                         SEQUENCE LISTING

<110>  Vorobiev, Alexei
       Lukhtanov , Eugeny
       Scarr, Noah
 
<120>  FUNCTIONALIZED 3-ALKYNYL PYRAZOLOPYRIMIDINE ANALOGUES AS 
       UNIVERSAL BASES AND METHODS OF USE

<130>  ELI-0118P1 (136520.273)

<140>  13/827,456
<141>  2013-03-14

<150>  US 61/466,755
<151>  2011-03-23

<150>  US 13/429,273
<151>  2012-03-23

<160>  60    

<170>  PatentIn version 3.5

<210>  1
<211>  15
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Duplex


<220>
<221>  misc_feature
<222>  (6)..(6)
<223>  n is 2'-deoxyinosine or 2-deoxy- 
       -D-ribofuranosyl-3-alkynyl-1H-pyrazolo[3,4-d]pyrimidin-4(5H)-one

<220>
<221>  misc_feature
<222>  (9)..(9)
<223>  n is 2'-deoxyinosine or 2-deoxy- 
       -D-ribofuranosyl-3-alkynyl-1H-pyrazolo[3,4-d]pyrimidin-4(5H)-one

<400>  1
gtaagnagnc ataac                                                        15


<210>  2
<211>  15
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Duplex


<220>
<221>  misc_feature
<222>  (6)..(6)
<223>  n is 2'-deoxyinosine or 2-deoxy- -D-ribofuranosyl- 
       3-alkynyl-1H-pyrazolo[3,4-d]pyrimidin-4(5H)-one

<400>  2
gtaagnagac ataac                                                        15


<210>  3
<211>  15
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Duplex


<220>
<221>  misc_feature
<222>  (9)..(9)
<223>  n is 2'-deoxyinosine or 2-deoxy- -D-ribofuranosyl- 
       3-alkynyl-1H-pyrazolo[3,4-d]pyrimidin-4(5H)-one

<400>  3
gtaagtagnc ataac                                                        15


<210>  4
<211>  19
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  ADV-1 primer


<220>
<221>  misc_feature
<222>  (12)..(12)
<223>  n is dI

<400>  4
ggcccgagat gngcatgta                                                    19


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

<220>
<223>  ADV-2 primer


<220>
<221>  misc_feature
<222>  (13)..(13)
<223>  n is dI

<400>  5
ggcccgagat gtncatgta                                                    19


<210>  6
<211>  19
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  ADV-3 primer


<220>
<221>  misc_feature
<222>  (14)..(14)
<223>  n is dI

<400>  6
ggcccgagat gtgnatgta                                                    19


<210>  7
<211>  19
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  ADV-4


<220>
<221>  misc_feature
<222>  (15)..(15)
<223>  n is dI

<400>  7
ggcccgagat gtgcntgta                                                    19


<210>  8
<211>  19
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  ADV-5 primer


<220>
<221>  misc_feature
<222>  (12)..(12)
<223>  n is I04

<400>  8
ggcccgagat gngcatgta                                                    19


<210>  9
<211>  19
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  ADV-6 primer


<220>
<221>  misc_feature
<222>  (13)..(13)
<223>  n is I04

<400>  9
ggcccgagat gtncatgta                                                    19


<210>  10
<211>  19
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  ADV-7 primer


<220>
<221>  misc_feature
<222>  (14)..(14)
<223>  n is I04

<400>  10
ggcccgagat gtgnatgta                                                    19


<210>  11
<211>  19
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  ADV-8 primer


<220>
<221>  misc_feature
<222>  (15)..(15)
<223>  n is I04

<400>  11
ggcccgagat gtgcntgta                                                    19


<210>  12
<211>  19
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  ADV-9 primer


<220>
<221>  misc_feature
<222>  (12)..(12)
<223>  n is I07

<400>  12
ggcccgagat gngcatgta                                                    19


<210>  13
<211>  19
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  ADV-10


<220>
<221>  misc_feature
<222>  (13)..(13)
<223>  n is I07

<400>  13
ggcccgagat gtncatgta                                                    19


<210>  14
<211>  19
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  ADV-11 primer


<220>
<221>  misc_feature
<222>  (14)..(14)
<223>  n is I07

<400>  14
ggcccgagat gtgnatgta                                                    19


<210>  15
<211>  19
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  ADV-12 primer


<220>
<221>  misc_feature
<222>  (15)..(15)
<223>  n is I07

<400>  15
ggcccgagat gtgcntgta                                                    19


<210>  16
<211>  19
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  ADV-L1 primer

<400>  16
ggcccgagat gtgcatgta                                                    19


<210>  17
<211>  19
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  ADV-L1

<400>  17
tacatgcaca tctcgggcc                                                    19


<210>  18
<211>  29
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  ADV-MGB-FAM primer


<220>
<221>  misc_feature
<222>  (1)..(1)
<223>  n is A conjugated to FAM and minor groove binder (MGB)

<400>  18
nataaatcat aagatggcta ccccttcga                                         29


<210>  19
<211>  12
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  target non-specific flap sequence

<400>  19
aataaatcat aa                                                           12


<210>  20
<211>  19
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  ADV-25 primer


<220>
<221>  misc_feature
<222>  (12)..(12)
<223>  n is dI

<220>
<221>  misc_feature
<222>  (14)..(14)
<223>  n is dI

<400>  20
ggcccgagat gngnatgta                                                    19


<210>  21
<211>  19
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  ADV-26 primer


<220>
<221>  misc_feature
<222>  (12)..(12)
<223>  n is dI

<220>
<221>  misc_feature
<222>  (15)..(15)
<223>  n is dI

<400>  21
ggcccgagat gngcntgta                                                    19


<210>  22
<211>  19
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  ADV-27 primer


<220>
<221>  misc_feature
<222>  (12)..(12)
<223>  n is dI

<220>
<221>  misc_feature
<222>  (16)..(16)
<223>  n is dI

<400>  22
ggcccgagat gngcangta                                                    19


<210>  23
<211>  19
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  ADV-28


<220>
<221>  misc_feature
<222>  (12)..(12)
<223>  n is dI

<220>
<221>  misc_feature
<222>  (17)..(17)
<223>  n is dI

<400>  23
ggcccgagat gngcatnta                                                    19


<210>  24
<211>  19
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  ADV-13 primer


<220>
<221>  misc_feature
<222>  (12)..(12)
<223>  n is I04

<220>
<221>  misc_feature
<222>  (14)..(14)
<223>  n is I04

<400>  24
ggcccgagat gngnatgta                                                    19


<210>  25
<211>  19
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  ADV-14 primer


<220>
<221>  misc_feature
<222>  (12)..(12)
<223>  n is I04

<220>
<221>  misc_feature
<222>  (15)..(15)
<223>  n is I04

<400>  25
ggcccgagat gngcntgta                                                    19


<210>  26
<211>  19
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  ADV-15 primer


<220>
<221>  misc_feature
<222>  (12)..(12)
<223>  n is I04

<220>
<221>  misc_feature
<222>  (16)..(16)
<223>  n is I04

<400>  26
ggcccgagat gngcangta                                                    19


<210>  27
<211>  19
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  ADV-16 primer


<220>
<221>  misc_feature
<222>  (12)..(12)
<223>  n is I04

<220>
<221>  misc_feature
<222>  (16)..(16)
<223>  n is I04

<220>
<221>  misc_feature
<222>  (17)..(17)
<223>  n is I04

<400>  27
ggcccgagat gngcatnta                                                    19


<210>  28
<211>  19
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  ADV-17 primer


<220>
<221>  misc_feature
<222>  (12)..(12)
<223>  n is I07

<220>
<221>  misc_feature
<222>  (14)..(14)
<223>  n is I07

<400>  28
ggcccgagat gngnatgta                                                    19


<210>  29
<211>  19
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  ADV-18


<220>
<221>  misc_feature
<222>  (12)..(12)
<223>  n is I07

<220>
<221>  misc_feature
<222>  (15)..(15)
<223>  n is I07

<400>  29
ggcccgagat gngcntgta                                                    19


<210>  30
<211>  19
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  ADV-19 primer


<220>
<221>  misc_feature
<222>  (12)..(12)
<223>  n is I07

<220>
<221>  misc_feature
<222>  (16)..(16)
<223>  n is I07

<400>  30
ggcccgagat gngcangta                                                    19


<210>  31
<211>  19
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  ADV-20


<220>
<221>  misc_feature
<222>  (12)..(12)
<223>  n is I07

<220>
<221>  misc_feature
<222>  (17)..(17)
<223>  n is I07

<400>  31
ggcccgagat gngcatnta                                                    19


<210>  32
<211>  19
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  ADV-29 primer


<220>
<221>  misc_feature
<222>  (18)..(18)
<223>  n is dI

<400>  32
ggcccgagat gtgcatgna                                                    19


<210>  33
<211>  19
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  ADV-30 primer


<220>
<221>  misc_feature
<222>  (19)..(19)
<223>  n is dI

<400>  33
ggcccgagat gtgcatgtn                                                    19


<210>  34
<211>  19
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  ADV-21


<220>
<221>  misc_feature
<222>  (18)..(18)
<223>  n is I04

<400>  34
ggcccgagat gtgcatgna                                                    19


<210>  35
<211>  19
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  ADV-22 primer


<220>
<221>  misc_feature
<222>  (19)..(19)
<223>  n is I04

<400>  35
ggcccgagat gtgcatgtn                                                    19


<210>  36
<211>  19
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  ADV-23 primer


<220>
<221>  misc_feature
<222>  (18)..(18)
<223>  n is I07

<400>  36
ggcccgagat gtgcatgna                                                    19


<210>  37
<211>  19
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  ADV-24 primer


<220>
<221>  misc_feature
<222>  (19)..(19)
<223>  n is I07

<400>  37
ggcccgagat gtgcatgtn                                                    19


<210>  38
<211>  19
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  ADV-32 primer


<220>
<221>  misc_feature
<222>  (9)..(9)
<223>  n is dI

<220>
<221>  misc_feature
<222>  (12)..(12)
<223>  n is dI

<220>
<221>  misc_feature
<222>  (15)..(15)
<223>  n is dI

<400>  38
ggcccgagnt gngcntgta                                                    19


<210>  39
<211>  19
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  ADV-31 primer


<220>
<221>  misc_feature
<222>  (10)..(10)
<223>  n is dI

<220>
<221>  misc_feature
<222>  (12)..(12)
<223>  n is dI

<220>
<221>  misc_feature
<222>  (15)..(15)
<223>  n is dI

<400>  39
ggcccgagan gngcntgta                                                    19


<210>  40
<211>  19
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  ADV-34 primer


<220>
<221>  misc_feature
<222>  (9)..(9)
<223>  n is I04

<220>
<221>  misc_feature
<222>  (12)..(12)
<223>  n is I04

<220>
<221>  misc_feature
<222>  (15)..(15)
<223>  n is I04

<400>  40
ggcccgagnt gngcntgta                                                    19


<210>  41
<211>  19
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  ADV-33 primer


<220>
<221>  misc_feature
<222>  (10)..(10)
<223>  n is I04

<220>
<221>  misc_feature
<222>  (12)..(12)
<223>  n is I04

<220>
<221>  misc_feature
<222>  (15)..(15)
<223>  n is I04

<400>  41
ggcccgagan gngcntgta                                                    19


<210>  42
<211>  19
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  ADV-36 primer


<220>
<221>  misc_feature
<222>  (9)..(9)
<223>  n is I07

<220>
<221>  misc_feature
<222>  (12)..(12)
<223>  n is I07

<220>
<221>  misc_feature
<222>  (15)..(15)
<223>  n is I07

<400>  42
ggcccgagnt gngcntgta                                                    19


<210>  43
<211>  19
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  ADV-35 primer


<220>
<221>  misc_feature
<222>  (10)..(10)
<223>  n is I07

<220>
<221>  misc_feature
<222>  (12)..(12)
<223>  n is I07

<220>
<221>  misc_feature
<222>  (15)..(15)
<223>  n is I07

<400>  43
ggcccgagan gngcntgta                                                    19


<210>  44
<211>  28
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  LGA-L23

<400>  44
gtatatttcc gttattttct aaagcact                                          28


<210>  45
<211>  28
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  LGA-L24


<220>
<221>  misc_feature
<222>  (6)..(6)
<223>  n is dI

<220>
<221>  misc_feature
<222>  (15)..(15)
<223>  n is dI

<220>
<221>  misc_feature
<222>  (18)..(18)
<223>  n is dI

<220>
<221>  misc_feature
<222>  (21)..(21)
<223>  n is dI

<220>
<221>  misc_feature
<222>  (23)..(23)
<223>  n is dI

<400>  45
gtatanttcc gttanttnct nangcact                                          28


<210>  46
<211>  29
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  LGA-L25


<220>
<221>  misc_feature
<222>  (6)..(6)
<223>  n is I07

<220>
<221>  misc_feature
<222>  (15)..(15)
<223>  n is I07

<220>
<221>  misc_feature
<222>  (18)..(18)
<223>  n is I07

<220>
<221>  misc_feature
<222>  (21)..(21)
<223>  n is I07

<220>
<221>  misc_feature
<222>  (23)..(23)
<223>  n is I07

<400>  46
gtatanttcc gttanttnct nangcactg                                         29


<210>  47
<211>  37
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  LGA-E3

<400>  47
aataaatcat aaggccaagg cgagatacta gtaaacc                                37


<210>  48
<211>  17
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  LGA-FAM5


<220>
<221>  misc_feature
<222>  (1)..(1)
<223>  n is Super G conjugated to FAM and minor groove binder (MGB)

<220>
<221>  misc_feature
<222>  (6)..(6)
<223>  n is Super A

<220>
<221>  misc_feature
<222>  (8)..(8)
<223>  n is Super T

<220>
<221>  misc_feature
<222>  (9)..(9)
<223>  n is Super T

<220>
<221>  misc_feature
<222>  (10)..(10)
<223>  n is Super T

<220>
<221>  misc_feature
<222>  (13)..(13)
<223>  n is Super A

<220>
<221>  misc_feature
<222>  (15)..(15)
<223>  n is Super A

<220>
<221>  misc_feature
<222>  (17)..(17)
<223>  n is G conjugated to Eclipse Dark Quencher (EDQ)

<400>  48
nataanannn gtntngn                                                      17


<210>  49
<211>  91
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Target sequence

<400>  49
acatgaggat tttgtatatt tccgttattt tctaaagcac tgtatattga taaaatttgt       60

atagggttta ctagtatctc gccttggcca t                                      91


<210>  50
<211>  38
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Natural F primer

<400>  50
gaggattttg tatatttccg ttattttcta aagcactg                               38


<210>  51
<211>  38
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  F I01 primer


<220>
<221>  misc_feature
<222>  (24)..(24)
<223>  n is dI

<220>
<221>  misc_feature
<222>  (27)..(27)
<223>  n is dI

<400>  51
gaggattttg tatatttccg ttanttncta aagcactg                               38


<210>  52
<211>  38
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  F I07 primer


<220>
<221>  misc_feature
<222>  (24)..(24)
<223>  n is I07

<220>
<221>  misc_feature
<222>  (27)..(27)
<223>  n is I07

<400>  52
gaggattttg tatatttccg ttanttncta aagcactg                               38


<210>  53
<211>  38
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Natural F primer (reverse strand)

<400>  53
cagtgcttta gaaaataacg gaaatataca aaatcctc                               38


<210>  54
<211>  38
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Amplicon complimentary to F I01 primer


<220>
<221>  misc_feature
<222>  (4)..(4)
<223>  n is A, C, T, or G

<220>
<221>  misc_feature
<222>  (34)..(35)
<223>  n is A, C, T, or G

<400>  54
cagngcttta gcaactaacg gaaatataca aaannctc                               38


<210>  55
<211>  38
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  Amplicon complimentary to F I07 primer


<220>
<221>  misc_feature
<222>  (3)..(5)
<223>  n is A, C, T, or G

<220>
<221>  misc_feature
<222>  (25)..(25)
<223>  n is A, C, T, or G

<220>
<221>  misc_feature
<222>  (38)..(38)
<223>  n is A, C, T, or G

<400>  55
cannncttta gcaactaacg gaaanataca aaatcctn                               38


<210>  56
<211>  12
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  5' DNA Duplex (Fig 20)


<220>
<221>  misc_feature
<222>  (7)..(7)
<223>  n is I07, I07-Pyr, I07-(Ac-Pyr)1, I07-(Ac-Pyr)2, or I07-Bu-Pyr

<400>  56
cttttangtc tt                                                           12


<210>  57
<211>  12
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  3' DNA duplex (Fig. 20)


<220>
<221>  misc_feature
<222>  (7)..(7)
<223>  n is A, C, T, or G

<400>  57
gaaaatncag aa                                                           12


<210>  58
<211>  15
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  DNA 15-mer (Fig. 21)


<220>
<221>  misc_feature
<222>  (6)..(6)
<223>  n is deoxyinosine, I04, I07, I07-Pyr, or I07-Acr

<400>  58
gtaagnagac ataac                                                        15


<210>  59
<211>  15
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  DNA 15-mer (Fig. 22)


<220>
<221>  misc_feature
<222>  (9)..(9)
<223>  n is deoxyinosine, I04, I07, I07-Pyr, or I07-Acr

<400>  59
gtaagtagnc ataac                                                        15


<210>  60
<211>  15
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  DNA 15-mer (Fig. 23)


<220>
<221>  misc_feature
<222>  (6)..(6)
<223>  n is deoxyinosine, I04, I07, I07-Pyr, or I07-Acr

<220>
<221>  misc_feature
<222>  (9)..(9)
<223>  n is deoxyinosine, I04, I07, I07-Pyr, or I07-Acr

<400>  60
gtaagnagnc ataac                                                        15


