The N 2 ‑Furfuryl-deoxyguanosine Adduct Does Not Alter the Structure of B‑DNA Pratibha P. Ghodke, † Kiran R. Gore, †,∥ S. Harikrishna, † Biswajit Samanta, † Jithesh Kottur, ‡,§ Deepak T. Nair,* ,§,⊥ and P. I. Pradeepkumar* ,† † Department of Chemistry, Indian Institute of Technology Bombay, Mumbai-400076, India ∥ Department of Chemistry, University of Mumbai, Mumbai-400098, India § Regional Centre for Biotechnology, NCR Biotech Science Cluster, Third Milestone, Faridabad-Gurgaon Expressway, Faridabad-121001, India ‡ Manipal University, Manipal-576104, India ⊥ National Centre for Biological Sciences (NCBS-TIFR), GKVK Campus, Bellary Road, Bangalore-560065, India * S Supporting Information ABSTRACT: N 2 -Furfuryl-deoxyguanosine (fdG) is carcino- genic DNA adduct that originates from furfuryl alcohol. It is also a stable structural mimic of the damage induced by the nitrofurazone family of antibiotics. For the structural and functional studies of this model N 2 -dG adduct, reliable and rapid access to fdG-modified DNAs are warranted. Toward this end, here we report the synthesis of fdG-modified DNAs using phosphoramidite chemistry involving only three steps. The functional integrity of the modified DNA has been verified by primer extension studies with DNA polymerases I and IV from E. coli. Introduction of fdG into a DNA duplex decreases the T m by ∼1.6 °C/modification. Molecular dynamics simulations of a DNA duplex bearing the fdG adduct revealed that though the overall B-DNA structure is maintained, this lesion can disrupt W−C H-bonding, stacking interactions, and minor groove hydrations to some extent at the modified site, and these effects lead to slight variations in the local base pair parameters. Overall, our studies show that fdG is tolerated at the minor groove of the DNA to a better extent compared with other bulky DNA damages, and this property will make it difficult for the DNA repair pathways to detect this adduct. ■ INTRODUCTION DNA damage is central to chemical carcinogenesis and occurs due to the continuous exposure to various endogenous and exogenous genotoxic agents. 1 Different carcinogens create a variety of metabolites, which can form significant modifications (adducts) in the DNA strands. 2 Such DNA adducts have the potential to inhibit the DNA replication process. 3 The presence of these adducts leads to recruitment of pathways and molecules that serve to neutralize their deleterious effects on replication and remove them from the genome. 4 One such event is DNA damage response (DDR), which eliminates various DNA adducts by various DNA repair mechanisms, thereby preventing the formation of lethal mutations. 4 Translesion synthesis (TLS) is a damage tolerance pathway in which the damage is bypassed with the assistance of specialized DNA polymerases (Y-family) to rescue DNA replication stalled at these lesions. 5 Failure to neutralize the deleterious effects of the damaged nucleotide on different genomic processes can lead to genetic instability, which generally leads to the death or oncogenic transformation of the cell. 4 The N 2 -position of the deoxyguanosine (dG) is one of the most susceptible sites in DNA, and a large number of adducts are known to form at this site from various genotoxic agents. 2 Many of the N 2 -dG adducts such as N 2 -benzo[a]pyrene, N 2 - carboxyethyl, N 2 -furfuryl (fdG, Figure 1), etc., are reported to be lethal to the cells. 6−9 The fdG adduct is caused by furfuryl alcohol (FFA, Figure 1), which is used as a flavoring agent. 10 Also, FFA has been detected in several foodstuffs such as coffee, red wine, rice cakes, cooked meat, and milk products. 11 It is mostly produced in heat-treated foods via thermal and acid- catalyzed dehydration of pentoses. 12 Moreover, it can be formed by reduction of hepatocarcinogenic agent furfural. 12 FFA is an established rodent carcinogen, and its carcinogenic effects on humans are being investigated. 13 Recently, FFA- induced fdG adduct has also been detected in human lung specimens. 10,13,14 The metabolic pathway of FFA follows bioactivation of furfuryl alcohol by endogenous sulfotrans- ferases to form a furfuryl sulfate intermediate (Figure 1). 13 This highly unstable intermediate generates an electrophilic carbon- ium ion, which is prone to react with nucleophilic sites on the DNA and forms furfuryl-modified DNA adducts. 13 fdG (Figure 1) and N 6 -furfuryl deoxyadenosine (fdA) are the main exocyclic Received: October 9, 2015 Published: December 9, 2015 Article pubs.acs.org/joc © 2015 American Chemical Society 502 DOI: 10.1021/acs.joc.5b02341 J. Org. Chem. 2016, 81, 502−511