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During the early stages of HIV-1 replication two viral enzymes are activated: reverse transcriptase (RT) and integrase (IN). RT catalyzes the synthesis of DNA copy of the viral genomic RNA, and IN stimulates the viral DNA integration into the cell genome. Inhibition of the activity of these proteins should completely block viral replication right after the infection. Earlier we have found that short single-stranded 11-mer 2’-O-methylated oligonucleotides (mODNs) conjugated to 2,4,5,7-tetrabromofluoresceine (eosin) inhibited the IN activity in vitro in nanomolar concentrations. Moreover the complexes of these compounds with a cell-penetrating peptide were shown to penetrate into HIV-1-infected cells, to block the viral replication at the reverse transcription step, and to lead to the emergence of drug resistance mutations known to confer a high level of virus resistance to non-nucleoside RT inhibitors. In the present work we study interactions of mODNs with RT in vitro. Their impact on the RT catalytic activity was evaluated. It was clarified that the mODNs conjugation with eosin significantly increased their inhibitory potency. The conjugates were able to inhibit the activity of RT-associated RNase H in submicromolar concentrations and DNA-dependent DNA-polymerase activity in low micromolar concentrations. The nucleotide sequence of the inhibitors had no significant impact on their capacity to inhibit both RT and IN. In addition, the inhibitors were still active against several RT mutants possessing resistance to non-nucleoside inhibitors (K103N/Y181C, V106A, Y188L). The ability of mODNs conjugates with eosin to block a direct binding of RT and IN was estimated. Thus we can consider these compounds as inhibitors of a new generation, capable to suppress the activity of two viral enzymes acting at early steps of HIV-1 infection and the interaction between them.