Position-specific Suppression and Enhancement of HIV-1 Integrase Reactions by Minor Groove Benzo[a]pyrene Diol Epoxide Deoxyguanine Adducts

Johnson, Allison A.; Sayer, Jane M.; Yagi, Haruhiko; Kalena, Govind P.; Amin, Ronak; Jerina, Donald M.; Pommier, ﻿Yves

doi:10.1074/jbc.m311263200

Cited by 8 publications

(12 citation statements)

References 31 publications

(41 reference statements)

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“…In the same assay, ST is achieved by insertion of the processed DNA into another identical duplex, resulting in a ladder of products migrating slower than the substrate DNA in denaturing sequencing gels. Here we present data from experiments using manganese so that our results are comparable with prior studies (7) and to create the most permissive conditions for integrase reactions. The data in Figs.…”

Section: Hiv-1supporting

confidence: 77%

“…7A). This position was not addressed in our prior study (7). Therefore, we wished to extend our minor groove footprinting through the end of the DNA.…”

Section: Effect Of Minor Groove Bap De Adducts Linked To the 3ј-procementioning

confidence: 99%

“…The hydrocarbon portion of the guanine N-2 adducts lies in the minor groove of the DNA and extends toward the 5Ј or 3Ј terminus of the adducted strand for the trans-(S) and trans-(R) adducts, respectively, where S and R refer to the absolute configuration at the point of attachment of the 2-amino group of the hydrocarbon (see Fig. 3, D and E) (7,16) We reported previously that a BaP DE dG adduct in the minor groove of the 3Ј-P site blocked 3Ј-P (7). Here we examined the effect of dG minor groove adducts attached to the 3Ј-processed dinucleotide, and we compared these results to those obtained with BaP DE adducts attached to the exocyclic N-6 amino group of adenines (Fig.…”

Section: Hiv-1mentioning

confidence: 99%

“…6B). We further examined the pattern of ST by labeling each strand at the 3Ј-end with 32 P to determine ST products specific for each strand of the acceptor duplex (7). Both the R and S adducts cause the formation of a strong 25-mer ST product corresponding to ST into the upper strand of the acceptor duplex DNA (Fig.…”

Section: Effect Of Sugar Modifications On Integrase Reactions-thementioning

confidence: 99%

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Effect of DNA Modifications on DNA Processing by HIV-1 Integrase and Inhibitor Binding

Johnson

Sayer

Yagi

et al. 2006

Journal of Biological Chemistry

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Integration of the viral cDNA into host chromosomes is required for viral replication. Human immunodeficiency virus integrase catalyzes two sequential reactions, 3-processing (3-P) and strand transfer (ST). The first integrase inhibitors are undergoing clinical trial, but interactions of inhibitors with integrase and DNA are not well understood in the absence of a co-crystal structure. To increase our understanding of integrase interactions with DNA, we examined integrase catalysis with oligonucleotides containing DNA backbone, base, and groove modifications placed at unique positions surrounding the 3-processing site. 3-Processing was blocked with substrates containing constrained sugars and ␣-anomeric residues, suggesting that integrase requires flexibility of the phosphodiester backbone at the 3-P site. Of several benzo[a]pyrene 7,8-diol 9,10-epoxide (BaP DE) adducts tested, only the adduct in the minor groove at the 3-P site inhibited 3-P, suggesting the importance of the minor groove contacts for 3-P. ST occurred in the presence of bulky BaP DE DNA adducts attached to the end of the viral DNA suggesting opening of the active site for ST. Positionspecific effects of these BaP DE DNA adducts were found for inhibition of integrase by diketo acids. Together, these results demonstrate the importance of DNA structure and specific contacts with the viral DNA processing site for inhibition by integrase inhibitors. HIV-12 integrase (integrase) catalyzes insertion of cDNA copies of the viral genome into human chromosomes. Integrase binds to the ends ("att" sites) of each viral long terminal repeat (LTR) through sequence-specific recognition of a conserved 5Ј-CA within the sequence 5Ј-GCAGT. In the first of two reactions, integrase cleaves the 3Ј-ends of the viral DNA, releasing the terminal 5Ј-GT dinucleotide (3Ј-processing, 3Ј-P). In the second reaction, the free 3Ј-hydroxyl of the conserved adenine provides the nucleophile for insertion of the viral cDNA into a chromosome (strand transfer, ST). Gap repair and ligation between the viral and cellular DNA are performed by cellular factors. (For recent reviews and insights on integration, see Refs. 1-5.)Determination of the molecular interactions between integrase and its DNA substrates (viral and chromosomal DNA) has proven challenging, and a co-crystal of these components remains elusive. Biochemical studies have revealed contact points between the viral DNA and integrase. Integrase has an absolute requirement for the conserved 5Ј-CA adjoining the 3Ј-P site (underlined in Fig. 1A). The efficiency of 3Ј-P is also dramatically decreased by changes to the G immediately 5Ј to the conserved CA dinucleotide (6 -8). The conserved adenine, substituted by 5-iododeoxyuracil as a photocross-linker, forms a photocross-link to Lys-159 of integrase (9). Residue Lys-159 also contacts the phosphate 5Ј to the conserved deoxyadenosine (10). Mutagenesis showed that Tyr-143 and probably Gln-148 interact with the 5Ј-overhang resulting from 3Ј-P (9, 11). Moreover, disulfide cross-linking ...

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Section: Hiv-1supporting

confidence: 77%

“…7A). This position was not addressed in our prior study (7). Therefore, we wished to extend our minor groove footprinting through the end of the DNA.…”

Section: Effect Of Minor Groove Bap De Adducts Linked To the 3ј-procementioning

confidence: 99%

Section: Hiv-1mentioning

confidence: 99%

Section: Effect Of Sugar Modifications On Integrase Reactions-thementioning

confidence: 99%

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Effect of DNA Modifications on DNA Processing by HIV-1 Integrase and Inhibitor Binding

Johnson

Sayer

Yagi

et al. 2006

Journal of Biological Chemistry

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“…ST-selective inhibitors, such as diketo acid and naphthyridine carboxamide derivatives (Hazuda et al, 2000(Hazuda et al, , 2004a, have been proposed to bind at the interface of the integrase-DNA complex . As part of our ongoing effort to characterize the molecular interactions between integrase, inhibitors, and the U5 LTR viral cDNA end (Johnson et al, 2004, here we describe the use of disulfide and Schiff base cross-linking (Mazumder et al, 1996) to examine interference upon cross-link formation of various integrase inhibitors.…”

mentioning

confidence: 99%

Probing HIV-1 Integrase Inhibitor Binding Sites with Position-Specific Integrase-DNA Cross-Linking Assays

Johnson¹,

Marchand²,

Patil³

et al. 2006

Mol Pharmacol

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HIV-1 integrase binds site-specifically to the ends of the viral cDNA. We used two HIV-1 integrase-DNA cross-linking assays to probe the binding sites of integrase inhibitors from different chemical families and with different strand transfer selectivities. The disulfide assay probes cross-linking between the integrase residue 148 and the 5Ј-terminal cytosine of the viral cDNA, and the Schiff base assay probes cross-linking between an integrase lysine residue and an abasic site placed at selected positions in the viral cDNA. Cross-linking interference by eight integrase inhibitors shows that the most potent cross-linking inhibitors are 3Ј-processing inhibitors, indicating that crosslinking assays probe the donor viral cDNA (donor binding site). In contrast, strand transfer-selective inhibitors provide weak cross-linking interference, consistent with their binding to a specific acceptor (cellular DNA) site. Docking and crystal structure studies illustrate specific integrase-inhibitor contacts that prevent cross-linking formation. Four inhibitors that prevented Schiff base cross-linking to the conserved 3Ј-terminal adenine position were examined for inhibition at various positions within the terminal 21 bases of the viral cDNA. Two of them selectively inhibited upper strand cross-linking, whereas the other two had a more global effect on integrase-DNA binding. These findings have implications for elucidating inhibitor binding sites and mechanisms of action. The cross-linking assays also provide clues to the molecular interactions between integrase and the viral cDNA.

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Insights into HIV‐1 Integrase–DNA Interactions

2011

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Position-specific Suppression and Enhancement of HIV-1 Integrase Reactions by Minor Groove Benzo[a]pyrene Diol Epoxide Deoxyguanine Adducts

Cited by 8 publications

References 31 publications

Effect of DNA Modifications on DNA Processing by HIV-1 Integrase and Inhibitor Binding

Effect of DNA Modifications on DNA Processing by HIV-1 Integrase and Inhibitor Binding

Probing HIV-1 Integrase Inhibitor Binding Sites with Position-Specific Integrase-DNA Cross-Linking Assays

Insights into HIV‐1 Integrase–DNA Interactions

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