**9. References**

382 Selected Topics in DNA Repair

sites [Tashiro et al., 2000]. RAD51 proteins have been identified in *Trypanosoma brucei* and *Plasmodium falciparum* parasites, which perform HRR to switch the expression of genes encoding surface membrane glycoproteins and generate antigenic variation [Conway et al., 2002; Freitas-Junior et al., 2000]. Furthermore, recombinational rearrangements are responsible for amplification of the multidrug resistance *pfmdr1* gene in *P. falciparum* [Triglia et al., 1991] demonstrating the relevance of HRR to generate genomic versatility and plasticity in protozoan parasites. Molecular analysis and functional assays confirmed that recombinant EhRAD51 is a *bonafide* recombinase that is able to catalyze specific ssDNA transfer to homologous dsDNA forming the three-stranded pairing molecule called Dloop structure. In addition, *E. histolytica RAD51* sequence conserves the typical architecture of RECA/RAD51 family members [Lopez-Casamichana et al., 2008]. Amino acid sequences multiple alignment of RAD51 orthologues from *E. histolytica, S. cerevisae, T. vaginalis*, *G. lamblia* and *P. falciparum* revealed that all these proteins share functional and structural conserved motifs (**Fig. 5C**). Each of them contains the putative polymerization motif (PM), which tethers individual subunits to form quaternary assemblies in human RAD51 protein [Bell, 2005]. We also identified the ATPase Walker A or phosphate binding loop (P-loop) and Walker B motifs residues, the ssDNA binding loops L1 and L2, as well as the ATP stacking motif or ATP cap at the C terminus, which are essential for nucleofilament assembling and ATP hydrolysis in RAD51/RECA-like recombinases [Shin

Protozoan parasites are continuously subjected to the effects of antiparasitic drugs and host immune system attacks, which can affect their genome stability and therefore, their survival. In order to maintain the integrity of their DNA molecules, parasites have developed several mechanisms that are efficient to detect and accurately repair damaged nucleotides. Bioinformatic analyses of fully sequenced genomes are useful to identify molecular machineries for DNA repair in protozoan parasites of clinical relevance such as *Entamoeba histolyica*, *Giardia lamblia*, *Plasmodium falciparum* and *Trichomonas vaginalis,*  which have a world-wide distribution with a high prevalence in developing countries. The computational data presented here provide new information on the evolution of DNA repair proteins and their potential relevance for DNA damage response in these major human pathogens. Future directions would include functional assays, as well as protein expression and protein-protein interactions analysis for the most relevant proteins, in order to contribute to the further elucidation of mechanisms regulating

rectangles) and DNA-binding domains (gray rectangles). **(B)**. Functional and structural domains of RAD50 proteins. Walker A (N terminus) and Walker B (C terminus) are marked in the ABC-ATPase domains (gray rectangles), while MRE11-binding sites flank Walker motifs (dark gray rectangles) and the CysXXCys hook domain (white rectangles) are labeled in the coiled-coil central regions. (**C)**. Functional and structural domains of RAD51 proteins. Polymerization motif (PM), as well as Walker A and B motifs, L1 and L2 regions and ATP cap appear as colored rectangles. Boxshade panels: black boxes, identical aa; grey boxes,

conserved substitutions.

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**7. Conclusions** 


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**17** 

*1,2Canada 3Ireland* 

**Mechanisms of Mutagenic** 

**DNA Nucleobase Damages and** 

*3School of Chemistry, National University of Ireland, Galway* 

**Their Chemical and Enzymatic Repairs** 

**Investigated by Quantum Chemical Methods** 

Eric A. C. Bushnell1, Jorge Llano2, Leif A. Eriksson3 and James W. Gauld1 *1University of Windsor, Department of Chemistry and Biochemistry, Windsor, Ontario 2Grant MacEwan University, Department of Physical Sciences, Edmonton, Alberta* 

A cells genetic information, its 'blueprint of life', is contained within its DNA. This biologically important molecule, however, can be attacked by high–energy ionizing radiation and oxidizing agents resulting in a range of possible damage. For instance, nucleobases can undergo chemical modifications or degradation such as oxidation, deamination, alkylation or be cleaved from the sugar-phosphate backbone. (De Bont & van Larebeke 2004; Friedberg et al. 2004; Hecht 1999; Kamiya et al. 1998; Labet et al. 2008a; Lindahl 1993; Lysetska et al. 2002; Neeley & Essigmann 2006; Rydberg & Lindahl 1982; Taylor 1994; Wang 2008) Similarly, the deoxyribose sugar moieties may also undergo various chemical modifications. These events can lead further to the formation of DNA– DNA or DNA–protein cross–links or DNA–strand breaks. (Kumar & Sevilla 2010; Lipfert et al. 2004) Importantly, damage to DNA can significantly affect its replication and transcription. This can ultimately result in cell apoptosis or protein mutations and

Experimentally, there have been numerous detailed *in vivo* and *in vitro* investigations into the processes and pathways involved in the damage of DNA. (See, for instance, Kumar & Sevilla 2010; Mishina et al. 2006, Wetmore et al. 2001) Radiolysis experiments with photometric, electrochemical and electron paramagnetic resonance detection, enzymatic inhibition and mutagenesis studies have identified a large number of reaction intermediates and rate constants for many damage and repair processes. For more in-depth reviews of experimental investigations on DNA damage processes the reader is also directed to relevant chapters in this present book. Unfortunately, however, many uncertainties and

Computational chemistry provides an alternate and also complementary approach for obtaining a deeper understanding of chemical processes. This is in part because it can not only be applied to systems that are amenable to experimental investigation but also to those

pathological diseases such as cancer. (Pages & Fuchs 2002)

questions still remain about DNA damage and repair.

**1. Introduction** 

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