Suse Broyde, Ph.D. - US grants

The goal for the research proposed here is to develop mathematical tools for computing three-dimensional structures of large biological molecules. In particular, modeling and large- scale minimization techniques will be devised to predict the conformations of single and doublestranded RNA and DNA molecules. The computational tools involve semi-empirical potential energy minimization and molecular dynamics, executed on the Cray X-MP and aided by interactive computer graphics on the Evans and Sutherland PS-330. The plan is to work on the following four areas of program development: (1) Global optimization strategies; test the determination Tunneling method of Levy and Gomez and a variant of the stochastic Simulated Annealing: (2) Faster manipulation of the pairwise interactions in the energy function; investigate the new method recently proposed by Greengard and Rokhlin which could reduce the order O(N2) computational complexity for an N - particle system to order O(N): (3) Implementation of molecular dynamics: dynamics simulations will enable an examination of the dynamic trajectories of the structures obtained from minimization; and: (4) Incorporation of solvent and metalions into the molecular model; this will provide a more realistic potential field to represent the molecular forces influencing the RNA and DNA in its natural milieu. The developed computational tools will yield the ability to investigate some intriquing problems of three-dimensional molecular structures. These problems include the dependence of DNA conformation on the nucleic acid base sequence and the structure and the complex folding patterns of single-stranded RNA. The minimizations and dynamics results will be used to make 16 mm films and videotapes that will reveal the dynamic range of structures and permit us to relate conformational features with known biological functions. This proposal projects to develop mathematical tools, using state-of-the-art optimization algorithms, for examination of dynamics simulation of solvent and metal-ion interaction in the biologically important molecular RNA and DNA. The Program Director for Computational Science and Engineering recommends support in the sum of $69,370 for a period of one year.

Structure of DNA modified by highly mutagenic and tumorigenic agents, and their less active analogs will be computed with our program DUPLEX, in order to define those conformational features that underlie the mutagenic and carcinogenic activity. We are especially interested in modification by polycyclic aromatic amines and hydrocarbons, with emphasis on the following issues: (1) chemical nature of the adduct, including ring size and substituent effects; (2) nature of base modified; (3) position of modification on a given base; (4) effect of neighboring base sequences. Aromatic amine adducts of highest priority are aniline (AN), 4- aminobiphenyl (ABP), 4-acetylaminobiphenyl (AABP), 2-aminofluorene (AF), 2- acetylaminofluorene (AAF) and 1-aminopyrene (AP) bound to guanine C-8, as well as ABP bound to adenine C-8. Next in priority are N-acetylbenzidine (NAB) and the cooked food mutagens Trp-P-2 and IQ, which also form adducts to guanine C-8. Among the polycyclic aromatic hydrocarbon adducts, our first priority remains the N-2 guanine adduct of the prototype highly tumorigenic (+) anti-benzo(a)pyrene 7, 8-diol-9, 10-epoxide (BPDE) and that of its much less active (-) anti analog. The N-2 guanine adducts of the highly tumorigenic (+) anti 5-methylchrysene-1, 2-diol-3, 4 epoxide, (+) 5- MCDE, and the much less active (+) 6-MCDE analog make up a similar pair of interest to us. The adenine N-6 and guanine N-2 adducts of (-) benzo(c)phenanthrene 3, 4-diol-1, 2-epoxide-2, (-)B(c)PHDE-2 which are apparently both highly mutagenic, are next in priority. Base sequences that are identified mutagenic hotspots are to be examined first. Of current interest are the CGC sequence, and sequences with purines adjacent to the modification. In single stranded or duplex trimers, we can investigate all sequence combinations surrounding the lesion to ascertain whether some conformational feature unique to a given sequence might predict a mutagenic hotspot. Both duplexes and single strands will be investigated. Our energy minimized structures are to be used as starting conformations for molecular dynamics simulations with the AMBER force field to provide for explicit solvent and salt incorporation. In addition, we have established collaborations with investigators who are using NMR techniques to study some of the modified DNAs, and are computing energy minimized structures that are within bounds of the experimental data. A number of new computational approaches are also planned including continued development of a build-up technique for prediction of modified DNA structures, molecular dynamics simulations with larger time steps, an effort to compute free energy rather than potential energy differences between conformers, and employment of a simulated annealing algorithm to diminish the multiple minimum problem. In addition, it is planned to automate and document DUPLEX, and release it to the scientific community.

This SGER award is for the preparation of the molecular mechanics program DUPLEX for release to the academic community of scientists. The program computes energy minimized structures of DNA, and of DNA covalently modified by foreign substances. It has several unique features that distinquish it from other state-of-the-art molecular mechanics. These features make it particularly valuable to scientists from various disciplines who wish to generate atomic resolution views of such DNAs. Urgent requests for the code have had to be deferred because the program is not ready for use by workers who cannot code in FORTRAN for a Cray Supercomputer. DUPLEX, fully documented and automated to operate without requirement for any FORTRAN coding will distributed via a suitable mechanism such as the Quantum Chemists' Program Exchange.//

Dr. Tamar Schlick is supported by a grant from the Theoretical and Computational Chemistry Program in the Chemistry Division, the Databases, Software Development and Computational Biology Program in the Division of Instrumentation and Resources, and the New Technologies Program in the Division of Advanced Scientific Computing to develop new computer algorithms for performing molecular mechanics and molecular dynamics calculations. These new algorithms will be used to predict nucleic acid and protein structures with the aid of supercomputers. In this research Schlick and coworkers will continue to address some of the fundamental computational and theoretical problems in the field of molecular modeling by: 1) devising more efficient nonlinear minimization techniques for complex large scale problems; 2) using larger time steps in molecular dynamics simulations; 3) including quantum-mechanical effects in molecular dynamics simulations; and 4) reducing the computation time for the pairwise nonbonded interactions. The algorithms which are developed will be used to study sequence-dependent folding pathways of closed circular DNA duplexes. The ultimate goal of this research is to explore the detailed folding pathways and important transitions in nucleic acids and proteins.

Structure of DNA modified by highly mutagenic and tumorigenic agents, and their less active analogs will be computed with our program DUPLEX, in order to define those conformational features that underlie the mutagenic and carcinogenic activity. We are especially interested in modification by polycyclic aromatic amines and hydrocarbons, with emphasis on the following issues: (1) chemical nature of the adduct, including ring size and substituent effects; (2) nature of base modified; (3) position of modification on a given base; (4) effect of neighboring base sequences. Aromatic amine adducts of highest priority are aniline (AN), 4- aminobiphenyl (ABP), 4-acetylaminobiphenyl (AABP), 2-aminofluorene (AF), 2- acetylaminofluorene (AAF) and 1-aminopyrene (AP) bound to guanine C-8, as well as ABP bound to adenine C-8. Next in priority are N-acetylbenzidine (NAB) and the cooked food mutagens Trp-P-2 and IQ, which also form adducts to guanine C-8. Among the polycyclic aromatic hydrocarbon adducts, our first priority remains the N-2 guanine adduct of the prototype highly tumorigenic (+) anti-benzo(a)pyrene 7, 8-diol-9, 10-epoxide (BPDE) and that of its much less active (-) anti analog. The N-2 guanine adducts of the highly tumorigenic (+) anti 5-methylchrysene-1, 2-diol-3, 4 epoxide, (+) 5- MCDE, and the much less active (+) 6-MCDE analog make up a similar pair of interest to us. The adenine N-6 and guanine N-2 adducts of (-) benzo(c)phenanthrene 3, 4-diol-1, 2-epoxide-2, (-)B(c)PHDE-2 which are apparently both highly mutagenic, are next in priority. Base sequences that are identified mutagenic hotspots are to be examined first. Of current interest are the CGC sequence, and sequences with purines adjacent to the modification. In single stranded or duplex trimers, we can investigate all sequence combinations surrounding the lesion to ascertain whether some conformational feature unique to a given sequence might predict a mutagenic hotspot. Both duplexes and single strands will be investigated. Our energy minimized structures are to be used as starting conformations for molecular dynamics simulations with the AMBER force field to provide for explicit solvent and salt incorporation. In addition, we have established collaborations with investigators who are using NMR techniques to study some of the modified DNAs, and are computing energy minimized structures that are within bounds of the experimental data. A number of new computational approaches are also planned including continued development of a build-up technique for prediction of modified DNA structures, molecular dynamics simulations with larger time steps, an effort to compute free energy rather than potential energy differences between conformers, and employment of a simulated annealing algorithm to diminish the multiple minimum problem. In addition, it is planned to automate and document DUPLEX, and release it to the scientific community.

Funds are sought for an IRIS Model 4D220 VGX Computer Graphics Workstation and accessories from Silicon Graphics Computer Systems. This workstation will be employed primarily by a group of five faculty and their associates who are all engaged in investigating mechanisms of synthesis and structural characterization of carcinogen-DNA adducts. The workstation will be employed in molecular modeling of reaction mechanisms and adduct conformations with the molecular modeling package INSIGHT/DISCOVER from Biosym Technologies, Inc. In addition, the workstation will be used to carry out molecular mechanics and molecular dynamics calculations for these adducts with our own program, DUPLEX, and with AMBER. Use of the IRIS workstation for the computation intensive molecular mechanics and dynamics calculations will alleviate supercomputing resource constraints, and will be far less costly. These computational efforts yield atomic resolution views of adducts in agreement with experimental data obtained in solution studies, and also offer plausible structural information for adducts where no data is at hand.

We are using minimized potential energy calculations with our program DUPLEX and molecular dynamics simulations with AMBER to determine the most stable conformations of DNA segments modified by the prototype mutagenic aromatic amines: 2-aminofluorene and 2- acetylaminofluorene. An extensive literature describes the genetic effects of this pair, which have been termed "superb tools for the exploration of the mechanisms of carcinogenesis". Our underlying hypothesis is that the structures of such damaged DNAs contribute to their mutagenic potential, and that an understanding of the details of structure will ultimately enable us to predict many of the genetic effects of chemical mutagens. The DNA species that we will examine model the stages of replication that lead to a mutagenic outcome, according to current theories. During the past few years, hypotheses have emerged which provide possible rationales for frameshift mutations (deletions in particular) and some base substitutions, in terms of the specific structures involved at the replications fork. Effects of the base sequence surrounding the modification on the nature of the structure of a particular chemical lesion will also be assessed, to gain insight into the sequence preferences ("hot spots" for the various kinds of mutagenic change. The results of the computations will produce atomic resolution views of the structures, together with their energy rankings. We expect that an examination of the changes produced in DNA by adducts derived from these amines will allow us to identify a well defined number of characteristic alterations. Our efforts at this stage will largely involve DNA alone, but in a few cases (as computational resources permit) we shall examine DNA in a complex with a fragment of a polymerase. As we gain understanding of the changes in DNA produced by AF and AAF modification, we will test our hypothesis by comparing our data with the growing collection of data on site-specific mutagenesis on these substances, and predicting nutational effects not yet tested experimentally.

DNA; chemical carcinogen; mutagens; carbopolycyclic compound; benzopyrenediol epoxide; adduct; conformation; active sites; DNA directed DNA polymerase; computer simulation; chemical structure function; molecular dynamics; gene deletion mutation; chemical carcinogenesis; DNA replication; carcinogen testing; mutagen testing; X ray crystallography; nuclear magnetic resonance spectroscopy;

DESCRIPTION: (provided by applicant) The human population is routinely exposed to a large number of environmental chemicals: some of them may initiate cancer while others, only slightly different in structure, are harmless. One prominent route by which carcinogens exert their effects is to react with DNA in a way that leads to a mutation in a vital cellular target. Insight into the mechanism by which a carcinogen-damaged DNA produces mutations is needed in order to identify potentially hazardous substances. In this project, intensive computer modeling is used to explore this process. Our efforts here are targeted particularly to frameshift mutations, whose contribution to carcinogenesis has perhaps been underemphasized. In particular, we will attempt to relate chemical structure to mutagenic effectiveness within the framework of the slippage/misalignment theory. This theory has successfully explained the sequence dependence of many frameshift mutations. We will work with four aromatic amines, members of a chemical class that has demonstrated an exceptional ability to induce frameshifts. Our selection includes acetylaminofluorene (AAF), chosen because of the extensive data based concerning its mutagenicity, 2-amino-1-methyl-6-phenylimidazo(4,5-b)pyridine (PhIP) and 2-amino-3-methyl-imidazo(4,5-f)quinoline (IQ), carcinogens that are formed during the cooking of protein-rich foods, and 1-aminopyrene (AP), the transformation product of a common pollutant present in diesel engine exhaust, urban air particulates, and a number of other sources. We will follow the behavior of modified DNA primer-template complexes as they proceed through the steps of extension, blockage, and/or misalignment within the active sites of selected polymerases for which suitable crystal structures are available. Our methods include the use of the programs DUPLEX (for molecular mechanics with modified DNA) and AMBER for molecular dynamics simulations with DNA in solution or in a polymerase. DUPLEX permits an extensive search of conformation space without the use of assumptions concerning the final structure. The molecular dynamics studies include explicit solvent and salt, and provide animation, but are more restricted in their search. Molecular dynamics trajectories yield ensembles of structures that will be used to compute free energy differences between conformers in solution, and binding free energies of polymerase-primer-template complexes.

DESCRIPTION (provided by applicant): The broad and long term goals of this research is to determine on a molecular level the etiology of cancer initiation by DNA damage, produced by environmental and endogenous chemicals to which the human population is widely exposed. The overall hypotheses are: (1) The specific formation of damaged DNA is critical in determining if it is repaired or not;(2) if repair fails, the DNA conformation within a replicative polymerase determines whether blockage, normal or mutagenic bypass occurs;(3) if normal replication is impeded, then the altered DNA will encounter one or more bypass polymerases, and the specific conformation of the altered DNA will determine whether a mutation which may initiate cancer occurs. The PI will test these hypotheses by determining structural, dynamic and thermodynamic properties for two groups of lesions: (1) a series derived from carcinogenic aromatic amines/amide presenting tobacco smoke, automobile exhaust and cooked foods that are capable of Watson-Crick pairing and stacking, and (2) a severely distorting group incapable of Watson-Crick pairing, with impaired stacking;these include a lesion derived from a prominent hormone replacement drug, and one produced by endogenous and exogenous reactive oxygen species. Specific aim 1 will determine detailed structural and thermodynamic properties of the lesions in duplex DNA as a function of adduct structure and thermodynamic factors that cause the adducts to impede replicative polymerases, and to delineate factors which could permit mutagenic or normal bypass of the lesions with lowered fidelity in Y-family bypass polymerases. Relevance to public health: this work will define precisely on a molecular level, the specific structural and energetic characteristics of DNA-containing lesions derived from carcinogenic environmental substances, and thus provided the molecular hallmarks that distinguish very harmful chemicals from benign ones. These studies will facilitate advances in biomonitoring of carcinogen - damaged DNA, since the structural and thermodynamic properties of the DNA lesions would provide a method for distinguishing highly genotoxic lesions from more benign ones.

DNA directed DNA polymerase; heat; model

A category of non-planar, twisted polycyclic aromatic hydrocarbons (PAHs), termed fjord region compounds, are extremely potent tumorigens; they include dibenzo[a,l]pyrene which has recently been cited as the most tumorigenic PAH yet identified. These pollutants are released into the environment as combustion products of a variety of fuels, and they contaminate food crops. They are biologically active at the low concentrations present in foods and urban air and are hazardous to the population at large. The origin of the extraordinary carcinogenic potencies of fjord PAHs remains unknown. However, it has recently been shown that several of the bulky DNA adducts that they produce after metabolic activation to diol epoxides, are resistant to nucleotide excision repair (NER), the principal cellular defense against such DNA lesions. Resistance to DNA repair of these adducts is deemed a critical cause for the extraordinary tumorigenicity of the parent chemicals, as they cause the mutations which initiate cancer. However, each environmental fjord PAH gives rise to a complex mixture of stereoisomeric guanine and adenine DNA adducts. Furthermore, the NER susceptibility of each such adduct may vary with DNA base sequence. In this multitude of lesions, the key repair-resistant ones that lead to cancer remain unidentified. Our broad, long-term objective is, working in tandem with our experimental collaborator Prof. N. Geacintov, to identify the NER-resistant adducts and their characteristics using innovative and state-of-the-art modeling methods: we hypothesize that NER-resistance is governed by the structural, dynamic and thermodynamic properties of the PAH-modified DNA. The fjord PAHs selected for detailed study are dibenzo[a,l]pyrene, benzo[g]chrysene, and benzo[c]phenanthrene; we investigate their adducts produced via the well established diol epoxide metabolic activation pathway. These PAHs represent aromatic systems of 6, 5, and 4 rings, respectively, a range optimal for the induction of tumors. We aim to investigate the many diol epoxide adducts of the three parent PAHs in selected sequences that we hypothesize will alter their NER-susceptibilities. We further aim to determine the characteristic properties and NER susceptibilities of lesions when organized within the histone protein environment of the nucleosome, the basic unit of chromatin structure in the cellular environment. This is an essential first step towards elucidating the functioning of the complex NER machinery in the context of chromatin. We will work hand-in-hand with our experimental collaborator Prof. N. Geacintov: NER data with human cell extracts and including lesion- containing nucleosomes will provide anchors for directly linking our findings with the experimental observations, and our analyses will point to important predictions that will be tested in his laboratory. Our studies will provide the next-generation of biomarkers for PAH exposure, facilitate design of better NER- resistant chemotherapeutics through our gained understanding of NER mechanisms, and advance our capability for genotoxic screening of adducts derived from PAHs present in our environment.

DESCRIPTION (provided by applicant): Polycyclic aromatic amines, heterocylic amines and nitroarenes are environmental carcinogens that are present in many cooked and broiled foods, notably meats, products of fuel combustion such as diesel exhaust, tobacco smoke, cooking oil fumes, coffee, tea and spices, and polluted air and water. Cancer is initiated when metabolites of these chemicals form DNA lesions that cause mutations during replication. Among the plethora of DNA adducts, it is essential to identify the most hazardous ones for purposes of biomonitoring and assessing the exposure risk of individuals to environmental carcinogens. Biomonitoring will be greatly improved by concentrating on those adducts that are the most persistent ones in vivo. We are focusing on a group of aromatic amine-, heterocyclic amine- and nitroarene-derived DNA adducts of varying sizes and shapes that stem from these metabolically activated environmental carcinogens. They have been identified in human cells and fluids, and in animal cells and tissues. We will investigate DNA adducts to dG-N2 that have been largely overlooked, but are often persistent in animal studies and adducts to dG-C8, for which animal studies suggest repair susceptibility in a number of cases. Our central hypothesis is that those adducts that entirely escape nucleotide excision repair (NER) are critical ones, as they will gradually accumulate in our DNA and cause cancer-initiating mutations. Our long-term goal is to determine the properties of adducts that govern repair resistance and susceptibility, and identify those adducts that resist NER. Our three Specific Aims test the hypothesis that the linkage site to guanine, the size and shape of the aromatic ring system and the sequence context of the adducts are the key factors that determine their NER susceptibility. We will utilize innovative molecular modeling approaches to elucidate the properties of the DNA lesions and determine the characteristics responsible for repair resistance or susceptibility. We will work hand-in-hand with our long-term collaborator N. Geacintov, who will perform NER studies with human HeLa cell extracts for our adducts. Our underlying hypothesis is that lesion-induced local stabilization of the DNA duplexes is the fundamental property that determines the NER resistance of a given lesion. Prior work has demonstrated, using melting points of duplexes as indicators of stability, that repair resistant adducts either cause minor stability decreases or stabilize modified double-stranded DNA. In contrast, DNA lesions that elicit NER are thermally destabilizing. We will investigate the adducts in uncomplexed DNA as well as when complexed with histone proteins in nucleosomes, the fundamental DNA-organization unit in the cellular environment. Our studies will provide the next-generation of biomarkers for exposure and risk of developing cancer, facilitate design of better NER-resistant chemotherapeutics through our gained understanding of NER mechanisms, and advance our capability for genotoxic screening of adducts derived from the polycyclic aromatic amines, heterocylic amines and nitroarenes present in our environment.

? DESCRIPTION (provided by applicant): The human genome is under constant attack from environmental pollutants, endogenous reactive oxidizing species that are secreted in human tissues during the inflammatory response, and ultraviolet components of sunlight. Among the exogenous cancer-causing environmental contaminants are polycyclic aromatic compounds that are byproducts of fossil fuel combustion found at toxic waste dumps and superfund sites, in airborne particulates, and in our food and water. The DNA lesions derived from polycyclic aromatic compounds, inflammation-related reactive oxidizing species, and ultraviolet light result in the accumulation of malignant mutations that lead to a variety of human cancers. However, not all DNA lesions are equally effective in promoting human diseases: while lesions can be excised by the human nucleotide excision repair (NER) mechanism, some DNA lesions are rapidly repaired, some are repaired slowly, and some are entirely resistant to NER and are therefore particularly genotoxic. The vital importance of NER is demonstrated in the devastating human disorder xeroderma pigmentosum, caused by mutations in various NER genes. However, why certain DNA lesions are NER-resistant and others are not when NER is normal, is not understood. The objective of this project is to provide mechanistic insights into this puzzling variability of DNA lesion repair, by focusing on the key step of lesion recognition in NER, to yield a molecular understanding of NER resistance. We hypothesize that how well a lesion is recognized is determined by the extent of destabilization or stabilization that it impose on DNA: stabilization leads to repair resistance and destabilization facilitates repair. We will dissect the structural, dynamic and thermodynamic properties for a selected set of DNA lesions that govern whether they are recognized by Rad4-Rad23, the yeast ortholog of the human XPC-RAD23B lesion recognition factor. In Aim 1 we will determine the extent that local thermodynamic stability of lesion-containing DNA regulates their recognition. In Aim 2 we will determine the molecular mechanism for productive binding of Rad4-Rad23 that successfully recognizes the lesions and correctly recruits subsequent NER factors, and how the binding pathway and free energies along this pathway depend on lesion structures. In Aim 3 we will investigate DNA complexed with histone proteins in nucleosomes, the fundamental packaging unit of DNA in cells. We will determine how access of the NER proteins to DNA lesions in nucleosomes is governed by the lesion's structural and dynamic properties to promote or inhibit repair. The novel insights into the DNA lesion recognition mechanisms of NER that we will gain may lead to the development of more effective, less NER- susceptible chemotherapeutic agents, since the efficacy of current drugs is impaired by NER. Furthermore, such understanding will help to identify the most genotoxic cancer-causing precursors among the many environmental contaminants, thus allowing for the development of better targeted abatement policies and biomonitoring methods of the associated health risks.

PROJECT SUMMARY The human genome is constantly attacked from sources that include environmental pollutants, other exogenous origins that include drug treatment, endogenous reactive oxygen species, and UV light. Among the lesions/adducts are ones derived from polycyclic aromatic compounds, widespread byproducts of fossil fuel combustion found at toxic waste dumps, superfund sites, in our air, food and water. The resulting DNA lesions cause mutations that lead to cancer. However, not all DNA lesions are equally carcinogenic, as their mutagenic propensities vary: a cascade of processes determines whether they are repaired, or survive for mutagenic or error-free bypass by DNA polymerases. Human nucleotide excision repair (NER) is a key mechanism for removal of many such DNA lesions. The vital importance of NER is demonstrated in the devastating human disorder xeroderma pigmentosum, caused by mutations in NER genes. Notably, some lesions are rapidly repaired, some slowly, and some are resistant and thus particularly genotoxic, a phenomenon that is poorly understood. Likewise, there is a gap in our understanding of the mechanisms underlying DNA lesion bypass by polymerases that can lead to a mutagenic or error-free outcome. The objective of this project is to provide mechanistic insights into the puzzling variability of DNA lesion mutagenicity, focusing on the key steps of lesion recognition for repair and mutagenic bypass, to yield integrated new molecular and dynamic understanding of lesion mutagenic proclivity in unprecedented atomistic detail, using molecular dynamics simulations. Our overall hypothesis is that the structure of the lesion and its base sequence context determine its overall mutagenic propensity. In Aim 1, we will utilize a selected set of DNA lesions/adducts whose structures differ greatly in size and shape, placed in differing sequence contexts, to determine structural, energetic and dynamic characteristics of the lesion-containing DNAs as they bind to Rad4/XPC, the yeast homolog of the human XPC lesion recognition protein. We will reveal how those that bind for productive recognition leading to excision differ from those that fail to do so. In Aim 2 we will determine how the human XPD helicase in TFIIH, that verifies the presence of lesions for NER by stalling, processes lesions of different sizes and shapes, and how XPD mutations that cause human disease inhibit XPD?s function. In Aim 3 we will determine how differing lesion structures in varying nucleosomal positions impose different distortions on the nucleosome and how selected histone acetylations modulate these distortions, to promote or inhibit access for repair. In Aim 4 we investigate endogenous and exogenous DNA peptide crosslink lesions, to determine how selected DNA bypass polymerases process them error-free or mutagenically, in differing DNA sequence contexts. Focusing on the most mutagenic lesions, our work will facilitate identification of appropriate biomarkers for determining risk of developing cancer, advance design of chemotherapy drugs that are less repaired, and yield a predictive tool to identify mutational hotspot sequences induced by different lesions in human tumors.