All Publications

  • High-resolution view of HIV-1 reverse transcriptase initiation complexes and inhibition by NNRTI drugs. Nature communications Ha, B., Larsen, K. P., Zhang, J., Fu, Z., Montabana, E., Jackson, L. N., Chen, D., Puglisi, E. V. 2021; 12 (1): 2500


    Reverse transcription of the HIV-1 viral RNA genome (vRNA) is an integral step in virus replication. Upon viral entry, HIV-1 reverse transcriptase (RT) initiates from a host tRNALys3 primer bound to the vRNA genome and is the target of key antivirals, such as non-nucleoside reverse transcriptase inhibitors (NNRTIs). Initiation proceeds slowly with discrete pausing events along the vRNA template. Despite prior medium-resolution structural characterization of reverse transcriptase initiation complexes (RTICs), higher-resolution structures of the RTIC are needed to understand the molecular mechanisms that underlie initiation. Here we report cryo-EM structures of the core RTIC, RTIC-nevirapine, and RTIC-efavirenz complexes at 2.8, 3.1, and 2.9A, respectively. In combination with biochemical studies, these data suggest a basis for rapid dissociation kinetics of RT from the vRNA-tRNALys3 initiation complex and reveal a specific structural mechanism of nucleic acid conformational stabilization during initiation. Finally, our results show that NNRTIs inhibit the RTIC and exacerbate discrete pausing during early reverse transcription.

    View details for DOI 10.1038/s41467-021-22628-9

    View details for PubMedID 33947853

  • Advances in understanding the initiation of HIV-1 reverse transcription. Current opinion in structural biology Krupkin, M. n., Jackson, L. N., Ha, B. n., Puglisi, E. V. 2020; 65: 175–83


    Many viruses, including Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) and Human Immunodeficiency Virus (HIV), use RNA as their genetic material. How viruses harness RNA structure and RNA-protein interactions to control their replication remains obscure. Recent advances in the characterization of HIV-1 reverse transcriptase, the enzyme that converts its single-stranded RNA genome into a double-stranded DNA copy, reveal how the reverse transcription complex evolves during initiation. Here we highlight these advances in HIV-1 structural biology and discuss how they are furthering our understanding of HIV and related ribonucleoprotein complexes implicated in viral disease.

    View details for DOI 10.1016/

    View details for PubMedID 32916568

  • Distinct Conformational States Underlie Pausing during Initiation of HIV-1 Reverse Transcription. Journal of molecular biology Larsen, K. P., Choi, J. n., Jackson, L. N., Kappel, K. n., Zhang, J. n., Ha, B. n., Chen, D. H., Puglisi, E. V. 2020


    A hallmark of the initiation step of HIV-1 reverse transcription, in which viral RNA genome is converted into double-stranded DNA, is that it is slow and non-processive. Biochemical studies have identified specific sites along the viral RNA genomic template in which reverse transcriptase (RT) stalls. These stalling points, which occur after the addition of 3 and 5 template dNTPs, may serve as checkpoints to regulate the precise timing of HIV-1 reverse transcription following viral entry. Structural studies of reverse transcriptase initiation complexes (RTICs) have revealed unique conformations that may explain the slow rate of incorporation, however, questions remain about the temporal evolution of the complex and features that contribute to strong pausing during initiation. Here we present cryo-electron microscopy (cryo-EM) and single-molecule characterization of an RTIC after three rounds of dNTP incorporation (+3), the first major pausing point during reverse transcription initiation. Cryo-EM structures of a + 3 extended RTIC reveal conformational heterogeneity within the RTIC core. Three distinct conformations were identified, two of which adopt unique, likely off-pathway, intermediates in the canonical polymerization cycle. Single-molecule Förster resonance energy transfer (smFRET) experiments confirm that the +3 RTIC is more structurally dynamic than earlier stage RTICs. These alternative conformations were selectively disrupted through structure-guided point mutations to shift smFRET populations back towards the on-pathway conformation. Our results support the hypothesis that conformational heterogeneity within the HIV-1 reverse transcriptase initiation complex during pausing serves as an additional means of regulating HIV-1 replication.

    View details for DOI 10.1016/j.jmb.2020.06.003

    View details for PubMedID 32512005

  • Crystal structures of a natural DNA polymerase that functions as an XNA reverse transcriptase NUCLEIC ACIDS RESEARCH Jackson, L. N., Chim, N., Shi, C., Chaput, J. C. 2019; 47 (13): 6973–83


    Replicative DNA polymerases are highly efficient enzymes that maintain stringent geometric control over shape and orientation of the template and incoming nucleoside triphosphate. In a surprising twist to this paradigm, a naturally occurring bacterial DNA polymerase I member isolated from Geobacillus stearothermophilus (Bst) exhibits an innate ability to reverse transcribe RNA and other synthetic congeners (XNAs) into DNA. This observation raises the interesting question of how a replicative DNA polymerase is able to recognize templates of diverse chemical composition. Here, we present crystal structures of natural Bst DNA polymerase that capture the post-translocated product of DNA synthesis on templates composed entirely of 2'-deoxy-2'-fluoro-β-d-arabino nucleic acid (FANA) and α-l-threofuranosyl nucleic acid (TNA). Analysis of the enzyme active site reveals the importance of structural plasticity as a possible mechanism for XNA-dependent DNA synthesis and provides insights into the construction of variants with improved activity.

    View details for DOI 10.1093/nar/gkz513

    View details for Web of Science ID 000490556600036

    View details for PubMedID 31170294

    View details for PubMedCentralID PMC6649750

  • Crystal structures of DNA polymerase I capture novel intermediates in the DNA synthesis pathway ELIFE Chim, N., Jackson, L. N., Trinh, A. M., Chaput, J. C. 2018; 7


    High resolution crystal structures of DNA polymerase intermediates are needed to study the mechanism of DNA synthesis in cells. Here we report five crystal structures of DNA polymerase I that capture new conformations for the polymerase translocation and nucleotide pre-insertion steps in the DNA synthesis pathway. We suggest that these new structures, along with previously solved structures, highlight the dynamic nature of the finger subdomain in the enzyme active site.

    View details for DOI 10.7554/eLife.40444

    View details for Web of Science ID 000449728600001

    View details for PubMedID 30338759

    View details for PubMedCentralID PMC6231770