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Panigrahi A, Vemuri H, Aggarwal M, Pitta K, Krishnan M. Sequence specificity, energetics and mechanism of mismatch recognition by DNA damage sensing protein Rad4/XPC. Nucleic Acids Res 2020; 48:2246-2257. [PMID: 32047903 PMCID: PMC7049735 DOI: 10.1093/nar/gkaa078] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 01/27/2020] [Accepted: 02/10/2020] [Indexed: 12/25/2022] Open
Abstract
The ultraviolet (UV) radiation-induced DNA lesions play a causal role in many prevalent genetic skin-related diseases and cancers. The damage sensing protein Rad4/XPC specifically recognizes and repairs these lesions with high fidelity and safeguards genome integrity. Despite considerable progress, the mechanistic details of the mode of action of Rad4/XPC in damage recognition remain obscure. The present study investigates the mechanism, energetics, dynamics, and the molecular basis for the sequence specificity of mismatch recognition by Rad4/XPC. We dissect the following three key molecular events that occur as Rad4/XPC tries to recognize and bind to DNA lesions/mismatches: (a) the association of Rad4/XPC with the damaged/mismatched DNA, (b) the insertion of a lesion-sensing β-hairpin of Rad4/XPC into the damage/mismatch site and (c) the flipping of a pair of nucleotide bases at the damage/mismatch site. Using suitable reaction coordinates, the free energy surfaces for these events are determined using molecular dynamics (MD) and umbrella sampling simulations on three mismatched (CCC/CCC, TTT/TTT and TAT/TAT mismatches) Rad4-DNA complexes. The study identifies the key determinants of the sequence-dependent specificity of Rad4 for the mismatches and explores the ramifications of specificity in the aforementioned events. The results unravel the molecular basis for the high specificity of Rad4 towards CCC/CCC mismatch and lower specificity for the TAT/TAT mismatch. A strong correlation between the depth of β-hairpin insertion into the DNA duplex and the degree of coupling between the hairpin insertion and the flipping of bases is also observed. The interplay of the conformational flexibility of mismatched bases, the depth of β-hairpin insertion, Rad4-DNA association energetics and the Rad4 specificity explored here complement recent experimental FRET studies on Rad4-DNA complexes.
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Affiliation(s)
- Abhinandan Panigrahi
- Center for Computational Natural Sciences and Bioinformatics (CCNSB), International Institute of Information Technology, Gachibowli, Hyderabad, Telangana 500032, India
| | - Hemanth Vemuri
- Center for Computational Natural Sciences and Bioinformatics (CCNSB), International Institute of Information Technology, Gachibowli, Hyderabad, Telangana 500032, India
| | - Madhur Aggarwal
- Center for Computational Natural Sciences and Bioinformatics (CCNSB), International Institute of Information Technology, Gachibowli, Hyderabad, Telangana 500032, India
| | - Kartheek Pitta
- Center for Computational Natural Sciences and Bioinformatics (CCNSB), International Institute of Information Technology, Gachibowli, Hyderabad, Telangana 500032, India
| | - Marimuthu Krishnan
- Center for Computational Natural Sciences and Bioinformatics (CCNSB), International Institute of Information Technology, Gachibowli, Hyderabad, Telangana 500032, India
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Toxicology of DNA Adducts Formed Upon Human Exposure to Carcinogens. ADVANCES IN MOLECULAR TOXICOLOGY 2016. [DOI: 10.1016/b978-0-12-804700-2.00007-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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3
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Sharma P, Manderville RA, Wetmore SD. Structural and energetic characterization of the major DNA adduct formed from the food mutagen ochratoxin A in the NarI hotspot sequence: influence of adduct ionization on the conformational preferences and implications for the NER propensity. Nucleic Acids Res 2014; 42:11831-45. [PMID: 25217592 PMCID: PMC4191402 DOI: 10.1093/nar/gku821] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The nephrotoxic food mutagen ochratoxin A (OTA) produces DNA adducts in rat kidneys, the major lesion being the C8-linked-2′-deoxyguanosine adduct (OTB-dG). Although research on other adducts stresses the importance of understanding the structure of the associated adducted DNA, site-specific incorporation of OTB-dG into DNA has yet to be attempted. The present work uses a robust computational approach to determine the conformational preferences of OTB-dG in three ionization states at three guanine positions in the NarI recognition sequence opposite cytosine. Representative adducted DNA helices were derived from over 2160 ns of simulation and ranked via free energies. For the first time, a close energetic separation between three distinct conformations is highlighted, which indicates OTA-adducted DNA likely adopts a mixture of conformations regardless of the sequence context. Nevertheless, the preferred conformation depends on the flanking bases and ionization state due to deviations in discrete local interactions at the lesion site. The structural characteristics of the lesion thus discerned have profound implications regarding its repair propensity and mutagenic outcomes, and support recent experiments suggesting the induction of double-strand breaks and deletion mutations upon OTA exposure. This combined structural and energetic characterization of the OTB-dG lesion in DNA will encourage future biochemical experiments on this potentially genotoxic lesion.
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Affiliation(s)
- Purshotam Sharma
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, T1K 3M4, Canada
| | - Richard A Manderville
- Department of Chemistry and Toxicology, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Stacey D Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, T1K 3M4, Canada
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Krasikova YS, Rechkunova NI, Maltseva EA, Anarbaev RO, Pestryakov PE, Sugasawa K, Min JH, Lavrik OI. Human and yeast DNA damage recognition complexes bind with high affinity DNA structures mimicking in size transcription bubble. J Mol Recognit 2014; 26:653-61. [PMID: 24277610 DOI: 10.1002/jmr.2308] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Revised: 07/26/2013] [Accepted: 08/06/2013] [Indexed: 02/05/2023]
Abstract
The human XPC-RAD23B complex and its yeast ortholog, Rad4-Rad23, are the primary initiators of global genome nucleotide excision repair. In this study, two types of DNA binding assays were used for the detailed analysis of interaction of these proteins with damaged DNA. An electrophoretic mobility shift assay revealed that human and yeast orthologs behave similarly in DNA binding. Quantitative analyses of XPC/Rad4 binding to the model DNA structures were performed using fluorescent depolarization measurements. The XPC-RAD23B and the Rad4-Rad23 proteins bind to the damaged 15 nt bubble-DNA structure mimicking in size the "transcription bubble" DNA intermediate with the highest affinity (KD values ~10(-10) M or less) that is reduced in the following order: damaged bubble > undamaged bubble > damaged duplex > undamaged duplex. The affinity of XPC/Rad4 for various DNAs was shown to correlate with DNA bending angle. The results obtained show clearly that more deviation from regular DNA structure leads to higher XPC/Rad4 affinity.
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Affiliation(s)
- Yuliya S Krasikova
- Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
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5
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Deligkaris C, Rodriguez JH. Non-covalent interactions of the carcinogen (+)-anti-BPDE with exon 1 of the human K-ras proto-oncogene. Phys Chem Chem Phys 2014; 16:6199-210. [PMID: 24562312 DOI: 10.1039/c3cp55049d] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Investigating the complementary, but different, effects of physical (non-covalent) and chemical (covalent) mutagen-DNA and carcinogen-DNA interactions is important for understanding possible mechanisms of development and prevention of mutagenesis and carcinogenesis. A highly mutagenic and carcinogenic metabolite of the polycyclic aromatic hydrocarbon benzo[α]pyrene, namely (+)-anti-BPDE, is known to undergo both physical and chemical complexation with DNA. Previous studies of BPDE-DNA complex formation have focused on processes that require substantial structural reorganization, such as intercalation, and consequently relatively long time scales. However, some initial processes which occur within shorter time scales, such as external non-covalent binding, and which do not require major DNA structural reorganization have not been thoroughly investigated. A detailed computational study of such initial BPDE-DNA interactions is needed to elucidate the temporal and structural origins of the major covalent adduct, a promutagenic, which is known to exist in an external (+)-trans-anti-BPDE-N(2)-dGuanosine configuration. Accordingly, the initial stages of external non-covalent BPDE-DNA binding are studied in this work as well as their relationship to subsequent formation of the major, also external, covalent adduct. To study mechanisms that occur prior to extensive DNA structural reorganization, we present a first and detailed codon by codon computational study of the non-covalent interactions of (+)-anti-BPDE with DNA. In particular, due to its relevance to carcinogenesis, the interaction of (+)-anti-BPDE with exon 1 of the human K-ras gene has been studied. External solvent-exposed non-covalent binding sites have been found which may be precursors of the major external trans adduct and, importantly, are located in codons 12 and 13 of the K-ras gene which are known to be key mutation hotspots. In addition, our study explains and correctly predicts preferential (+)-anti-BPDE binding at minor groove guanosines. A subtle combination of van der Waals and hydrogen bonding interactions has been found to be a primary factor in preferentially positioning (+)-anti-BPDE toward the 5' position of a guanosine's strand, consistent with proton NMR observations for the major trans adduct, and at 5'-TGG-3' sequences which are known to yield high binding probability.
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Affiliation(s)
- Christos Deligkaris
- Department of Physics, Theoretical and Computational Biomolecular Physics Group, Purdue University, West Lafayette, IN 47907, USA.
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6
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Rodríguez FA, Liu Z, Lin CH, Ding S, Cai Y, Kolbanovskiy A, Kolbanovskiy M, Amin S, Broyde S, Geacintov NE. Nuclear magnetic resonance studies of an N2-guanine adduct derived from the tumorigen dibenzo[a,l]pyrene in DNA: impact of adduct stereochemistry, size, and local DNA sequence on solution conformations. Biochemistry 2014; 53:1827-41. [PMID: 24617538 PMCID: PMC3985812 DOI: 10.1021/bi4017044] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
![]()
The
dimensions and arrangements of aromatic rings (topology) in
adducts derived from the reactions of polycyclic aromatic hydrocarbon
(PAH) diol epoxide metabolites with DNA influence the distortions
and stabilities of double-stranded DNA, and hence their recognition
and processing by the human nucleotide excision repair (NER) system.
Dibenzo[a,l]pyrene (DB[a,l]P) is a highly tumorigenic six-ring PAH, which
contains a nonplanar and aromatic fjord region that is absent in the
structurally related bay region five-ring PAH benzo[a]pyrene (B[a]P). The PAH diol epoxide–DNA
adducts formed include the stereoisomeric 14S and
14Rtrans-anti-DB[a,l]P-N2-dG
and the stereochemically analogous 10S- and 10R-B[a]P-N2-dG
(B[a]P-dG) guanine adducts. However, nuclear magnetic
resonance (NMR) solution studies of the 14S-DB[a,l]P-N2-dG
adduct in DNA have not yet been presented. Here we have investigated
the 14S-DB[a,l]P-N2-dG adduct in two different sequence contexts
using NMR methods with distance-restrained molecular dynamics simulations.
In duplexes with dC opposite the adduct deleted, a well-resolved base-displaced
intercalative adduct conformation can be observed. In full duplexes,
in contrast to the intercalated 14R stereoisomeric
adduct, the bulky DB[a,l]P residue
in the 14S adduct is positioned in a greatly widened
and distorted minor groove, with significant disruptions and distortions
of base pairing at the lesion site and two 5′-side adjacent
base pairs. These unique structural features are significantly different
from those of the stereochemically analogous but smaller B[a]P-dG adduct. The greater size and different topology of
the DB[a,l]P aromatic ring system
lead to greater structurally destabilizing DNA distortions that are
partially compensated by stabilizing DB[a,l]P-DNA van der Waals interactions, whose combined effects
impact the NER response to the adduct. These structural results broaden
our understanding of the structure–function relationship in
NER.
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Affiliation(s)
- Fabián A Rodríguez
- Department of Chemistry, New York University , New York, New York 10003, United States
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7
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Minero AS, Lukashevich OV, Cherepanova NA, Kolbanovskiy A, Geacintov NE, Gromova ES. Probing murine methyltransfease Dnmt3a interactions with benzo[a]pyrene-modified DNA by fluorescence methods. FEBS J 2012; 279:3965-80. [PMID: 22913541 DOI: 10.1111/j.1742-4658.2012.08756.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2012] [Revised: 07/30/2012] [Accepted: 08/06/2012] [Indexed: 11/29/2022]
Abstract
The impact of bulky carcinogen-DNA adducts positioned at or near recognition sites (CpG) of eukaryotic DNA methyltransferases on their catalytic activities is poorly understood. In the present study, we employed site-specifically modified 30-mer oligodeoxyribonucleotides containing stereoisomeric benzo[a]pyrene diol epoxide (B[a]PDE)-derived guanine (B[a]PDE-N(2)-dG) or adenine (B[a]PDE-N(6)-dA) adducts of different conformations as substrates of the catalytic domain of murine Dnmt3a (Dnmt3a-CD). The fluorescence of these lesions was used to examine interactions between Dnmt3a-CD and DNA. In B[a]PDE-DNA•Dnmt3a-CD complexes, the intensity of fluorescence of the covalently bound B[a]PDE residues is enhanced relative to the protein-free value when the B[a]PDE is positioned in the minor groove [(+)- and (-)-trans-B[a]PDE-N(2)-dG adducts in the CpG site] and when it is intercalated on the 5'-side of the CpG site [(+)-trans-B[a]PDE-N(6)-dA adduct]. The fluorescence of B[a]PDE-modified DNA•Dnmt3a-CD complexes exhibits only small changes when the B[a]PDE is intercalated with base displacement in (+)- and (-)-cis-B[a]PDE-N(2)-dG adducts and without base displacement in the (-)-trans-B[a]PDE-N(6)-dA adduct. The initial rates of methylation were significantly reduced by the minor groove trans-B[a]PDE-N(2)-dG adducts, regardless of their position in the substrate and by the intercalated cis-B[a]PDE-N(2)-dG adducts within the CpG site. The observed changes in fluorescence and methylation rates are consistent with the flipping of the target cytosine and a catalytic loop motion within the DNA•Dnmt3a-CD complexes. In the presence of the regulatory factor Dnmt3L, an enhancement of both methylation rates and fluorescence was observed, which is consistent with a Dnmt3L-mediated displacement of the catalytic loop towards the CpG site.
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Affiliation(s)
- Antonio S Minero
- Department of Chemistry, Moscow State University, Moscow, Russia
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8
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Zhou P, Tian F, Ren Y, Shang Z. Systematic classification and analysis of themes in protein-DNA recognition. J Chem Inf Model 2010; 50:1476-88. [PMID: 20726602 DOI: 10.1021/ci100145d] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Protein-DNA recognition plays a central role in the regulation of gene expression. With the rapidly increasing number of protein-DNA complex structures available at atomic resolution in recent years, a systematic, complete, and intuitive framework to clarify the intrinsic relationship between the global binding modes of these complexes is needed. In this work, we modified, extended, and applied previously defined RNA-recognition themes to describe protein-DNA recognition and used a protocol that incorporates automatic methods into manual inspection to plant a comprehensive classification tree for currently available high-quality protein-DNA structures. Further, a nonredundant (representative) data set consisting of 200 thematically diverse complexes was extracted from the leaves of the classification tree by using a locally sensitive interface comparison algorithm. On the basis of the representative data set, various physical and chemical properties associated with protein-DNA interactions were analyzed using empirical or semiempirical methods. We also examined the individual energetic components involved in protein-DNA interactions and highlighted the importance of conformational entropy, which has been almost completely ignored in previous studies of protein-DNA binding energy.
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Affiliation(s)
- Peng Zhou
- Department of Chemistry, Zhejiang University, Hangzhou 310027, China, College of Bioengineering, Chongqing University, Chongqing 400044, China
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9
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Tian F, Yang L, Lv F, Luo X, Pan Y. Why OppA protein can bind sequence-independent peptides? A combination of QM/MM, PB/SA, and structure-based QSAR analyses. Amino Acids 2010; 40:493-503. [DOI: 10.1007/s00726-010-0661-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2010] [Accepted: 06/12/2010] [Indexed: 01/21/2023]
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10
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Millán-Pacheco C, Capistrán VM, Pastor N. On the consequences of placing amino groups at the TBP-DNA interface. Does TATA really matter? J Mol Recognit 2009; 22:453-64. [DOI: 10.1002/jmr.963] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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11
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Cai Y, Patel DJ, Geacintov NE, Broyde S. Differential nucleotide excision repair susceptibility of bulky DNA adducts in different sequence contexts: hierarchies of recognition signals. J Mol Biol 2008; 385:30-44. [PMID: 18948114 DOI: 10.1016/j.jmb.2008.09.087] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2008] [Revised: 09/24/2008] [Accepted: 09/26/2008] [Indexed: 11/26/2022]
Abstract
The structural origin underlying differential nucleotide excision repair (NER) susceptibilities of bulky DNA lesions remains a challenging problem. We investigated the 10S (+)-trans-anti-[BP]-N(2)-2'-deoxyguanosine (G*) adduct in double-stranded DNA. This adduct arises from the reaction, in vitro and in vivo, of a major genotoxic metabolite of benzo[a]pyrene (BP), (+)-(7R,8S,9S,10R)-7,8-dihydroxy-9,10-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene, with the exocyclic amino group of guanine. Removal of this lesion by the NER apparatus in cell-free extracts has been found to depend on the base sequence context in which the lesion is embedded, providing an excellent opportunity for elucidating the properties of the damaged DNA duplexes that favor NER. While the BP ring system is in the B-DNA minor groove, 5' directed along the modified strand, there are orientational distinctions that are sequence dependent and are governed by flanking amino groups [Nucleic Acids Res.35 (2007), 1555-1568]. To elucidate sequence-governed NER susceptibility, we conducted molecular dynamics simulations for the 5'-...CG*GC..., 5'-...CGG*C..., and 5'-...TCG*CT... adduct-containing duplexes. We also investigated the 5'-...CG*IC... and 5'-...CIG*C... sequences, which contain "I" (2'-deoxyinosine), with hydrogen replacing the amino group in 2'-deoxyguanosine, to further characterize the structural and dynamic roles of the flanking amino groups in the damaged duplexes. Our results pinpoint explicit roles for the amino groups in tandem GG sequences on the efficiency of NER and suggest a hierarchy of destabilizing structural features that differentially facilitate NER of the BP lesion in the sequence contexts investigated. Furthermore, combinations of several locally destabilizing features in the hierarchy, consistent with a multipartite model, may provide a relatively strong recognition signal.
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Affiliation(s)
- Yuqin Cai
- Department of Chemistry, New York University, New York, NY 10003, USA
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12
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Mattsson A, Jernström B, Cotgreave IA, Bajak E. H2AX phosphorylation in A549 cells induced by the bulky and stable DNA adducts of benzo[a]pyrene and dibenzo[a,l]pyrene diol epoxides. Chem Biol Interact 2008; 177:40-7. [PMID: 18848825 DOI: 10.1016/j.cbi.2008.09.015] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2008] [Revised: 09/04/2008] [Accepted: 09/04/2008] [Indexed: 01/15/2023]
Abstract
Early events in the cellular response to DNA damage, such as double strand breaks, rely on lesion recognition and activation of proteins involved in maintenance of genomic stability. One important component of this process is the phosphorylation of the histone variant H2AX. To investigate factors explaining the variation in carcinogenic potency between different categories of polycyclic aromatic hydrocarbons (PAHs), we have studied the phosphorylation of H2AX (H2AXgamma). A549 cells were exposed to benzo[a]pyrene diol epoxide [(+)-anti-BPDE] (a bay-region PAH) and dibenzo[a,l]pyrene diol epoxide [(-)-anti-DBPDE] (a fjord-region PAH) and H2AXgamma was studied using immunocytochemistry and Western blot. Hydrogen peroxide (H(2)O(2)) was used to induce oxidative DNA damage and strand breaks. As showed with single cell gel electrophoresis, neither of the diol epoxides resulted in DNA strand breaks relative to H(2)O(2). Visualisation of H2AXgamma formation demonstrated that the proportion of cells exhibiting H2AXgamma staining at 1h differed between BPDE, 40% followed by a decline, and DBPDE, <10% followed by an increase. With H(2)O(2) treatment, almost all cells demonstrated H2AXgamma at 1h. Western blot analysis of the H2AXgamma formation also showed concentration and time-dependent response patterns. The kinetics of H2AXgamma formation correlated with the previously observed kinetics of elimination of BPDE and DBPDE adducts. Thus, the extent of H2AXgamma formation and persistence was related to both the number of adducts and their structural features.
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Affiliation(s)
- Ase Mattsson
- Institute of Environmental Medicine, Division of Biochemical Toxicology, Karolinska Institutet, Box 210, S-171 77 Stockholm, Sweden
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13
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Sliding of alkylating anticancer drugs along the minor groove of DNA: new insights on sequence selectivity. Biophys J 2008; 94:550-61. [PMID: 18160662 DOI: 10.1529/biophysj.107.113308] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Currently, little is known about the molecular recognition pathways between DNA-alkylating anticancer drugs and their targets despite their pharmacological relevance. In the framework of classical molecular dynamics simulations, here we use umbrella sampling to map the potential of mean force (PMF) associated with sliding along the DNA minor groove of two of these compounds. These are an indole derivative of duocarmycin (DSI) and the putative reactive form of anthramycin (anhydro-anthramycin, IMI). Twenty-three configurations were considered for each drug/DNA complex, corresponding to a movement along approximately 3 basepairs. The alkylation site turns out to be the most favorable for DSI, while a barrier of approximately 6 kcal/mol separates the reactive configuration of IMI.DNA from the absolute minimum. An analysis of various contributions to the PMF reveals that solvent effects play an important role for the largest and more flexible drug DSI. Instead, the PMF of IMI.DNA overall correlates with changes in the binding enthalpy. Implications of these results on the sequence selectivity of the two drugs are discussed.
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14
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Cai Y, Patel DJ, Geacintov NE, Broyde S. Dynamics of a benzo[a]pyrene-derived guanine DNA lesion in TGT and CGC sequence contexts: enhanced mobility in TGT explains conformational heterogeneity, flexible bending, and greater susceptibility to nucleotide excision repair. J Mol Biol 2007; 374:292-305. [PMID: 17942115 DOI: 10.1016/j.jmb.2007.09.034] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2007] [Revised: 08/07/2007] [Accepted: 09/04/2007] [Indexed: 11/19/2022]
Abstract
The nucleotide excision repair (NER) machinery excises a variety of bulky DNA lesions, but with varying efficiencies. The structural features of the DNA lesions that govern these differences are not well understood. An intriguing model system for studying structure-function relationships in NER is the major adduct derived from the reaction of the highly tumorigenic metabolite of benzo[a]pyrene, (+)-anti-benzo[a]pyrene diol epoxide, with the exocyclic amino group of guanine ((+)-trans-anti-[BP]-N(2)-dG, or G*). The rates of incision of the stereochemically identical lesions catalyzed by the prokaryotic UvrABC system was shown to be greater by a factor of 2.3+/-0.3 in the TG*T than in the CG*C sequence context [Biochemistry 46 (2007) 7006-7015]. Here we employ molecular dynamics simulations to elucidate the origin of the greater excision efficiency in the TG*T case and, more broadly, to delineate structural parameters that enhance NER. Our results show that the BP aromatic ring system is 5'-directed along the modified strand in the B-DNA minor groove in both sequence contexts. However, the TG*T modified duplex is much more dynamically flexible, featuring more perturbed and mobile Watson-Crick hydrogen bonding adjacent to the lesion, a greater impairment in stacking interactions, more dynamic local roll/bending, and more minor groove flexibility. These characteristics explain a number of experimental observations concerning the (+)-trans-anti-[BP]-N(2)-dG adduct in double-stranded DNA with the TG*T sequence context: its conformational heterogeneity in NMR solution studies, its highly flexible bend, and its lower thermal stability. By contrast, the CG*C modified duplex is characterized by a single BP conformation and a rigid bend. While current recognition models of bulky lesions by NER factors have stressed the importance of impaired Watson-Crick pairing/stacking and bending, our results highlight the likelihood of an important role for the local dynamics in the vicinity of the lesion.
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Affiliation(s)
- Yuqin Cai
- Department of Chemistry, New York University, New York, NY 10003, USA
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15
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Konidala P, Niemeyer B. Molecular dynamics simulations of pea (Pisum sativum) lectin structure with octyl glucoside detergents: the ligand interactions and dynamics. Biophys Chem 2007; 128:215-30. [PMID: 17532552 DOI: 10.1016/j.bpc.2007.04.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2007] [Revised: 04/18/2007] [Accepted: 04/18/2007] [Indexed: 11/23/2022]
Abstract
The mitogenic pea (Pisum sativum) lectin is a legume protein of non-immunoglobulin nature capable of specific recognition of glucose derivatives without altering its structure. Molecular dynamics simulations were performed in a realistic environment to investigate the structure and interaction properties of pea lectin with various concentrations of n-octyl-beta-d-glucopyranoside (OG) detergent monomers distributed inside explicit solvent cell. In addition, the diffusion coefficients of the ligands (OG, Ca2+, Mn2+, and Cl-) and the water molecules were also reported. The structural flexibility of the lectin was conserved in all simulations. The self-assembly of OG monomers into a small micelle at the hydrophobic site of the lectin was noticed in the simulation with 20 OG monomers. The interaction energy analysis concludes that the lectin was appropriately termed an adaptive structure. One or rarely two binding sites were observed at an instant in each simulation that were electrostatically favoured for the OG to interact with the surface amino acid residues. Enhanced binding of OG to the pea lectin was quantified in the system containing only Ca2+ divalent ions. Interestingly, no binding was observed in the simulation without divalent ions. Furthermore, the lectin-ligand complex was stabilized by multiple hydrogen bonds and at least one water bridge. Finally, the work was also in accordance with the published work elsewhere that the simulations performed with different initial conditions and using higher nonbonded cutoffs for the van der Waals and electrostatic interactions provide more accurate information and clues than the single large simulation of the biomolecular system of interest.
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Affiliation(s)
- Praveen Konidala
- Institute of Thermodynamics, Helmut-Schmidt-University / University of the Federal Armed Forces Hamburg, Holstenhofweg 85, D-22043 Hamburg, Germany
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16
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Mocquet V, Kropachev K, Kolbanovskiy M, Kolbanovskiy A, Tapias A, Cai Y, Broyde S, Geacintov NE, Egly JM. The human DNA repair factor XPC-HR23B distinguishes stereoisomeric benzo[a]pyrenyl-DNA lesions. EMBO J 2007; 26:2923-32. [PMID: 17525733 PMCID: PMC1894768 DOI: 10.1038/sj.emboj.7601730] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2006] [Accepted: 04/30/2007] [Indexed: 12/27/2022] Open
Abstract
Benzo[a]pyrene (B[a]P), a known environmental pollutant and tobacco smoke carcinogen, is metabolically activated to highly tumorigenic B[a]P diol epoxide derivatives that predominantly form N(2)-guanine adducts in cellular DNA. Although nucleotide excision repair (NER) is an important cellular defense mechanism, the molecular basis of recognition of these bulky lesions is poorly understood. In order to investigate the effects of DNA adduct structure on NER, three stereoisomeric and conformationally different B[a]P-N(2)-dG lesions were site specifically incorporated into identical 135-mer duplexes and their response to purified NER factors was investigated. Using a permanganate footprinting assay, the NER lesion recognition factor XPC/HR23B exhibits, in each case, remarkably different patterns of helix opening that is also markedly distinct in the case of an intra-strand crosslinked cisplatin adduct. The different extents of helix distortions, as well as differences in the overall binding of XPC/HR23B to double-stranded DNA containing either of the three stereoisomeric B[a]P-N(2)-dG lesions, are correlated with dual incisions catalyzed by a reconstituted incision system of six purified NER factors, and by the full NER apparatus in cell-free nuclear extracts.
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Affiliation(s)
- Vincent Mocquet
- Chemistry Department, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, Strasbourg, France
| | | | | | | | - Angels Tapias
- Chemistry Department, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, Strasbourg, France
| | - Yuqin Cai
- Chemistry Department, New York University, New York, NY, USA
| | - Suse Broyde
- Biology Department, New York University, New York, NY, USA
| | - Nicholas E Geacintov
- Chemistry Department, New York University, New York, NY, USA
- Chemistry Department, New York University, 31 Washington Place, New York, NY 10003-5180, USA. Tel.: +1 212 998 8407; Fax: +1 212 998 8421; E-mail:
| | - Jean-Marc Egly
- Chemistry Department, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, Strasbourg, France
- Chemistry Department, New York University, 31 Washington Place, New York, NY 10003-5180, USA. Tel.: +1 212 998 8407; Fax: +1 212 998 8421; E-mail:
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17
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Yingling YG, Shapiro BA. The impact of dyskeratosis congenita mutations on the structure and dynamics of the human telomerase RNA pseudoknot domain. J Biomol Struct Dyn 2007; 24:303-20. [PMID: 17206847 DOI: 10.1080/07391102.2007.10531238] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
The pseudoknot domain is a functionally crucial part of telomerase RNA and influences the activity and stability of the ribonucleoprotein complex. Autosomal dominant dyskeratosis congenita (DKC) is an inherited disease that is linked to mutations in telomerase RNA and impairs telomerase function. In this paper, we present a computational prediction of the influence of two base DKC mutations on the structure, dynamics, and stability of the pseudoknot domain. We use molecular dynamics simulations, MM-GBSA free energy calculations, static analysis, and melting simulations analysis. Our results show that the DKC mutations stabilize the hairpin form and destabilize the pseudoknot form of telomerase RNA. Moreover, the P3 region of the predicted DKC-mutated pseudoknot structure is unstable and fails to form as a defined helical stem. We directly compare our predictions with experimental observations by calculating the enthalpy of folding and melting profiles for each structure. The enthalpy values are in very good agreement with values determined by thermal denaturation experiments. The melting simulations and simulations at elevated temperatures show the existence of an intermediate structure, which involves the formation of two UU base pairs observed in the hairpin form of the pseudoknot domain.
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Affiliation(s)
- Yaroslava G Yingling
- Center for Cancer Research Nanobiology Program, National Cancer Institute, NCI-Frederick National Institutes of Health, Building 469, Room 150, Frederick, MD 21702, USA
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18
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Rodríguez FA, Cai Y, Lin C, Tang Y, Kolbanovskiy A, Amin S, Patel DJ, Broyde S, Geacintov NE. Exocyclic amino groups of flanking guanines govern sequence-dependent adduct conformations and local structural distortions for minor groove-aligned benzo[a]pyrenyl-guanine lesions in a GG mutation hotspot context. Nucleic Acids Res 2007; 35:1555-68. [PMID: 17287290 PMCID: PMC1865068 DOI: 10.1093/nar/gkm022] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The environmental carcinogen benzo[a]pyrene (BP) is metabolized to reactive diol epoxides that bind to cellular DNA by predominantly forming N2-guanine adducts (G*). Mutation hotspots for these adducts are frequently found in 5′- ··· GG ··· dinucleotide sequences, but their origins are poorly understood. Here we used high resolution NMR and molecular dynamics simulations to investigate differences in G* adduct conformations in 5′- ··· CG*GC ··· and 5′- ··· CGG* C··· sequence contexts in otherwise identical 12-mer duplexes. The BP rings are positioned 5′ along the modified strand in the minor groove in both cases. However, subtle orientational differences cause strong distinctions in structural distortions of the DNA duplexes, because the exocyclic amino groups of flanking guanines on both strands compete for space with the BP rings in the minor groove, acting as guideposts for placement of the BP. In the 5′- ··· CGG* C ··· case, the 5′-flanking G · C base pair is severely untwisted, concomitant with a bend deduced from electrophoretic mobility. In the 5′- ··· CG*GC ··· context, there is no untwisting, but there is significant destabilization of the 5′-flanking Watson–Crick base pair. The minor groove width opens near the lesion in both cases, but more for 5′- ··· CGG*C···. Differential sequence-dependent removal rates of this lesion result and may contribute to the mutation hotspot phenomenon.
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Affiliation(s)
- Fabián A. Rodríguez
- Department of Chemistry and Biology, New York University, New York, NY, USA, Department of Pharmacology, Penn State College of Medicine, Hershey, PA, USA and Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Yuqin Cai
- Department of Chemistry and Biology, New York University, New York, NY, USA, Department of Pharmacology, Penn State College of Medicine, Hershey, PA, USA and Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Chin Lin
- Department of Chemistry and Biology, New York University, New York, NY, USA, Department of Pharmacology, Penn State College of Medicine, Hershey, PA, USA and Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Yijin Tang
- Department of Chemistry and Biology, New York University, New York, NY, USA, Department of Pharmacology, Penn State College of Medicine, Hershey, PA, USA and Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Alexander Kolbanovskiy
- Department of Chemistry and Biology, New York University, New York, NY, USA, Department of Pharmacology, Penn State College of Medicine, Hershey, PA, USA and Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Shantu Amin
- Department of Chemistry and Biology, New York University, New York, NY, USA, Department of Pharmacology, Penn State College of Medicine, Hershey, PA, USA and Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Dinshaw J. Patel
- Department of Chemistry and Biology, New York University, New York, NY, USA, Department of Pharmacology, Penn State College of Medicine, Hershey, PA, USA and Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Suse Broyde
- Department of Chemistry and Biology, New York University, New York, NY, USA, Department of Pharmacology, Penn State College of Medicine, Hershey, PA, USA and Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Nicholas E. Geacintov
- Department of Chemistry and Biology, New York University, New York, NY, USA, Department of Pharmacology, Penn State College of Medicine, Hershey, PA, USA and Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
- *To whom correspondence should be addressed. +1 212 998 8407+1 212 998 8421
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19
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Jia L, Shafirovich V, Shapiro R, Geacintov NE, Broyde S. Flexible 5-guanidino-4-nitroimidazole DNA lesions: structures and thermodynamics. Biochemistry 2006; 45:6644-55. [PMID: 16716075 PMCID: PMC2527740 DOI: 10.1021/bi0601757] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
5-Guanidino-4-nitroimidazole (NI), derived from guanine oxidation by reactive oxygen and nitrogen species, contains an unusual flexible ring-opened structure, with nitro and guanidino groups which possess multiple hydrogen bonding capabilities. In vitro primer extension experiments with bacterial and mammalian polymerases show that NI incorporates C as well as A and G opposite the lesion, depending on the polymerase. To elucidate structural and thermodynamic properties of the mutagenic NI lesion, we have investigated the structure of the modified base itself and the NI-containing nucleoside with high-level quantum mechanical calculations and have employed molecular modeling and molecular dynamics simulations in solution for the lesion in B-DNA duplexes, with four partner bases opposite the NI. Our results show that NI adopts a planar structure at the damaged base level. However, in the nucleoside and in DNA duplexes, steric hindrance between the guanidino group and its linked sugar causes NI to be nonplanar. The NI lesion can adopt both syn and anti conformations on the DNA duplex level, with the guanidino group positioned in the DNA major and minor grooves, respectively; the specific preference depends on the partner base. On the basis of hydrogen bonding and stacking interactions, groove dimensions, and bending, we find that the least distorted NI-modified duplex contains partner C, consistent with observed incorporation of C opposite NI. However, hydrogen bonding interactions between NI and partner G or A are also found, which would be compatible with the observed mismatches.
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Affiliation(s)
- Lei Jia
- Department of Chemistry, New York University, New York, New York 10003, USA
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20
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Carcinogenicity of benzo[a]pyrene diol epoxide stereoisomers: A linear free energy relationship study. ACTA ACUST UNITED AC 2006. [DOI: 10.1016/j.theochem.2006.02.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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21
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Chapter 6 Molecular Modeling and Atomistic Simulation of Nucleic Acids. ACTA ACUST UNITED AC 2005. [DOI: 10.1016/s1574-1400(05)01006-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
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22
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Abstract
In moving towards the simulation of larger nucleic acid assemblies over longer timescales that include more accurate representations of the environment, we are nearing the end of an era characterized by single nanosecond molecular dynamics simulation of nucleic acids. We are excited by the promise and predictability of the modeling methods, yet remain prudently cautious of sampling and force field limitations. Highlights include the accurate representation of subtle drug-DNA interactions, the detailed study of modified and unusual nucleic acid structures, insight into the influence of dynamics on the structure of DNA, and exploration of the interaction of solvent and ions with nucleic acids.
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Affiliation(s)
- Thomas E Cheatham
- Department of Medicinal Chemistry, University of Utah, 2000 East, 30 South, Skaggs Hall 201, Salt Lake City, Utah 84112, USA.
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23
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Johnson AA, Sayer JM, Yagi H, Kalena GP, Amin R, Jerina DM, Pommier Y. Position-specific suppression and enhancement of HIV-1 integrase reactions by minor groove benzo[a]pyrene diol epoxide deoxyguanine adducts: implications for molecular interactions between integrase and substrates. J Biol Chem 2003; 279:7947-55. [PMID: 14627697 DOI: 10.1074/jbc.m311263200] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The viral protein HIV-1 integrase is required for insertion of the viral genome into human chromosomes and for viral replication. Integration proceeds in two consecutive integrase-mediated reactions: 3'-processing and strand transfer. To investigate the DNA minor groove interactions of integrase relative to known sites of integrase action, we synthesized oligodeoxynucleotides containing single covalent adducts of known absolute configuration derived from trans-opening of benzo-[a]pyrene 7,8-diol 9,10-epoxide by the exocyclic 2-amino group of deoxyguanosine at specific positions in a duplex sequence corresponding to the terminus of the viral U5 DNA. Because the orientations of the hydrocarbon in the minor groove are known from NMR solution structures of duplex oligonucleotides containing these deoxyguanosine adducts, a detailed analysis of the relationship between the position of minor groove ligands and integrase interactions is possible. Adducts placed in the DNA minor groove two or three nucleotides from the 3'-processing site inhibited both 3'-processing and strand transfer. Inosine substitution showed that the guanine 2-amino group is required for efficient 3'-processing at one of these positions and for efficient strand transfer at the other. Mapping of the integration sites on both strands of the DNA substrates indicated that the adducts both inhibit strand transfer specifically at the minor groove bound sites and enhance integration at sites up to six nucleotides away from the adducts. These experiments demonstrate the importance of position-specific minor groove contacts for both the integrase-mediated 3'-processing and strand transfer reactions.
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MESH Headings
- 7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide/analogs & derivatives
- 7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide/chemistry
- 7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide/pharmacology
- Binding Sites
- DNA/chemistry
- DNA/metabolism
- DNA, Viral/chemistry
- Deoxyguanosine/analogs & derivatives
- Deoxyguanosine/chemistry
- Deoxyguanosine/pharmacology
- HIV Integrase/metabolism
- Magnetic Resonance Spectroscopy
- Recombinant Proteins
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Affiliation(s)
- Allison A Johnson
- Laboratory of Molecular Pharmacology, Center for Cancer Research, NCI, and Laboratory of Bioorganic Chemistry, NIDDK, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland 20892, USA
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