Deamination of cytidine residues in viral DNA is a major mechanism by which 
APOBEC3G (A3G) inhibits vif-deficient human immunodeficiency virus type 1 
(HIV-1) replication. dC-to-dU transition following RNase-H activity leads to 
viral cDNA degradation, production of non-functional proteins, formation of 
undesired stop codons and decreased viral protein synthesis. Here, we 
demonstrate that A3G provides an additional layer of defense against HIV-1 
infection dependent on inhibition of proviral transcription. HIV-1 transcription 
elongation is regulated by the trans-activation response (TAR) element, a short 
stem-loop RNA structure required for elongation factors binding. Vif-deficient 
HIV-1-infected cells accumulate short viral transcripts and produce lower 
amounts of full-length HIV-1 transcripts due to A3G deamination of the TAR 
apical loop cytidine, highlighting the requirement for TAR loop integrity in 
HIV-1 transcription. We further show that free single-stranded DNA (ssDNA) 
termini are not essential for A3G activity and a gap of CCC motif blocked with 
juxtaposed DNA or RNA on either or 3'+5' ends is sufficient for A3G deamination. 
These results identify A3G as an efficient mutator and that deamination of 
(-)SSDNA results in an early block of HIV-1 transcription.