Immune focusing and enhanced neutralization induced by HIV-1 gp140 chemical cross-linking.

Experimental vaccine antigens based upon the HIV-1 envelope glycoproteins (Env) have failed to induce neutralizing antibodies (NAbs) against the majority of circulating viral strains as a result of antibody evasion mechanisms, including amino acid variability and conformational instability. A potential vaccine design strategy is to stabilize Env, thereby focusing antibody responses on constitutively exposed, conserved surfaces, such as the CD4 binding site (CD4bs). Here, we show that a largely trimeric form of soluble Env can be stably cross-linked with glutaraldehyde (GLA) without global modification of antigenicity. Cross-linking largely conserved binding of all potent broadly neutralizing antibodies (bNAbs) tested, including CD4bs-specific VRC01 and HJ16, but reduced binding of several non- or weakly neutralizing antibodies and soluble CD4 (sCD4). Adjuvanted administration of cross-linked or unmodified gp140 to rabbits generated indistinguishable total gp140-specific serum IgG binding titers. However, sera from animals receiving cross-linked gp140 showed significantly increased CD4bs-specific antibody binding compared to animals receiving unmodified gp140. Moreover, peptide mapping of sera from animals receiving cross-linked gp140 revealed increased binding to gp120 C1 and V1V2 regions. Finally, neutralization titers were significantly elevated in sera from animals receiving cross-linked gp140 rather than unmodified gp140. We conclude that cross-linking favors antigen stability, imparts antigenic modifications that selectively refocus antibody specificity and improves induction of NAbs, and might be a useful strategy for future vaccine design.

Characteristics of superficially-porous silica particles for fast HPLC: some performance comparisons with sub-2-microm particles.

Columns of 2.7-microm fused-core (superficially porous) Type B silica particles allow very fast separations of small molecules at pressures available in most high-performance liquid chromatography instruments. These highly-purified particles with 1.7-microm solid silica cores and 0.5-microm-thick shells of 9 nm pores exhibit efficiencies that rival those of totally porous sub-2-microm particles but at one-half to one-third of the column back pressure. This presentation describes other operating features of fused-core particle columns, including sample loading characteristics and packed bed stability. The superior mass transfer (kinetic) properties of the fused-core particles result in much-improved separation efficiency at higher mobile phase velocities, especially for > 600 molecular weight solutes.

The art and science of forming packed analytical high-performance liquid chromatography columns.

Columns of packed particles still are the most popular devices for high-performance liquid chromatography (HPLC) separations because of their great utility, excellent performance and wide variety. However, the forming of packed beds for efficient, stable columns traditionally has been an art where the basics of how to form optimum beds generally was not well understood. The recent development of monolith rods was introduced in part to overcome the difficulty of producing stable beds of packing particles. However, these materials are less versatile than packed particle columns. Technology developments in recent years have produced a better understanding among those skilled in the practice of how to form optimized packed beds, and this has led to widely available, high-quality commercial columns. This presentation discusses the developments that led to the present state of column packing technology. Important steps in the packing of efficient, stable beds are described. The key step of selecting the best solvent for the slurry packing method is emphasized. Factors affecting the mechanical stability of packed columns also are discussed. The early art of packing columns now has evolved into a more scientific approach that allows the packing of good columns with a minimum of effort and time.

Physical mapping of HIV reverse transcriptase to the 5' end of RNA primers.

Enzymatic analysis of RNA cleavage products has suggested that human immunodeficiency virus (HIV) reverse transcriptase (RT) binds to the 5' end of RNAs that are recessed on a longer DNA template (RNA primers) yet binds to the 3' end of DNA primers. One concern is that RT molecules bound at the 3' end of RNA would not be easily detected because RT may not catalyze substantial RNA extension or cleavage when bound to the 3' end. We used physical mapping to show that RT binds preferentially to the 5' end of RNA primers. An HIV-RT that lacked RNase H activity (HIV-RT(E478Q)) was incubated with the RNA-DNA hybrid followed by the addition of Escherichia coli RNase H. RT protected a approximately 23-base region at the 5' end of the RNA and 4 additional bases on the DNA strand. This footprint correlated well with the crystal structure of HIV-RT. No protection of the RNA 3' end was observed, although when dNTPs were included, low levels of extension occurred, indicating that RT can bind this end. Wild-type HIV-RT cleaved the RNA and then extended a small portion of the cleaved fragments, suggesting that very small RNAs may be bound similar to DNA primers.

Primer-dependent synthesis by poliovirus RNA-dependent RNA polymerase (3D(pol)).

Properties of poliovirus RNA-dependent RNA polymerase (3D(pol)) including optimal conditions for primer extension, processivity and the rate of dissociation from primer-template (k(off)) were examined in the presence and absence of viral protein 3AB. Primer-dependent polymerization was examined on templates of 407 or 1499 nt primed such that fully extended products would be 296 or 1388 nt, respectively. Maximal primer extension was achieved with low rNTP concentrations (50-100 microM) using pH 7 and low (<1 mM) MgCl(2) and KCl (<20 mM) concentrations. However, high activity (about half maximal) was also observed with 500 microM rNTPs providing that higher MgCl(2) levels (3-5 mM) were used. The enhancement observed with the former conditions appeared to result from a large increase in the initial level or active enzyme that associated with the primer. 3AB increased the number of extended primers at all conditions with no apparent change in processivity. The k(off) values for the polymerase bound to primer-template were 0.011 +/- 0.005 and 0.037 +/- 0.006 min(-1) (average of four or more experiments +/- SD) in the presence or absence of 3AB, respectively. The decrease in the presence of 3AB suggested an enhancement of polymerase binding or stability. However, binding was tight even without 3AB, consistent with the highly processive (at least several hundred nucleotides) nature of 3D(pol). The results support a mechanism whereby 3AB enhances the ability of 3D(pol) to form a productive complex with the primer-template. Once formed, this complex is very stable resulting in highly processive synthesis.

Determination of the mutation rate of poliovirus RNA-dependent RNA polymerase.

The fidelity of poliovirus RNA-dependent RNA polymerase (3D(pol)) was determined using a system based on the fidelity of synthesis of the alpha-lac gene which codes for a subunit of beta-galactosidase. Synthesis products are screened for mutations by an alpha-complementation assay, in which the protein product from alpha-lac is used in trans to complement beta-galactosidase activity in bacteria that do not express alpha-Lac. Several polymerases have been analyzed by this approach allowing comparisons to be drawn. The assay included RNA synthesis by 3D(pol) on an RNA template that coded for the N-terminal region of alpha-Lac. The product of this reaction was used as a template for a second round of 3D(pol) synthesis and the resulting RNA was reverse transcribed to DNA by MMLV-RT. The DNA was amplified by PCR and inserted into a vector used to transform Escherichia coli. The bacteria were screened for beta-galactosidase activity by blue-white phenotype analysis with white or faint blue colonies scored as errors made during synthesis on alpha-lac. Results showed a mutation rate for 3D(pol) corresponding to approximately 4.5x10(-4) errors per base (one error in approximately 2200 bases). Analysis of mutations showed that base substitutions occurred with greater frequency than deletions and insertions.

In vitro strand transfer from broken RNAs results in mismatch but not frameshift mutations.

An in vitro system to compare the fidelity of strand transfers from truncated vs full-length RNAs was constructed. A donor RNA, on which reverse transcriptase (RT)-directed DNA synthesis was initiated, shared homology with an acceptor RNA, to which DNAs initiated on the donor could transfer. All RNAs were derived from the N-terminal portion of the alpha-lac gene. On full-length donors, transfers occurred when DNAs migrated to the acceptor prior to being completed on the donor. On donors that were truncated, most transfers occurred after DNAs reached the end of the donor. Transfer products were amplified by PCR and used to replace the corresponding region in a vector containing the alpha-lac gene. Transformed Escherichia coli were screened for alpha-complementation by blue-white phenotype analysis, with white colonies scored as those with errors in alpha-lac. These errors were derived from RT synthesis and strand transfer. The mutant colony frequency approximately doubled for transfer products derived from truncated donors (0.026+/-0.005 vs. 0.053+/-0.011 (three experiments +/- SD), for full-length vs. truncated, respectively). The increases resulted from additional non-template-directed bases (mostly thymidines) added to the DNAs before transfer. Sequence analysis of DNAs synthesized on truncated donors showed that about 60% had additions (20/34); however, those without additions transferred at a much higher rate than those with. Transfer of the DNAs with additions always resulted in substitutions; no frameshifts were observed. Results are consistent with RT adding nontemplated nucleotides at template termini. Transfer and subsequent extension of these products is severely inhibited relative to products without additions. The potential relevance of these findings to retrovirus replication is discussed.

Human immunodeficiency virus reverse transcriptase base misincorporations can promote strand transfer.

A system to determine if HIV-reverse transcriptase (RT) base misincorporations can promote strand transfer was constructed. A donor RNA, on which RT-directed DNA synthesis was initiated, shared homology over a 119 base internal region with an acceptor RNA, to which DNAs initiated on the donor could transfer. Products completed on the donor in the presence or absence of acceptor were isolated and PCR was used to amplify these DNAs. PCR products were ligated into a vector which had this same region (near the N-terminus of the alpha-lac gene) removed. Transformed E. coli were screened in an alpha-complementation assay by blue-white phenotype analysis with white colonies scored as those with errors in plasmid-derived alpha-lac. The frequence of white colonies +/- standard deviations was 0.031 +/- 0.006 and 0.0037 +/- 0.009, for plasmids with inserts derived from donor-directed products synthesized with 100 microM dNTPs in the presence and absence of acceptor template, respectively. Statistical analysis indicated a lower white colony frequency in the presence of acceptor (p = 0.0025). The lower frequency with acceptor implies that a portion of the errors made on the donor are transferred to the acceptor suggesting that base misincorporations can induce strand transfer.

Kinetic analysis of the effect of HIV nucleocapsid protein (NCp) on internal strand transfer reactions.

The mechanism of HIV reverse transcriptase (RT) catalyzed strand transfer synthesis (i.e., switching of the primer to a new template) from internal regions on RNA templates in the presence and absence of HIV nucleocapsid protein (NCp) was investigated. Two different systems each consisting of DNA-primed RNA donor (on which primer extension initiated) and acceptor (to which DNAs initiated on the donor could transfer) templates were used to determine kinetic parameters of strand transfer. The donor and acceptor shared an internal region of homology where homologous strand transfer could occur. The rate of strand transfer at various acceptor concentrations was determined by monitoring the production of transfer products over time. These rates were used to construct Lineweaver-Burk plots. In each system, NCp increased the Vmax about 3-fold while the Km for acceptor template was decreased severalfold. NCp's effects on RT extension ranged from no effect to inhibition depending on the primer-template used. The lowered Km shows that NCp increases the affinity of the acceptor template for the transferring DNA. Vmax increases despite the inhibition of RT extension. The increased Vmax implies a stimulatory mechanism that cannot be mimicked by high acceptor concentrations. Therefore, NCp does not act by merely increasing the effective concentration of nucleic acids.

Evaluation of the human arrestin gene in patients with retinitis pigmentosa and stationary night blindness.

PURPOSE: To establish the DNA sequence of the coding regions of the human arrestin locus and to determine whether defects in this sequence are present among patients with retinitis pigmentosa (RP) or types of stationary night blindness in addition to Oguchi disease. METHODS: The human genomic locus encoding arrestin was cloned in bacteriophage and P1 vectors. The sequence of the intron DNA flanking each exon was determined from these clones. Single-strand conformation polymorphism analysis and direct genomic sequencing techniques were used to screen 272 unrelated patients, comprising 177 patients with autosomal dominant RP, 85 with recessive RP, and 10 with stationary night blindness. RESULTS: The arrestin gene is divided into 16 exons ranging in size from 10 bp to 194 bp, with the open reading frame spanning exons 2 through 16. The authors identified several discrepancies between the genomic sequence the authors obtained and the previously published cDNA and genomic sequences. In the set of patients with dominant RP, the authors found one of three heterozygous missense changes (Arg84Cys, Thr125Met, and Val378Ile) in each of four unrelated patients; none of these changes cosegregated with disease in the respective families. In the set of patients with recessive RP, the authors found one of two heterozygous missense changes in each of two unrelated patients with recessive RP (Pro364Leu and Arg384Cys). One of the patients was the offspring of a consanguineous marriage; because the Arg384Cys change in him was heterozygous, it is unlikely to have been the cause of his RP. Cosegregation studies could not be performed on the patient with the Pro364Leu change. The authors confirmed the existence of two previously described polymorphisms (Ile76Val and a multiallelic polymorphism at codon 403), and the authors identified several silent polymorphisms and rare sequence variants. No sequence changes, other than polymorphic changes also found in some patients with RP, were identified in the patients with stationary night blindness. CONCLUSIONS: We found no evidence that mutations in arrestin are a cause of RP or stationary night blindness other than Oguchi disease. According to the genomic sequence obtained, a region in exon 8 that has been postulated to represent the site of interaction between arrestin and rhodopsin is 100% conserved between humans and all other mammals studied to date.

High fidelity of internal strand transfer catalyzed by human immunodeficiency virus reverse transcriptase.

A system to study the fidelity of internal strand transfer events was constructed. A donor RNA, on which reverse transcriptase (RT)-directed DNA synthesis was initiated, shared homology with an acceptor RNA, to which DNAs initiated on the donor could transfer. The homology occurred over a 119-base internal region of the donor which coded for the N-terminal portion of the alpha-lac gene. Polymerase chain reaction (PCR) was used to amplify DNA synthesis products. The PCR products were then digested with PvuII and EcoRI and ligated into a vector which had this same region excised. Transformed Escherichia coli were screened for the ability to produce a functional beta-galactosidase protein by blue-white phenotype analysis with white colonies scored as those with errors in alpha-lac. Products synthesized on the donor were used to assess the error rate of human immunodeficiency virus-RT while products transferring to and subsequently extended on the acceptor (transfer products) were used to monitor transfer fidelity. Human immunodeficiency virus-RT made approximately 1 error per 7500 bases copied in the assay. Nucleocapsid protein (NCp), although stimulating strand transfer 3-fold, had no effect on RT fidelity. Transfer products in the absence of NCp had essentially the same amount of errors as donor-directed products while those produced with NCp showed a slight increase in error frequency. Overall, strand transfer events on this template were highly accurate. Since experiments with other templates have suggested that transfer is error prone, the fidelity of strand transfer may be highly sequence dependent.

Stability of silica-based, endcapped columns with pH 7 and 11 mobile phases for reversed-phase high-performance liquid chromatography.

The goal of this study was to define practical conditions and limitations of using silica-based, endcapped bonded-phase columns in intermediate and higher pH environments for developing rugged HPLC methods. Bonded-phase degradation in this pH range is a result mainly of silica support dissolution; covalently-bound silane ligands are hydrolyzed very slowly if at all from silica supports at intermediate and higher pH. Based on rates of silica support dissolution determined by chemical measurements and comparable chromatographic studies, we now find that endcapping alkyl-bonded stationary phases increases column longevity at pH 7, compared to non-endcapped columns. As previously determined for non-endcapped packings, we also find that the type of silica support determines the stability of bonded-phase packings. Silicas made by the sol-gel process are more resistant to dissolution than supports made by a silicate-gel (xerogel) process. In addition, endcapping methods apparently affect column stability, with double-endcapping methods apparently superior to single-endcapping approaches. Degradation rates for several endcapped commercial bonded-phase C8 columns were found to be quite variable in highly aggressive pH 7 accelerated-lifetime tests. Column stability in the pH 7-11 range is enhanced by using buffers other than phosphate in the mobile phase, and by excluding higher column temperatures. Certain silica-based endcapped bonded-phase columns can be used for developing rugged methods to at least pH 11 when used with organic buffers at < or = 40 degrees C.

The mechanism of retroviral recombination: the role of sequences proximal to the point of strand transfer.

Transfer of nascent DNA from an RNA template (donor) to the homologous region of a second RNA template (acceptor) was studied. The templates were designed to assess the roles of the sequences proximal (3' relative to the transferring DNA) to the point of transfer. The donor template was primed with a specific 18 nucleotide DNA such that extension by reverse transcriptase to the end of the template produced a 79 nucleotide product. Homologous strand transfer and subsequent extension on the acceptors produced longer products allowing distinction between strand transfer and donor-directed synthesis. The donor and one particular acceptor shared a region of homology which included 8 tandem 5'-CAGU-3' repeats followed at the 3' end by a 17 nucleotide region of random homologous sequence. Derivatives of the acceptor either completely lacked the 17 nucleotide region or were progressively truncated resulting in a shorter region. With the acceptor lacking this region, prominent transfer products differing in length by 4 nucleotides were observed. Presumably this occurs because the transferring DNA can base-pair with several copies of the repeat elements of the acceptor. Addition of 5 or more of the 17 random nucleotides to the 3' end of the acceptor resulted in transfer products of essentially one length, and consistent with the transferring DNA correctly base-pairing with the 3' nucleotides. Results suggest that the transferring DNA interacts with the acceptor over several bases to form the most energetically stable hybrid duplex prior to extension on the acceptor. Hybrids formed from shorter interactions between the 3' end of the DNA and acceptor are either realinged prior to extension or precluded due to the mechanism of transfer.

Strand transfer is enhanced by mismatched nucleotides at the 3' primer terminus: a possible link between HIV reverse transcriptase fidelity and recombination.

Strand transfer catalyzed by HIV reverse transcriptase (RT) was examined. The system consisted of a 142 nt RNA (donor) to which a 50 nt DNA primer was hybridized. The primer bound such that its 3' terminal nucleotide hybridized to the 12th nt from the 5' end of the donor. The 3' terminal nucleotide on the primer was either a G, A or T residue. Since the corresponding nucleotide of the donor was a C, the G formed a matched terminus and the A or T a mismatched terminus. The efficiency with which DNA bound to the donor transferred to a second RNA, termed acceptor, was monitored. The acceptor was homologous to the donor for all but the last 9 nt at the 5' end of the donor. Therefore, homologous strand transfer could occur at any point prior to the DNA being extended into the nonhomologous region on the donor. Strand transfer occurred approximately twice as efficiently with the mismatched versus matched substrates. The mismatched nucleotide was fixed into transfer products indicating that excision of the mismatch was not required for RT extension or transfer. Results suggest that base misincorporations by RT may promote recombination by enhancing strand transfer.

Interaction of human immunodeficiency virus nucleocapsid protein with a structure mimicking a replication intermediate. Effects on stability, reverse transcriptase binding, and strand transfer.

The interaction of human immunodeficiency virus (HIV) nucleocapsid protein (NCp) with a substrate closely mimicking a retrovirus replication intermediate was studied. The heteroduplex substrate consisted of a DNA and RNA of 80 and 63 nucleotides, respectively. The nucleotides at the 3' end of the DNA were complementary to those at the 3' end of the RNA such that a hybrid region of 30 base pairs could form. HIV-reverse transcriptase (RT) extended the DNA and cleaved the RNA strand of the substrate. The rates of extension and cleavage were significantly decreased when the substrate was prebound with NCp before HIV-RT addition. In assays assessing the integrity of the substrate by measuring release of the DNA strand from the heteroduplex, prebinding with NCp protected the substrate when HIV-RT was added, a result consistent with resistance to RT-mediated cleavage. In contrast, NCp significantly decreased the thermal stability of the substrate as judged by incubation of the substrate at various temperatures. In strand transfer assays, a 189-nucleotide RNA (acceptor) with an internal region complementary to all 80 nucleotides of the substrate DNA was incubated with the substrate in the presence or absence of NCp. Nucleocapsid protein stimulated strand transfer in which the substrate RNA was displaced upon binding of the DNA to the acceptor. Results are discussed with respect to the role of NCp in retroviral recombination.

The orientation of binding of human immunodeficiency virus reverse transcriptase on nucleic acid hybrids.

The binding of HIV reverse transcriptase (RT) to heteroduplexes was examined using a substrate consisting of a 42 nt chimeric nucleic acid composed. (5'-->3') of 23 nt of RNA and 19 of DNA. This chimera was hybridized to an internal region of a relatively long complementary DNA or RNA. When the chimera was bound to DNA and conditions limiting cleavage to a single binding event between the enzyme and substrate were employed initial RNase H-directed cleavages occurred 19-21 nt from the chimera 5'-terminus. A 42 nt strand identical in sequence to the chimera and composed of only RNA was cleaved at the same locations. Reducing the length of the DNA portion of the chimera from 19 to 7 nt did not alter the cleavage positions, suggesting that cleavage was not coordinated by the DNA 3'-terminus. Under the same conditions cleavage was not detected when the chimera was bound to RNA. In contrast, addition of dNTPs to the DNA 3'-terminus of the chimera occurred only when the chimera was bound to RNA. The results support preferable binding of RT to RNA-DNA versus DNA-DNA hybrid regions and a model in which the orientation of binding to heteroduplexes is 5'-->3' (relative to the RNA strand), polymerase to RNase H active site, with sites associated with the DNA and RNA strand respectively.

Human immunodeficiency virus nucleocapsid protein stimulates strand transfer from internal regions of heteropolymeric RNA templates.

We have examined the influence of HIV nucleocapsid protein (NCp) on strand transfer from internal regions of a heteropolymeric RNA template. The system consisted of a DNA-primed 225 nucleotide RNA donor template, on which reverse transcriptase initiated primer extension, and a 189 nucleotide RNA acceptor template, to which extended primers could transfer. The last 133 nucleotides on the 3' end of the acceptor were homologous to an internal region on the donor, limiting homologous strand transfer to this region. Primers extended to the end of the donor were 212 nucleotides while those transferred to, and extended on the acceptor were 259 nucleotides in length. The rate of strand transfer and the level of transfer products increased several-fold when nucleocapsid was included in the reactions. The increase was due, at least in part, to the transfer to, and extension on the acceptor, of incompletely elongated primer-extension products that were "chased" into transfer products in the presence of nucleocapsid. Nucleocapsid did not directly influence reverse transcriptase elongation as the enzyme processivity (number of nucleotides incorporated before the enzyme dissociates from the primer-template) was approximately the same in the presence and absence of nucleocapsid.

Kinetic analysis of the catalysis of strand transfer from internal regions of heteropolymeric RNA templates by human immunodeficiency virus reverse transcriptase.

The kinetic mechanism of HIV reverse transcriptase catalyzed strand transfer synthesis (i.e. switching of the primer to a new template) from internal regions of natural sequence RNA was investigated. The system consisted of a 142 nucleotide RNA template (donor), primed with a specific 20 nucleotide DNA oligonucleotide that was used to initiate synthesis. An RNA with homology to an internal region of the donor was used as acceptor template. Using 32P-labeled DNA oligonucleotide, the primer-extension products made from full-length synthesis on the donor (108 bases in length) or homologous transfer to and extension on the acceptor (155 bases) were monitored. Results indicated that the maximum efficiency of transfer (the ratio of transfer products to donor-directed+transfer products x 100) in this particular system was about 25% while the theoretical Vmax for the rate of appearance of transfer products at infinite acceptor concentration was about 20-fold lower than the measured rate for full-length donor-directed products. The Km for acceptor template in the transfer reaction was about 8 nM. Experiments using the above donor template hybridized to a specific DNA that has been shown to transfer to the acceptor indicated that RNase H-mediated rapid release of this DNA from the donor while subsequent association with the acceptor was relatively slow.

Characterization of an RNase H deficient mutant of human immunodeficiency virus-1 reverse transcriptase having an aspartate to asparagine change at position 498.

It has been proposed that Asp-443, Glu-478, and Asp-498 are important in RNase H mediated catalysis by human immunodeficiency virus-1 reverse transcriptase (Davies J.F., Hostomska, Z. Hostomsky, Z., Jordan, S.R. and Matthews, D.A. (1991) Science 251, 88-95; Mizrahi, V., Usdin, M.T., Harington, A. and Dudding, L.R. (1990) Nucleic Acids Res. 18, 5359-5363). Single point mutations at either position 443 (Mizrahi, V., Usdin, M.T., Harington, A. and Dudding, L.R. (1990) Nucleic Acids Res. 18, 5359-5363) or 478 (Schatz, O., Cromme, F.V., Grüninger-Leitch, F. and Le Grice, S.F.J. (1989) FEBS Lett. 257, 311-314) severely inhibit RNase H activity but have only small effects on polymerase activity. We show here that a single mutation at position 498 of Asp to Asn (mutant D498N) results in a stable enzyme with a 20-fold reduction in the ratio of RNase H to polymerase activity. The mutant and wild type enzymes were equally processive, paused in the same locations, and extended primers at the same rate during DNA synthesis on a heteropolymeric RNA template. The rate of elongation on the homopolymeric template poly(rA) was also the same. The results indicate that the mutation does not affect normally measured catalytic parameters of the polymerase function of the enzyme. D498N catalyzed strand transfer synthesis on homopolymeric, but not heteropolymeric templates, indicating that RNase H activity is not required for the former activity, but is for the latter.

Quantitative analysis of RNA cleavage during RNA-directed DNA synthesis by human immunodeficiency and avian myeloblastosis virus reverse transcriptases.

We have determined the extent of RNA cleavage carried out during DNA synthesis by either human immunodeficiency virus (HIV) or avian myeloblastosis virus (AMV) reverse transcriptases (RTs). Conditions were chosen that allowed the analysis of the cleavage and synthesis performed by the RT during one binding event on a given template-primer. The maximum quantity of ribonuclease H (RNase H) sensitive template RNA left after synthesis by the RTs was determined by treatment with Escherichia coli RNase H. RNA cleavage products that were expected to be too short to remain hybridized, less than 13 nucleotides in length, were quantitated. Results showed that HIV- and AMV-RT degraded about 80% and less than 20%, respectively, of the potentially degradable RNA to these short products. Survival of longer, hybridized RNA was not a result of synthesis by a population of RTs that had selectively lost RNase H activity. Using an assay that evaluated the proportion of primers extended versus RNA templates cleaved during primer-extension by the RTs, we determined that essentially each molecule of HIV- and AMV-RT with polymerase also has RNase H activity. The results indicate that although both HIV- and AMV-RTs cleave the RNA template during synthesis, the number of cleavages per nucleotide addition with HIV-RT is much greater. They also suggest that some hybridized RNA segments remain right after the passage of the RT making the first DNA strand. In vivo, these segments would have to be cleaved or displaced in later reactions before second strand DNA synthesis could be completed.