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Table 2 Analysis of U5-PBS from viruses following extended in vitro culture in PBMC

From: Preferences for the selection of unique tRNA primers revealed from analysis of HIV-1 replication in peripheral blood mononuclear cells

Virus

U5-PBS

 

Days Post-Culture

 

Ile3

  

NL4-3-Ile-AC

15' AGTCAGTGTTTATCAGCTCTAGCAG 2TGGTGGCCCGTACGGGGA TTGAAA 3'

Input5

0

 

Ile

  
 

45' ************************* ****************** ****** 3'

PCR Product6

21

 

Lys, 3

  
 

5' ************************* TGGCGCCCGAACAGGGAC -***** 3'

6/7 TA Clones7

35

 

Lys,1,2

  
 

5' ************************* TGGCGCCCAACGTGGGGC -***** 3'

1/7 TA Clones

35

 

Lys, 3

  
 

5' ************************* TGGCGCCCGAACAGGGAC -***** 3'

PCR Product

73

 

Met

  

NL4-3-Met-AC 5

5' AGTCAGTGTTGTGAGACTGTAGCAG TGGTGCCCCGTGTGAGGC GAAAGC 3'

Input

0

 

Met

  
 

5' ************************* ****************** ****** 3'

5/10 TA Clones

35

 

5' ************************* *****************A ****** 3'

3/10 TA Clones

35

 

5' ********************* *A* * ****************** ****** 3'

1/10 TA Clones

35

 

5' ************************* *******T********** ****** 3'

1/10 TA Clones

35

 

Met

  
 

5' ************************* ****************** A***** 3'

6/9 TA Clones

63

 

5' ************************* *****************A A***** 3'

2/9 TA CIones

63

 

5' *********C*****G********* ****************** A***** 3'

1/9 TA CIones

63

  1. 1. The U5-loop is in bold type.
  2. 2. Spaces separate the PBS (indicated in bold type) from flanking sequence.
  3. 3. PBS complementary to the 3' terminal 18-nucleotide sequence of the indicated host tRNA.
  4. 4. Asterisks represent conserved nucleotides.
  5. 5. "Input" refers to the clone that was used to initiate viral infection in PBMCs.
  6. 6. PCR product that was sequenced directly.
  7. 7. Refers to TA clones of PCR product that is cloned into the Promega, P-Gem T-Easy Vector System I, to isolate individual colonies for sequencing.