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. 2013 Mar 27;10(4):540–552. doi: 10.4161/rna.24133

Table 1. Phylogenetic analysis of 16 RNA structures in the HIV-1 genome.

name positiona subtype Prototype sequenceb nt differencesc RNA structure
          ΔG (kcal/mol)d
 Conservatione
A
 1076–1142
 NL4–3
  
  
 -22.9
 +
gag, p24
 A
 2/6 (33%)
 4
 -22.9
 +
 
 B
 23/235 (10%)
 1
 -22.9
 +
 
 C
 12/397 (3%)
 9
 -16.1
 -
 
 D
 6/49 (12%)
 4
 -21.3
 +
B
 1459–1522
 NL4–3
  
  
 -12.5
 -
gag, p2
 A
 1/6 (17%)
 13 (3 del)
 -8.0
 -
 
 B
 7/371 (2%)
 2
 -15.0
 -
 
 C
 3/399 (1%)
 23 (4 del)
 -11.3
 -
 
 D
 2/51 (4%)
 15
 -11.3
 -
C
 1823–1859
 NL4–3
  
  
 -19.1
 +
gag, p6
 A
 2/6 (33%)
 11
 -7.9
 1/2Bf
pol, prot
 B
 41/371 (11%)
 2
 -18.1
 +
 
 C
 11/399 (3%)
 10
 -17.1
 -
 
 D
 3/51 (6%)
 5
 -17.5
 +
D
 2388–2484
 NL4–3
  
  
 -23.1
 -
pol, RT
 A
 1/6 (17%)
 10
 -34.1
 -
 
 B
 7/235 (3%)
 2
 -21.7
 -
 
 C
 10/397 (3%)
 8
 -27.5
 -
 
 D
 1/49 (2%)
 6
 -21.4
 -
E
POL1
 2619–2686
 NL4–3
  
  
 -20.7
 +
pol, RT
 A
 1/6 (17%)
 6
 -9.2
 +
 
 B
 39/235 (17%)
 1
 -18.5
 +
 
 C
 26/397 (7%)
 4
 -17.4
 1/2Bf
 
 D
 6/49 (12%)
 3
 -15.0
 1/2Bf
 
 CPZ
 1/9 (9%)
 26
 -12.4
 +
F
POL2
 2781–2835
 NL4–3
  
  
 -23.2
 +
pol, RT
 A
 2/6 (33%)
 6
 -14.5
 1/2Af
 
 B
 53/235 (21%)
 0
 -23.2
 +
 
 C
 122/397 (31%)
 4
 -20.2
 +
 
 D
 8/49 (16%)
 3
 -17.6
 +
 
 CPZ
 8/49 (16%)
 3
 -17.6
 +
G
 3285–3358
 NL4–3
  
  
 -23.4
 -
pol, RT
 A
 1/6 (17%)
 8
 -25.2
 -
 
 B
 25/235 (11%)
 1
 -23.9
 -
 
 C
 55/396 (14%)
 5
 -22.5
 1/2Bf
 
 D
 4/49 (8%)
 3
 -23.9
 -
H
POL3
 3606–3639
 NL4–3
  
  
 -5.8
 +
pol, RNase H
 A
 1/6 (17%)
 6
 -5.1
 +
 
 B
 59/235 (25%)
 2
 -2.0
 +
 
 C
 140/395 (35%)
 1
 -5.8
 +
 
 D
 17/49 (35%)
 1
 -5.8
 +
 
 CPZ
 17/49 (35%)
 1
 -5.8
 +
I
 5303–5343
 NL4–3
  
  
 -12.3
 -
vpr
 A
 3/6 (50%)
 5
 -3.9
 -
 
 B
 35/234 (15%)
 1
 -9.8
 -
 
 C
 78/397 (20%)
 6
 -4.5
 -
 
 D
 6/49 (12%)
 3
 -4.5
 -
J
 5530–5581
 NL4–3
  
  
 -12.4
 +
tat(1), rev(1)
 A
 1/6 (17%)
 14
 -14.7
 -
 
 B
 6/371 (2%)
 4
 -10.1
 -
 
 C
 17/399 (4%)
 12
 -14.9
 -
 
 D
 2/51 (4%)
 11
 -6.9
 -
K
 5600–5645
 NL4–3
  
  
 -7.6
 -
 
 A
 1/6 (17%)
 21
 -6.5
 -
 
 B
 2/235 (1%)
 7
 -8.8
 -
 
 C
 3/397 (1%)
 30
 -0.4
 -
 
 D
 2/49 (4%)
 8
 -8.8
 -
L
 6536–6598
 NL4–3
  
  
 -17.8
 -
env, gp120
 A
 1/6 (17%)
 11
 -10.3
 -
 
 B
 6/371 (2%)
 4
 -8.8
 -
 
 C
 5/398 (1%)
 13
 -8.4
 -
 
 D
 2/51 (4%)
 9
 -11.6
 -
M
 6982–7016
 NL4–3
  
  
 -7.9
 +
env, gp120
 A
 1/6 (17%)
 17
 -1.3
 -
 
 B
 1/235 (< 1%)
 14
 0.7
 -
 
 C
 1/397 (< 1%)
 17 (7 del)
 -0.6
 -
 
 D
 1/49 (2%)
 13
 -1.7
 -
N
 8455–8505
 NL4–3
  
  
 -18.3
 +
nef, LTR
 A
 1/6 (17%)
 11
 -11.8
 -
 
 B
 24/370 (7%)
 partial del
 -1.6
 -
 
 C
 8/399 (2%)
 13
 -15.0
 +
 
 D
 4/51 (8%)
 7
 -13.4
 -
O
NEF1
 8723–8773
 NL4–3
  
  
 -26.6
 +
nef, LTR
 A
 1/6 (17%)
 8
 -13.3
 1/2Bf
 
 B
 16/219 (7%)
 2
 -19.0
 +
 
 C
 49/396 (12%)
 4
 -25.1
 +
 
 D
 9/48 (19%)
 4
 -19.6
 +
 
 CPZ
 1/11 (9%)
 10
 -17.5
 +
P 8867–8906
 NL4–3
  
  
 -19.5
 +
nef, LTR
 A
 3/6 (50%)
 13
 -11.0
 +
 
 B
 15/59 (25%)
 6
 -7.1
 +
 
 C
 2/25 (8%)
 14
 -6.0
 -
  D 1/4 (25%) 11 -3.9 -

a) NL4-3 coordinates

b) Number of virus isolates that match the exact prototype sequence, which was identified by PrimAlign (Los Alamos HIV database)

c) Compared with NL4-3

d) Calculated by mfold for the prototype sequence

e) Structural similarity between SHAPE model2 and predicted mfold structure; structure maintained = +; structure changed = -

f) 1/2A = only first domain maintained, 1/2B = only second domain maintained.