Table 3S: Digestion Products Obtained by Treating HIV-1 5 -UTR with A) Mung Bean Nuclease
Position / Sequence / Exp. Mass / From seq.
G1:A21-U37:C58 / 5'-TpGGUCUCUCUGGUUAGACCAGA-3' 5'-pUCUCUGGCUAACUAGGGAACCC-3' / 13979.7 / 13979.7
G1:A21-C38:C58 / 5'-TpGGUCUCUCUGGUUAGACCAGA-3' 5'-pCUCUGGCUAACUAGGGAACCC-3' / 13673.7 / 13673.7
G1:A21-U37:C56 / 5'-TpGGUCUCUCUGGUUAGACCAGA-3' 5'-pUCUCUGGCUAACUAGGGAAC-3' / 13369.7 / 13369.6
G1:A19 / 5'-TpGGUCUCUCUGGUUAGACCA-3' / 6251.69 / 6251.70
G1:G20 / 5'-TpGGUCUCUCUGGUUAGACCAG-3' / 6596.74 / 6596.74
G1:U22 / 5'-TpGGUCUCUCUGGUUAGACCAGAU-3' / 7231.82 / 7231.82
G1:C23 / 5'-TpGGUCUCUCUGGUUAGACCAGAUC-3' / 7536.86 / 7536.86
G1:U24 / 5'-TpGGUCUCUCUGGUUAGACCAGAUCU-3' / 7842.89 / 7842.89
G1:U30 / 5'-TpGGUCUCUCUGGUUAGACCAGAUCUGAGCCU-3' / 9778.15 / 9778.14
G1:G31 / 5'-TpGGUCUCUCUGGUUAGACCAGAUCUGAGCCUG-3' / 10123.2 / 10123.2
U30:A74 / 5'-pUGGGAGCUCUCUGGCUAACUAGGGAACCCACUGCUUAAGCCUCAA-3' / 14458.9 / 14458.9
G31:A76 / 5'-pGGGAGCUCUCUGGCUAACUAGGGAACCCACUGCUUAAGCCUCAAUA-3' / 14787.9 / 14788.0
G32:A74 / 5'-pGGAGCUCUCUGGCUAACUAGGGAACCCACUGCUUAAGCCUCAA-3' / 13807.8 / 13807.8
G32:U75 / 5'-pGGAGCUCUCUGGCUAACUAGGGAACCCACUGCUUAAGCCUCAAU-3' / 14113.9 / 14113.9
G32:A76 / 5'-pGGAGCUCUCUGGCUAACUAGGGAACCCACUGCUUAAGCCUCAAUA-3' / 14442.8 / 14442.9
A55:A66 / 5'-pACCCACUGCUUA-3' / 3793.54 / 3793.50
A67:C72 / 5'-pAGCCUC-3' / 1913.26 / 1913.26
A78:C95 / 5'-pAGCUUGCCUUGAGUGCUC-3' / 5762.70 / 5762.71
A78:A96 / 5'-pAGCUUGCCUUGAGUGCUCA-3' / 6091.75 / 6091.76
G79:C95 / 5'-pGCUUGCCUUGAGUGCUC-3' / 5433.65 / 5433.66
U87:G116 / 5'-pUGAGUGCUCAAAGUAGUGUGUGCCCGUCUG-3' / 9698.18 / 9698.22
G99:C151 / 5'-pGUAGUGUGUGCCCGUCUGUUGUGUGACUCUGGUAACUAGAGAUCCCUCAGACC-3' / 17017.1 / 17017.1
G102:C151 / 5'-pGUGUGUGCCCGUCUGUUGUGUGACUCUGGUAACUAGAGAUCCCUCAGACC-3' / 16037.0 / 16037.0
U105:U115 / 5'-pUGUGCCCGUCU-3' / 3497.42 / 3497.42
G108:G119-G335:G346 / 5'-pGCCCGUCUGUUG-3' 5'-pGAUGGGUGCGAG-3' / 7850.99 / 7851.01
C109:A124 / 5'-pCCCGUCUGUUGUGUGA-3' / 5128.61 / 5128.62
U128:C179 / 5'-pUGGUAACUAGAGAUCCCUCAGACCCUUUUAGUCAGUGUGGAAAAUCUCUAGC-3' / 16671.1 / 16671.1
A133:C151 / 5'-pACUAGAGAUCCCUCAGACC-3' / 6080.83 / 6080.83
A138:U155-C352:G367 / 5'-pAGAUCCCUCAGACCCUUU-3' 5'-pCGGUAUUAAGCGGGGG-3' / 10983.5 / 10983.4
U154:C179 / 5'-pUUUAGUCAGUGUGGAAAAUCUCUAGC-3' / 8366.07 / 8366.05
U154:A180 / 5'-pUUUAGUCAGUGUGGAAAAUCUCUAGCA-3' / 8695.11 / 8695.11
U154:C189 / 5'-pUUUAGUCAGUGUGGAAAAUCUCUAGCAGUGGCGCCC-3' / 11601.5 / 11601.5
U154:G190 / 5'-pUUUAGUCAGUGUGGAAAAUCUCUAGCAGUGGCGCCCG-3' / 11946.5 / 11946.5
U155:A180 / 5'-pUUAGUCAGUGUGGAAAAUCUCUAGCA-3' / 8389.08 / 8389.08
U155:C188 / 5'-pUUAGUCAGUGUGGAAAAUCUCUAGCAGUGGCGCC-3' / 10990.4 / 10990.4
U155:C189 / 5'-pUUAGUCAGUGUGGAAAAUCUCUAGCAGUGGCGCCC-3' / 11295.5 / 11295.5
U155:G190 / 5'-pUUAGUCAGUGUGGAAAAUCUCUAGCAGUGGCGCCCG-3' / 11640.5 / 11640.5
U155:A191 / 5'-pUUAGUCAGUGUGGAAAAUCUCUAGCAGUGGCGCCCGA-3' / 11969.5 / 11969.6
U155:C199 / 5'-pUUAGUCAGUGUGGAAAAUCUCUAGCAGUGGCGCCCGAACAGGGAC-3' / 14602.0 / 14601.9
U155:U200 / 5'-pUUAGUCAGUGUGGAAAAUCUCUAGCAGUGGCGCCCGAACAGGGACU-3' / 14908.0 / 14908.0
U155:U201 / 5'-pUUAGUCAGUGUGGAAAAUCUCUAGCAGUGGCGCCCGAACAGGGACUU-3' / 15214.0 / 15214.0
U155:G202 / 5'-pUUAGUCAGUGUGGAAAAUCUCUAGCAGUGGCGCCCGAACAGGGACUUG-3' / 15559.1 / 15559.0
U156:C188 / 5'-pUAGUCAGUGUGGAAAAUCUCUAGCAGUGGCGCC-3' / 10684.4 / 10684.4
U156:C189 / 5'-pUAGUCAGUGUGGAAAAUCUCUAGCAGUGGCGCCC-3' / 10989.4 / 10989.4
A157:C188 / 5'-pAGUCAGUGUGGAAAAUCUCUAGCAGUGGCGCC-3' / 10378.3 / 10378.4
U159:G190 / 5'-pUCAGUGUGGAAAAUCUCUAGCAGUGGCGCCCG-3' / 10354.4 / 10354.4
G183:C189 / 5'-pGGCGCCC-3' / 2273.31 / 2273.32
A192:G202 / 5'-pACAGGGACUUG-3' / 3607.49 / 3607.49
C193:G202 / 5'-pCAGGGACUUG-3' / 3278.43 / 3278.44
A205:G224 / 5'-pAGCGAAAGUAAAGCCAGAGG-3' / 6615.96 / 6615.96
G206:G224 / 5'-pGCGAAAGUAAAGCCAGAGG-3' / 6286.91 / 6286.91
U288:U307 / 5'-pUGGUGAGUACGCCAAAAAUU-3' / 6491.88 / 6491.87
G290:G317 / 5'-pGUGAGUACGCCAAAAAUUUUGACUAGCG-3' / 9062.20 / 9062.20
U291:G317 / 5'-pUGAGUACGCCAAAAAUUUUGACUAGCG-3' / 8717.15 / 8717.15
G294:G317 / 5'-pGUACGCCAAAAAUUUUGACUAGCG-3' / 7737.02 / 7737.02
G335:G346 / 5'-pGAUGGGUGCGAG-3' / 4008.53 / 4008.54
U337:A347 / 5'-pUGGGUGCGAGA-3' / 3663.49 / 3663.49
C362:G369 / 5'-pCGGGGGAG-3' / 2722.38 / 2722.39
b) HIV-1 5’-UTR digestion by V1 nuclease
Position / Sequence / Exp mass. / From seq.
G1:C18 / 5'-TpGGUCUCUCUGGUUAGACC-3' / 5922.64 / 5922.64
G1:A19 / 5'-TpGGUCUCUCUGGUUAGACCA-3' / 6251.69 / 6251.70
G1:C23 / 5'-TpGGUCUCUCUGGUUAGACCAGAUC-3' / 7536.85 / 7536.86
G1:U24 / 5'-TpGGUCUCUCUGGUUAGACCAGAUCU-3' / 7842.88 / 7842.89
G1:C60 / 5'-TpGGUCUCUCUGGUUAGACCAGAUCUGAGCCUGGGAGCUCUCUGGCUAACUAGGGAACCCAC-3' / 19462.4 / 19462.4
U9:A19 / 5'-pUGGUUAGACCA-3' / 3568.46 / 3568.47
G25:U37 / 5'-pGAGCCUGGGAGCU-3' / 4273.56 / 4273.58
G25:C60 / 5'-pGAGCCUGGGAGCUCUCUGGCUAACUAGGGAACCCAC-3' / 11637.5 / 11637.6
C38:U49 / 5'-pCUCUGGCUAACU-3' / 3810.48 / 3810.48
U64:G92 / 5'-pUUAAGCCUCAAUAAAGCUUGCCUUGAGUG-3' / 9305.19 / 9305.19
C70:G92 / 5'-pCUCAAUAAAGCUUGCCUUGAGUG-3' / 7384.93 / 7384.94
U71:U94 / 5'-pUCAAUAAAGCUUGCCUUGAGUGCU-3' / 7690.96 / 7690.97
C72:U86 / 5'-pCAAUAAAGCUUGCCU-3' / 4797.63 / 4797.64
G90:G102 / 5'-pGUGCUCAAAGUAG-3' / 4242.57 / 4242.57
A96:C111 / 5'-pAAAGUAGUGUGUGCCC-3' / 5198.68 / 5198.68
A96:G119 / 5'-pAAAGUAGUGUGUGCCCGUCUGUUG-3' / 7762.92 / 7762.97
C110:U126 / 5'-pCCGUCUGUUGUGUGACU-3' / 5434.64 / 5434.64
C111:U126 / 5'-pCGUCUGUUGUGUGACU-3' / 5129.59 / 5129.60
G112:U126 / 5'-pGUCUGUUGUGUGACU-3' / 4824.56 / 4824.56
C114:U126 / 5'-pCUGUUGUGUGACU-3' / 4173.48 / 4173.49
G116:U126 / 5'-pGUUGUGUGACU-3' / 3562.41 / 3562.42
U126:C144 / 5'-pUCUGGUAACUAGAGAUCCC-3' / 6098.79 / 6098.80
U126:C173 / 5'-pUCUGGUAACUAGAGAUCCCUCAGACCCUUUUAGUCAGUGUGGAAAAUC-3' / 15385.9 / 15386.0
U128:C142 / 5'-pUGGUAACUAGAGAUC-3' / 4877.64 / 4877.65
U128:C143 / 5'-pUGGUAACUAGAGAUCC-3' / 5182.68 / 5182.69
U128:U174 / 5'-pUGGUAACUAGAGAUCCCUCAGACCCUUUUAGUCAGUGUGGAAAAUCU-3' / 15080.9 / 15080.9
G129:U145 / 5'-pGGUAACUAGAGAUCCCU-3' / 5487.73 / 5487.73
U135:U145 / 5'-pUAGAGAUCCCU-3' / 3528.46 / 3528.46
C146:U159 / 5'-pCAGACCCUUUUAGU-3' / 4445.54 / 4445.56
C146:G167 / 5'-pCAGACCCUUUUAGUCAGUGUGG-3' / 7071.88 / 7071.89
A147:C173 / 5'-pAGACCCUUUUAGUCAGUGUGGAAAAUC-3' / 8694.12 / 8694.12
G148:U174 / 5'-pGACCCUUUUAGUCAGUGUGGAAAAUCU-3' / 8671.16 / 8671.10
A149:G162 / 5'-pACCCUUUUAGUCAG-3' / 4445.55 / 4445.56
A161:U182 / 5'-pAGUGUGGAAAAUCUCUAGCAGU-3' / 7142.93 / 7142.94
A170:G186 / 5'-pAAUCUCUAGCAGUGGCG-3' / 5503.72 / 5503.72
C175:U200 / 5'-pCUAGCAGUGGCGCCCGAACAGGGACU-3' / 8456.15 / 8456.16
U176:C188 / 5'-pUAGCAGUGGCGCC-3' / 4233.55 / 4233.57
G186:G202 / 5'-pGCCCGAACAGGGACUUG-3' / 5541.76 / 5541.76
C188:G202 / 5'-pCCGAACAGGGACUUG-3' / 4891.67 / 4891.68
C189:G202 / 5'-pCGAACAGGGACUUG-3' / 4586.63 / 4586.63
G190:G202 / 5'-pGAACAGGGACUUG-3' / 4281.59 / 4281.59
A198:C219 / 5'-pACUUGAAAGCGAAAGUAAAGCC-3' / 7171.98 / 7172.01
U201:C219 / 5'-pUGAAAGCGAAAGUAAAGCC-3' / 6231.89 / 6231.90
A209:C219 / 5'-pAAAGUAAAGCC-3' / 3598.52 / 3598.53
A216:U250 / 5'-pAGCCAGAGGAGAUCUCUCGACGCAGGACUCGGCUU-3' / 11332.5 / 11332.5
A222:C238 / 5'-pAGGAGAUCUCUCGACGC-3' / 5502.75 / 5502.74
A222:A256 / 5'-pAGGAGAUCUCUCGACGCAGGACUCGGCUUGCUGAA-3' / 11333.5 / 11333.5
G246:A263 / 5'-pGGCUUGCUGAAGCGCGCA-3' / 5863.78 / 5863.78
U250:A263 / 5'-pUGCUGAAGCGCGCA-3' / 4562.62 / 4562.62
U250:A268 / 5'-pUGCUGAAGCGCGCACGGCA-3' / 6191.84 / 6191.85
G285:A302 / 5'-pGACUGGUGAGUACGCCAA-3' / 5871.79 / 5871.80
C287:A301 / 5'-pCUGGUGAGUACGCCA-3' / 4868.64 / 4868.65
G289:A302 / 5'-pGGUGAGUACGCCAA-3' / 4586.62 / 4586.63
G290:A301 / 5'-pGUGAGUACGCCA-3' / 3912.50 / 3912.53
A301:U323 / 5'-pAAAAAUUUUGACUAGCGGAGGCU-3' / 7471.99 / 7471.99
A301:G338 / 5'-pAAAAAUUUUGACUAGCGGAGGCUAGAAGGAGAGAGAUG-3' / 12496.7 / 12496.7
G338:C362 / 5'-pGGGUGCGAGAGCGUCGGUAUUAAGC-3' / 8209.06 / 8209.09
G344:C362 / 5'-pGAGAGCGUCGGUAUUAAGC-3' / 6217.82 / 6217.83
G350:C362 / 5'-pGUCGGUAUUAAGC-3' / 4219.54 / 4219.54
Table 3S: Digestion products obtained by treating HIV-1 5’-UTR with a) Mung bean nuclease and b) V1 nuclease. Dashes are used to indicate duplex products. Monoisotopic masses are reported in mass units.
3.