Table 3S: Digestion Products Obtained by Treating HIV-1 5 -UTR with A) Mung Bean Nuclease

a) HIV-1 5’-UTR digestion by Mung bean nuclease Exp. From Position Sequence Mass seq. 5'-TpGGUCUCUCUGGUUAGACCAGA-3' 13979. 13979. G1:A21-U37:C58 5'-pUCUCUGGCUAACUAGGGAACCC-3' 7 7 5'-TpGGUCUCUCUGGUUAGACCAGA-3' 13673. G1:A21-C38:C58 13673.7 5'-pCUCUGGCUAACUAGGGAACCC-3' 7 5'-TpGGUCUCUCUGGUUAGACCAGA-3' 13369. G1:A21-U37:C56 13369.7 5'-pUCUCUGGCUAACUAGGGAAC-3' 6 6251.7 G1:A19 5'-TpGGUCUCUCUGGUUAGACCA-3' 6251.69 0 6596.7 G1:G20 5'-TpGGUCUCUCUGGUUAGACCAG-3' 6596.74 4 7231.8 G1:U22 5'-TpGGUCUCUCUGGUUAGACCAGAU-3' 7231.82 2 7536.8 G1:C23 5'-TpGGUCUCUCUGGUUAGACCAGAUC-3' 7536.86 6 7842.8 G1:U24 5'-TpGGUCUCUCUGGUUAGACCAGAUCU-3' 7842.89 9 9778.1 G1:U30 5'-TpGGUCUCUCUGGUUAGACCAGAUCUGAGCCU-3' 9778.15 4 10123. G1:G31 5'-TpGGUCUCUCUGGUUAGACCAGAUCUGAGCCUG-3' 10123.2 2 14458. U30:A74 5'-pUGGGAGCUCUCUGGCUAACUAGGGAACCCACUGCUUAAGCCUCAA-3' 14458.9 9 14788. G31:A76 5'-pGGGAGCUCUCUGGCUAACUAGGGAACCCACUGCUUAAGCCUCAAUA-3' 14787.9 0 13807. G32:A74 5'-pGGAGCUCUCUGGCUAACUAGGGAACCCACUGCUUAAGCCUCAA-3' 13807.8 8 14113. G32:U75 5'-pGGAGCUCUCUGGCUAACUAGGGAACCCACUGCUUAAGCCUCAAU-3' 14113.9 9 14442. G32:A76 5'-pGGAGCUCUCUGGCUAACUAGGGAACCCACUGCUUAAGCCUCAAUA-3' 14442.8 9 3793.5 A55:A66 5'-pACCCACUGCUUA-3' 3793.54 0 1913.2 A67:C72 5'-pAGCCUC-3' 1913.26 6 5762.7 A78:C95 5'-pAGCUUGCCUUGAGUGCUC-3' 5762.70 1 6091.7 A78:A96 5'-pAGCUUGCCUUGAGUGCUCA-3' 6091.75 6 5433.6 G79:C95 5'-pGCUUGCCUUGAGUGCUC-3' 5433.65 6 9698.2 U87:G116 5'-pUGAGUGCUCAAAGUAGUGUGUGCCCGUCUG-3' 9698.18 2 17017. G99:C151 5'-pGUAGUGUGUGCCCGUCUGUUGUGUGACUCUGGUAACUAGAGAUCCCUCAGACC-3' 17017.1 1 16037. G102:C151 5'-pGUGUGUGCCCGUCUGUUGUGUGACUCUGGUAACUAGAGAUCCCUCAGACC-3' 16037.0 0 3497.4 U105:U115 5'-pUGUGCCCGUCU-3' 3497.42 2 G108:G119- 5'-pGCCCGUCUGUUG-3' 7851.0 7850.99 G335:G346 5'-pGAUGGGUGCGAG-3' 1 5128.6 C109:A124 5'-pCCCGUCUGUUGUGUGA-3' 5128.61 2 16671. U128:C179 5'-pUGGUAACUAGAGAUCCCUCAGACCCUUUUAGUCAGUGUGGAAAAUCUCUAGC-3' 16671.1 1 6080.8 A133:C151 5'-pACUAGAGAUCCCUCAGACC-3' 6080.83 3 A138:U155- 5'-pAGAUCCCUCAGACCCUUU-3' 10983. 10983.5 C352:G367 5'-pCGGUAUUAAGCGGGGG-3' 4 8366.0 U154:C179 5'-pUUUAGUCAGUGUGGAAAAUCUCUAGC-3' 8366.07 5 8695.1 U154:A180 5'-pUUUAGUCAGUGUGGAAAAUCUCUAGCA-3' 8695.11 1 11601. U154:C189 5'-pUUUAGUCAGUGUGGAAAAUCUCUAGCAGUGGCGCCC-3' 11601.5 5 11946. U154:G190 5'-pUUUAGUCAGUGUGGAAAAUCUCUAGCAGUGGCGCCCG-3' 11946.5 5 8389.0 U155:A180 5'-pUUAGUCAGUGUGGAAAAUCUCUAGCA-3' 8389.08 8 10990. U155:C188 5'-pUUAGUCAGUGUGGAAAAUCUCUAGCAGUGGCGCC-3' 10990.4 4 11295. U155:C189 5'-pUUAGUCAGUGUGGAAAAUCUCUAGCAGUGGCGCCC-3' 11295.5 5 11640. U155:G190 5'-pUUAGUCAGUGUGGAAAAUCUCUAGCAGUGGCGCCCG-3' 11640.5 5 11969. U155:A191 5'-pUUAGUCAGUGUGGAAAAUCUCUAGCAGUGGCGCCCGA-3' 11969.5 6 14601. U155:C199 5'-pUUAGUCAGUGUGGAAAAUCUCUAGCAGUGGCGCCCGAACAGGGAC-3' 14602.0 9 14908. U155:U200 5'-pUUAGUCAGUGUGGAAAAUCUCUAGCAGUGGCGCCCGAACAGGGACU-3' 14908.0 0 15214. U155:U201 5'-pUUAGUCAGUGUGGAAAAUCUCUAGCAGUGGCGCCCGAACAGGGACUU-3' 15214.0 0 15559. U155:G202 5'-pUUAGUCAGUGUGGAAAAUCUCUAGCAGUGGCGCCCGAACAGGGACUUG-3' 15559.1 0 10684. U156:C188 5'-pUAGUCAGUGUGGAAAAUCUCUAGCAGUGGCGCC-3' 10684.4 4 10989. U156:C189 5'-pUAGUCAGUGUGGAAAAUCUCUAGCAGUGGCGCCC-3' 10989.4 4 10378. A157:C188 5'-pAGUCAGUGUGGAAAAUCUCUAGCAGUGGCGCC-3' 10378.3 4 10354. U159:G190 5'-pUCAGUGUGGAAAAUCUCUAGCAGUGGCGCCCG-3' 10354.4 4 2273.3 G183:C189 5'-pGGCGCCC-3' 2273.31 2 3607.4 A192:G202 5'-pACAGGGACUUG-3' 3607.49 9 3278.4 C193:G202 5'-pCAGGGACUUG-3' 3278.43 4 A205:G224 5'-pAGCGAAAGUAAAGCCAGAGG-3' 6615.96 6615.9

2. 6 6286.9 G206:G224 5'-pGCGAAAGUAAAGCCAGAGG-3' 6286.91 1 6491.8 U288:U307 5'-pUGGUGAGUACGCCAAAAAUU-3' 6491.88 7 9062.2 G290:G317 5'-pGUGAGUACGCCAAAAAUUUUGACUAGCG-3' 9062.20 0 8717.1 U291:G317 5'-pUGAGUACGCCAAAAAUUUUGACUAGCG-3' 8717.15 5 7737.0 G294:G317 5'-pGUACGCCAAAAAUUUUGACUAGCG-3' 7737.02 2 4008.5 G335:G346 5'-pGAUGGGUGCGAG-3' 4008.53 4 3663.4 U337:A347 5'-pUGGGUGCGAGA-3' 3663.49 9 2722.3 C362:G369 5'-pCGGGGGAG-3' 2722.38 9

3. b) HIV-1 5’-UTR digestion by V1 nuclease Exp Position Sequence From seq. mass. 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

4. 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.