaatatac gaacgagttc gtgatgatta ccaattgcat      780

tggacttcaa caaattggaa aggtaccaat actaaagata aatggacaga tcgttcttca      840

gaaagatata aaatcgattg ggaaaaagaa gaaatgacaa attaa                      885


<210>  2
<211>  293
<212>  PRT
<213>  Staphylococcus aureus

<400>  2

Ala Asp Ser Asp Ile Asn Ile Lys Thr Gly Thr Thr Asp Ile Gly Ser 
1               5                   10                  15      


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


Gly Met His Lys Lys Val Phe Tyr Ser Phe Ile Asp Asp Lys Asn His 
        35                  40                  45              


Asn Lys Lys Leu Leu Val Ile Arg Thr Lys Gly Thr Ile Ala Gly Gln 
    50                  55                  60                  


Tyr Arg Val Tyr Ser Glu Glu Gly Ala Asn Lys Ser Gly Leu Ala Trp 
65                  70                  75                  80  


Pro Ser Ala Phe Lys Val Gln Leu Gln Leu Pro Asp Asn Glu Val Ala 
                85                  90                  95      


Gln Ile Ser Asp Tyr Tyr Pro Arg Asn Ser Ile Asp Thr Lys Asn Tyr 
            100                 105                 110         


Met Ser Thr Leu Thr Tyr Gly Phe Asn Gly Asn Val Thr Gly Asp Asp 
        115                 120                 125             


Thr Gly Lys Ile Gly Gly Leu Ile Gly Ala Asn Val Ser Ile Gly His 
    130                 135                 140                 


Thr Leu Asn Tyr Val Gln Pro Asp Phe Lys Thr Ile Leu Glu Ser Pro 
145                 150                 155                 160 


Thr Asp Lys Lys Val Gly Trp Lys Val Ile Phe Asn Asn Met Val Asn 
                165                 170                 175     


Gln Asn Trp Gly Pro Tyr Asp Arg Asp Ser Trp Asn Pro Val Tyr Gly 
            180                 185                 190         


Asn Gln Leu Phe Met Lys Thr Arg Asn Gly Ser Met Lys Ala Ala Asp 
        195                 200                 205             


Asn Phe Leu Asp Pro Asn Lys Ala Ser Ser Leu Leu Ser Ser Gly Phe 
    210                 215                 220                 


Ser Pro Asp Phe Ala Thr Val Ile Thr Met Asp Arg Lys Ala Ser Lys 
225                 230                 235                 240 


Gln Gln Thr Asn Ile Asp Val Ile Tyr Glu Arg Val Arg Asp Asp Tyr 
                245                 250                 255     


Gln Leu His Trp Thr Ser Thr Asn Trp Lys Gly Thr Asn Thr Lys Asp 
            260                 265                 270         


Lys Trp Thr Asp Arg Ser Ser Glu Arg Tyr Lys Ile Asp Trp Glu Lys 
        275                 280                 285             


Glu Glu Met Thr Asn 
    290             


<210>  3
<211>  1830
<212>  DNA
<213>  Bacteriophage phi29

<400>  3
atgaaacaca tgccgcgtaa aatgtatagc tgcgcgtttg aaaccacgac caaagtggaa       60

gattgtcgcg tttgggccta tggctacatg aacatcgaag atcattctga atacaaaatc      120

ggtaacagtc tggatgaatt tatggcatgg gtgctgaaag ttcaggcgga tctgtacttc      180

cacaacctga aatttgatgg cgcattcatt atcaactggc tggaacgtaa tggctttaaa      240

tggagcgcgg atggtctgcc gaacacgtat aataccatta tctctcgtat gggccagtgg      300

tatatgattg atatctgcct gggctacaaa ggtaaacgca aaattcatac cgtgatctat      360

gatagcctga aaaaactgcc gtttccggtg aagaaaattg cgaaagattt caaactgacg      420

gttctgaaag gcgatattga ttatcacaaa gaacgtccgg ttggttacaa aatcaccccg      480

gaagaatacg catacatcaa aaacgatatc cagatcatcg cagaagcgct gctgattcag      540

tttaaacagg gcctggatcg catgaccgcg ggcagtgata gcctgaaagg tttcaaagat      600

atcatcacga ccaaaaaatt caaaaaagtg ttcccgacgc tgagcctggg tctggataaa      660

gaagttcgtt atgcctaccg cggcggtttt acctggctga acgatcgttt caaagaaaaa      720

gaaattggcg agggtatggt gtttgatgtt aatagtctgt atccggcaca gatgtacagc      780

cgcctgctgc cgtatggcga accgatcgtg ttcgagggta aatatgtttg ggatgaagat      840

tacccgctgc atattcagca catccgttgt gaatttgaac tgaaagaagg ctatattccg      900

accattcaga tcaaacgtag tcgcttctat aagggtaacg aatacctgaa aagctctggc      960

ggtgaaatcg cggatctgtg gctgagtaac gtggatctgg aactgatgaa agaacactac     1020

gatctgtaca acgttgaata catcagcggc ctgaaattta aagccacgac cggtctgttc     1080

aaagatttca tcgataaatg gacctacatc aaaacgacct ctgaaggcgc gattaaacag     1140

ctggccaaac tgatgctgaa cagcctgtat ggcaaattcg cctctaatcc ggatgtgacc     1200

ggtaaagttc cgtacctgaa agaaaatggc gcactgggtt ttcgcctggg cgaagaagaa     1260

acgaaagatc cggtgtatac cccgatgggt gttttcatta cggcctgggc acgttacacg     1320

accatcaccg cggcccaggc atgctatgat cgcattatct actgtgatac cgattctatt     1380

catctgacgg gcaccgaaat cccggatgtg attaaagata tcgttgatcc gaaaaaactg     1440

ggttattggg cccacgaaag tacgtttaaa cgtgcaaaat acctgcgcca gaaaacctac     1500

atccaggata tctacatgaa agaagtggat ggcaaactgg ttgaaggttc tccggatgat     1560

tacaccgata tcaaattcag tgtgaaatgc gccggcatga cggataaaat caaaaaagaa     1620

gtgaccttcg aaaacttcaa agttggtttc agccgcaaaa tgaaaccgaa accggtgcag     1680

gttccgggcg gtgtggttct ggtggatgat acgtttacca ttaaatctgg cggtagtgcg     1740

tggagccatc cgcagttcga aaaaggcggt ggctctggtg gcggttctgg cggtagtgcc     1800

tggagccacc cgcagtttga aaaataataa                                      1830


<210>  4
<211>  608
<212>  PRT
<213>  Bacteriophage phi29

<400>  4

Met Lys His Met Pro Arg Lys Met Tyr Ser Cys Ala Phe Glu Thr Thr 
1               5                   10                  15      


Thr Lys Val Glu Asp Cys Arg Val Trp Ala Tyr Gly Tyr Met Asn Ile 
            20                  25                  30          


Glu Asp His Ser Glu Tyr Lys Ile Gly Asn Ser Leu Asp Glu Phe Met 
        35                  40                  45              


Ala Trp Val Leu Lys Val Gln Ala Asp Leu Tyr Phe His Asn Leu Lys 
    50                  55                  60                  


Phe Asp Gly Ala Phe Ile Ile Asn Trp Leu Glu Arg Asn Gly Phe Lys 
65                  70                  75                  80  


Trp Ser Ala Asp Gly Leu Pro Asn Thr Tyr Asn Thr Ile Ile Ser Arg 
                85                  90                  95      


Met Gly Gln Trp Tyr Met Ile Asp Ile Cys Leu Gly Tyr Lys Gly Lys 
            100                 105                 110         


Arg Lys Ile His Thr Val Ile Tyr Asp Ser Leu Lys Lys Leu Pro Phe 
        115                 120                 125             


Pro Val Lys Lys Ile Ala Lys Asp Phe Lys Leu Thr Val Leu Lys Gly 
    130                 135                 140                 


Asp Ile Asp Tyr His Lys Glu Arg Pro Val Gly Tyr Lys Ile Thr Pro 
145                 150                 155                 160 


Glu Glu Tyr Ala Tyr Ile Lys Asn Asp Ile Gln Ile Ile Ala Glu Ala 
                165                 170                 175     


Leu Leu Ile Gln Phe Lys Gln Gly Leu Asp Arg Met Thr Ala Gly Ser 
            180                 185                 190         


Asp Ser Leu Lys Gly Phe Lys Asp Ile Ile Thr Thr Lys Lys Phe Lys 
        195                 200                 205             


Lys Val Phe Pro Thr Leu Ser Leu Gly Leu Asp Lys Glu Val Arg Tyr 
    210                 215                 220                 


Ala Tyr Arg Gly Gly Phe Thr Trp Leu Asn Asp Arg Phe Lys Glu Lys 
225                 230                 235                 240 


Glu Ile Gly Glu Gly Met Val Phe Asp Val Asn Ser Leu Tyr Pro Ala 
                245                 250                 255     


Gln Met Tyr Ser Arg Leu Leu Pro Tyr Gly Glu Pro Ile Val Phe Glu 
            260                 265                 270         


Gly Lys Tyr Val Trp Asp Glu Asp Tyr Pro Leu His Ile Gln His Ile 
        275                 280                 285             


Arg Cys Glu Phe Glu Leu Lys Glu Gly Tyr Ile Pro Thr Ile Gln Ile 
    290                 295                 300                 


Lys Arg Ser Arg Phe Tyr Lys Gly Asn Glu Tyr Leu Lys Ser Ser Gly 
305                 310                 315                 320 


Gly Glu Ile Ala Asp Leu Trp Leu Ser Asn Val Asp Leu Glu Leu Met 
                325                 330                 335     


Lys Glu His Tyr Asp Leu Tyr Asn Val Glu Tyr Ile Ser Gly Leu Lys 
            340                 345                 350         


Phe Lys Ala Thr Thr Gly Leu Phe Lys Asp Phe Ile Asp Lys Trp Thr 
        355                 360                 365             


Tyr Ile Lys Thr Thr Ser Glu Gly Ala Ile Lys Gln Leu Ala Lys Leu 
    370                 375                 380                 


Met Leu Asn Ser Leu Tyr Gly Lys Phe Ala Ser Asn Pro Asp Val Thr 
385                 390                 395                 400 


Gly Lys Val Pro Tyr Leu Lys Glu Asn Gly Ala Leu Gly Phe Arg Leu 
                405                 410                 415     


Gly Glu Glu Glu Thr Lys Asp Pro Val Tyr Thr Pro Met Gly Val Phe 
            420                 425                 430         


Ile Thr Ala Trp Ala Arg Tyr Thr Thr Ile Thr Ala Ala Gln Ala Cys 
        435                 440                 445             


Tyr Asp Arg Ile Ile Tyr Cys Asp Thr Asp Ser Ile His Leu Thr Gly 
    450                 455                 460                 


Thr Glu Ile Pro Asp Val Ile Lys Asp Ile Val Asp Pro Lys Lys Leu 
465                 470                 475                 480 


Gly Tyr Trp Ala His Glu Ser Thr Phe Lys Arg Ala Lys Tyr Leu Arg 
                485                 490                 495     


Gln Lys Thr Tyr Ile Gln Asp Ile Tyr Met Lys Glu Val Asp Gly Lys 
            500                 505                 510         


Leu Val Glu Gly Ser Pro Asp Asp Tyr Thr Asp Ile Lys Phe Ser Val 
        515                 520                 525             


Lys Cys Ala Gly Met Thr Asp Lys Ile Lys Lys Glu Val Thr Phe Glu 
    530                 535                 540                 


Asn Phe Lys Val Gly Phe Ser Arg Lys Met Lys Pro Lys Pro Val Gln 
545                 550                 555                 560 


Val Pro Gly Gly Val Val Leu Val Asp Asp Thr Phe Thr Ile Lys Ser 
                565                 570                 575     


Gly Gly Ser Ala Trp Ser His Pro Gln Phe Glu Lys Gly Gly Gly Ser 
            580                 585                 590         


Gly Gly Gly Ser Gly Gly Ser Ala Trp Ser His Pro Gln Phe Glu Lys 
        595                 600                 605             


<210>  5
<211>  67
<212>  DNA
<213>  Synthetic


<220>
<221>  misc_feature
<222>  (19)..(23)
<223>  n is abasic nucleotide

<400>  5
actatcatta tctacatcnn nnncatcact actccgcatg caggtagcct tttggctacc       60

tgcatgc                                                                 67


<210>  6
<211>  67
<212>  DNA
<213>  Synthetic


<220>
<221>  misc_feature
<222>  (25)..(29)
<223>  n is abasic nucleotide

<400>  6
actatcatta tctacatcca ttacnnnnnt actccgcatg caggtagcct tttggctacc       60

tgcatgc                                                                 67


<210>  7
<211>  67
<212>  DNA
<213>  Synthetic


<220>
<221>  misc_feature
<222>  (24)..(28)
<223>  n is abasic nucleotide

<400>  7
actatcatta tctacatcca ttannnnnct actccgcatg caggtagcct tttggctacc       60

tgcatgc                                                                 67


<210>  8
<211>  67
<212>  DNA
<213>  Synthetic


<220>
<221>  misc_feature
<222>  (23)..(27)
<223>  n is abasic nucleotide

<400>  8
actatcatta tctacatcca ttnnnnnact actccgcatg caggtagcct tttggctacc       60

tgcatgc                                                                 67


<210>  9
<211>  67
<212>  DNA
<213>  Synthetic


<220>
<221>  misc_feature
<222>  (22)..(26)
<223>  n is abasic nucleotide

<400>  9
actatcatta tctacatcca tnnnnncact actccgcatg caggtagcct tttggctacc       60

tgcatgc                                                                 67


<210>  10
<211>  67
<212>  DNA
<213>  Synthetic


<220>
<221>  misc_feature
<222>  (21)..(25)
<223>  n is abasic nucleotide

<400>  10
actatcatta tctacatcca nnnnntcact actccgcatg caggtagcct tttggctacc       60

tgcatgc                                                                 67


<210>  11
<211>  67
<212>  DNA
<213>  Synthetic


<220>
<221>  misc_feature
<222>  (20)..(24)
<223>  n is abasic nucleotide

<400>  11
actatcatta tctacatccn nnnnatcact actccgcatg caggtagcct tttggctacc       60

tgcatgc                                                                 67


<210>  12
<211>  67
<212>  DNA
<213>  Synthetic


<220>
<221>  misc_feature
<222>  (19)..(23)
<223>  n is abasic nucleotide

<400>  12
actatcatta tctacatcnn nnncatcact actccgcatg caggtagcct tttggctacc       60

tgcatgc                                                                 67


<210>  13
<211>  67
<212>  DNA
<213>  Synthetic


<220>
<221>  misc_feature
<222>  (18)..(22)
<223>  n is abasic nucleotide

<400>  13
actatcatta tctacatnnn nnacatcact actccgcatg caggtagcct tttggctacc       60

tgcatgc                                                                 67


<210>  14
<211>  67
<212>  DNA
<213>  Synthetic


<220>
<221>  misc_feature
<222>  (17)..(21)
<223>  n is abasic nucleotide

<400>  14
actatcatta tctacannnn ntacatcact actccgcatg caggtagcct tttggctacc       60

tgcatgc                                                                 67


<210>  15
<211>  67
<212>  DNA
<213>  Synthetic


<220>
<221>  misc_feature
<222>  (16)..(20)
<223>  n is abasic nucleotide

<400>  15
actatcatta tctacnnnnn ttacatcact actccgcatg caggtagcct tttggctacc       60

tgcatgc                                                                 67


<210>  16
<211>  67
<212>  DNA
<213>  Synthetic


<220>
<221>  misc_feature
<222>  (15)..(19)
<223>  n is abasic nucleotide

<400>  16
actatcatta tctannnnna ttacatcact actccgcatg caggtagcct tttggctacc       60

tgcatgc                                                                 67


<210>  17
<211>  67
<212>  DNA
<213>  Synthetic


<220>
<221>  misc_feature
<222>  (14)..(18)
<223>  n is abasic nucleotide

<400>  17
actatcatta tctnnnnnca ttacatcact actccgcatg caggtagcct tttggctacc       60

tgcatgc                                                                 67


<210>  18
<211>  63
<212>  DNA
<213>  Synthetic


<220>
<221>  misc_feature
<222>  (9)..(13)
<223>  n is abasic nucleotide

<400>  18
tctacatcnn nnncacacat cacacaacca cgcatgcagg tagccttttg gctacctgca       60

tgc                                                                     63


<210>  19
<211>  67
<212>  DNA
<213>  Synthetic


<220>
<221>  misc_feature
<222>  (16)..(20)
<223>  n is abasic nucleotide

<400>  19
actatcatta tctacnnnnn ttacatcact actccgcatg caggtagcct tttggctacc       60

tgcatgc                                                                 67


<210>  20
<211>  73
<212>  DNA
<213>  Synthetic


<220>
<221>  misc_feature
<222>  (19)..(23)
<223>  n is abasic nucleotide

<400>  20
actatcatta tctacatcnn nnncacacat cacacaacca cgcatgcagg tagccttttg       60

gctacctgca tgc                                                          73


<210>  21
<211>  85
<212>  DNA
<213>  Synthetic


<220>
<221>  misc_feature
<222>  (24)..(28)
<223>  n is abasic nucleotide

<400>  21
ctcacctatc cttccactca actnnnnntc tacatccatt acatcactac tccgcatgca       60

ggtagccttt tggctacctg catgc                                             85


<210>  22
<211>  94
<212>  DNA
<213>  Synthetic


<220>
<221>  misc_feature
<222>  (40)..(44)
<223>  n is abasic nucleotide

<220>
<221>  misc_feature
<222>  (93)..(93)
<223>  n is abasic nucleotide

<400>  22
ctcacctatc cttccactca tactatcatt atctacatcn nnnntaccat tcattcagat       60

ctcactatcg cattctcatg caggtcgtag ccns                                   94


<210>  23
<211>  23
<212>  DNA
<213>  Synthetic

<400>  23
ggctacgacc tgcatgagaa tgc                                               23


<210>  24
<211>  32
<212>  DNA
<213>  Synthetic


<220>
<221>  misc_feature
<222>  (25)..(31)
<223>  n is abasic nucleotide

<400>  24
atagtgagat ctgaatgaat ggtannnnnn ns                                     32


<210>  25
<211>  108
<212>  DNA
<213>  Synthetic


<220>
<221>  misc_feature
<222>  (31)..(35)
<223>  n is abasic nucleotide

<220>
<221>  misc_feature
<222>  (71)..(75)
<223>  n is abasic nucleotide

<400>  25
tatctacatc tatctacatc tatctacatc nnnnntacca ttcattcaga tctcactatc       60

tatctacatc nnnnntatcc atctctatct cacctatcct tccactca                   108


<210>  26
<211>  33
<212>  DNA
<213>  Synthetic


<220>
<221>  misc_feature
<222>  (26)..(32)
<223>  n is abasic nucleotide

<400>  26
gatagtgaga tctgaatgaa tggtannnnn nns                                    33


<210>  27
<211>  34
<212>  DNA
<213>  Synthetic


<220>
<221>  misc_feature
<222>  (1)..(2)
<223>  n is abasic nucleotide

<220>
<221>  misc_feature
<222>  (27)..(33)
<223>  n is abasic nucleotide

<400>  27
nnatagtgag atctgaatga atggtannnn nnns                                   34


<210>  28
<211>  70
<212>  DNA
<213>  Synthetic


<220>
<221>  misc_feature
<222>  (16)..(20)
<223>  n is abasic nucleotide

<220>
<221>  misc_feature
<222>  (69)..(69)
<223>  n is abasic nucleotide

<400>  28
atcattatct acatcnnnnn taccattcat tcagatctca ctatcgcatt ctcatgcagg       60

tcgtagccns                                                              70


