Submitted by Geandra Rodrigues (geandrar@gmail.com) on 2018-01-10T14:27:33Z No. of bitstreams: 1 sirleiaparecidajulião.pdf: 1501615 bytes, checksum: c915a860117fdc2bf5cd1ba90fdab0b9 (MD5) / Approved for entry into archive by Adriana Oliveira (adriana.oliveira@ufjf.edu.br) on 2018-01-22T16:11:44Z (GMT) No. of bitstreams: 1 sirleiaparecidajulião.pdf: 1501615 bytes, checksum: c915a860117fdc2bf5cd1ba90fdab0b9 (MD5) / Made available in DSpace on 2018-01-22T16:11:44Z (GMT). No. of bitstreams: 1 sirleiaparecidajulião.pdf: 1501615 bytes, checksum: c915a860117fdc2bf5cd1ba90fdab0b9 (MD5) Previous issue date: 2017-08-11 / Lippia alba é uma espécie medicinal com ampla diversidade fenotípica, incluindo a composição do óleo essencial. A variação genética é provavelmente a principal causa dessa variação. A espécie foi descrita como um complexo poliploide com cinco números cromossômicos (2n=30, 38, 45, 60 e 90). Devido à importância econômica e à variação genética natural, essa espécie representa um excelente modelo em estudos sobre estabilidade genômica. Este trabalho teve como objetivo investigar a estabilidade genômica de 22 acessos naturais cultivados in vitro durante sete anos e em acessos poliploides sintéticos obtidos a partir da duplicação cromossômica de um acesso diploide natural usando colchicina. Para analisar a estabilidade do genoma de plantas cultivadas a longo prazo, foram analisadas quatro plantas (três mantidas in vitro e uma no campo) de 22 acessos. O tamanho do genoma foi verificado por citometria de fluxo e oito marcadores ISSR foram utilizados para verificara estabilidade em nível de sequencia de DNA. Para avaliar a estabilidade genômica após a poliploidização, onze plantas poliploides sintéticas, sendo 5 tetraploides (4X) e 6 mixoploides (2X / 4X) foram comparadas com a planta matriz diploide. As comparações foram baseadas no conteúdo de DNA, contagem cromossômica, marcadores moleculares ISSR e SSR e no perfil químico do óleo essencial. A comparação entre as plantas mantidas in vitro e as respectivas plantas mantidas no campo mostrou que 13 dos 22 acessos sofreram uma pequena redução no tamanho do genoma. Os marcadores ISSR detectaram polimorfismos na sequência de DNA variando de 1,61 a 33,87%. Somente três acessos não apresentaram bandas polimórficas. O número de bandas polimórficas entre os outros 19 acessos variou de um a 21. A análise da ploidia das plantas poliploides sintéticas realizada em folhas e raízes confirmou a estabilidade das plantas tetraploides. As plantas mixoploides apresentaram um único pico G1 correspondente a plantas triploides. A análise cromossômica revelou 60 cromossomos com 12 sítios de DNAr 45S nas plantas tetraploides e 9 sítios de DNAr 45S nos 45 cromossomos observados nas plantas triploides. Os marcadores ISSR mostraram polimorfismo entre a planta matriz diploide e as plantas poliploides sintéticas. A taxa de polimorfismo variou de 1,81 a 5,45% nas plantas tetraploides e de 43,63 a 56,36% nas plantas triploides. Alterações no tamanho dos alelos de microssatélites também foram detectadas. A planta matriz diploide apresentou dez alelos, três dos quais foram compartilhados com as plantas triploides e sete com as plantas tetraploides. Todas as plantas triploides apresentaram 13 alelos, sendo dez deles correspondentes a alelos novos. O número de alelos detectados nas plantas tetraploides variou de oito a 11 e o número de alelos novos como consequência da poliploidização variou de dois a quatro. O componente majoritário detectado no óleo essencial da planta matriz diploide e das plantas tetraploides foi o citral e nas plantas triploides foi o linalol. A instabilidade genômica detectada em L. alba após sete anos de cultura in vitro pode ser devido à consequência da instabilidade do genoma natural combinada com a cultura in vitro a longo prazo. Os efeitos da poliploidização que resultam em reorganização genômica e alterações fisiológicas podem explicar a variação observada nas plantas poliploides sintéticas. / Lippia alba is a medicinal species with a broad phenotypic diversity, including the essential oil composition. Genetic variation is probably the main cause of this variation. The species is a polyploid complex with five chromosome numbers (2n = 30, 38, 45, 60 and 90). Due to the economic importance and the natural genetic variation, this species represents an excellent model in studies on the genomic stability. This work aimed to investigate the genomic stability of 22 natural accessions grown in vitro for 7 years and in synthetic polyploid accessions obtained from the chromosome duplication of a natural diploid access using colchicine. To analyze the genome stability of long-term cultivated plants, four replicates (three maintained in vitro and one in the field) of 22 accessions were analyzed. The size of the genome was verified by flow cytometry and eight ISSR markers checked for stability in the DNA sequence. To evaluate the effect of polyploidization, eleven synthetic polyploid plants composed of 5 tetraploids (4X) and 6 mixoploids (2X/4X) were compared with the diploid parent plant. The comparisons were based on DNA content, chromosomal count, molecular markers ISSR and SSR, and chemical profile of the essential oil. The comparison between the plants maintained in vitro and the respective plants maintained in the field showed that 13 of the 22 accessions suffered a small reduction in the size of the genome. ISSR markers detected polymorphisms in the DNA sequence ranging from 1.61 to 33.87%. Only three accessions did not present polymorphic bands. The number of polymorphic bands among the other 19 accesses ranged from 1 to 21. Analysis of the ploidy of the synthetic polyploid plants carried out on leaves and roots confirmed the stability of the tetraploid plants. The mixoploid plants presented a single G1 peak corresponding to triploid plants. The chromosome analysis showed 60 chromosomes with twelve 45S rDNA sites in the synthetic tetraploids and nine 45S rDNA sites over the 45 chromosomes observed in the synthetics triploid plants. ISSR markers showed polymorphism between the diploid parent plant and synthetic polyploid plants. The polymorphism rate varied from 1.81 to 5.45% in the tetraploid plants and from 43.63 to 56.36% in the triploid plants. Changes in the size of the microsatellite alleles were also detected. The diploid parental plant presented 10 alleles, of which 3 were shared with the triploid plants and 7 with the tetraploid plants. All triploid plants had 13 alleles, 10 of which correspond to new alleles. The number of alleles detected in tetraploid plants ranged from 8 to 11 and the number of new alleles as a consequence of polyploidization ranged from 2 to 4. The major component detected in the essential oil of the parental diploid plant and the tetraploid plants was the citral and the triploid plants was the linalool. The genetic instability detected in L. alba after seven years of in vitro culture may be due to the consequence of natural genome instability combined with long-term in vitro culture. The effects of polyploidization that result in genomic reorganization and physiological changes may explain the variation observed in synthetic polyploid plants.

A via de sinalização da GTPase RhoA atua em diversos processos celulares. Para avaliar o comportamento de RhoA, após estresse causado por radiação ultravioleta, foram gerados clones mutantes que expressam RhoA em seu estado constitutivamente ativo e dominante negativo. Após exposição das linhagens à radiação ultravioleta, observou-se uma maior sensibilidade e um maior tempo de recuperação das linhagens quando a atividade de RhoA é reduzida. Estes prejuízos no reparo prejudicaram a proliferação e sobrevivência celular quando da deficiência na atividade de RhoA. Em linhagens deficientes na via de NER, percebemos que estas linhagens possuem uma capacidade ainda mais reduzida de reparo quando a atividade de RhoA é inibida. / The RhoA GTPase signaling pathway acts on many cellular processes. To evaluate this possible RhoA function after stress caused by ultraviolet radiation, mutant clones expressing RhoA in its constitutively active or dominant negative forms were generated. After exposure of the cells to ultraviolet radiation, cell lines showed a higher sensitivity and a delayed recovery capacity when the RhoA activity is reduced. The impaired repair reduced the cells proliferation and survival under RhoA deficiency. In cell lines deficient in NER pathway, we notice that these cell lines, have a further reduced ability to repair damaged DNA under RhoA inhibition.

Les membres de la famille SMC (Structural Maintenance of Chromosomes), présents dans tous les domaines de la vie, sont impliqués dans des processus allant de la cohésion des chromatides-sœurs jusqu’à la réparation de l’ADN. Chacun des membres de cette famille, composée de 6 membres (Smc1 à Smc6), s’associe avec un autre membre ainsi qu’à des sous-unités non-SMC pour former 3 complexes : cohésine, condensine et Smc5-6. L’implication du complexe Smc5-6 dans plusieurs aspects du maintien de l’intégrité génomique est bien démontrée. Néanmoins, une question fondamentale concernant ce complexe demeure encore sans réponse: comment peut-il être impliqué dans autant d’aspects de la vie d’une cellule? Encore à ce jour, il est difficile de répondre à cette question en raison du manque d’information disponible au sujet des activités biochimiques de ce complexe. C’est pourquoi l’objectif de ce travail consiste en la caractérisation biochimique du complexe Smc5-6. La biochimie de cohésine et condensine suggère diverses possibilités en ce qui a trait aux activités biochimiques du complexe Smc5-6. La première étape de mon projet fut donc d’élaborer une procédure pour la purification de Smc5 et Smc6 après surexpression en levure. Après plusieurs expériences, il apparut clair que les deux protéines possèdent une activité de liaison à l’ADN simple brin (ADNsb) ainsi qu’à l’ADN double brins (ADNdb) et que, même si les protéines peuvent se lier aux deux types d’ADN, elles possèdent une plus grande affinité pour l’ADNsb. De plus, ces expériences permirent de démontrer que l’interaction entre Smc5 ou Smc6 et l’ADNsb est très stable, alors que l’interaction avec l’ADNdb ne l’est pas. Suite à l’obtention de ces résultats, la seconde étape fut la détermination de la ou des partie(s) de Smc5 et Smc6 permettant la liaison à l’ADN. Pour répondre à cette question, une dissection moléculaire fut réalisée, suivi d’une caractérisation des différents domaines constituants Smc5 et Smc6. De cette façon, il fut possible de démontrer qu’il existe deux sites de liaison à l’ADN sur Smc5 et Smc6 ; le premier site se trouvant dans le domaine «hinge» ainsi que dans la région adjacente du domaine «coiled-coil» et le second au niveau de la tête ATPase des deux protéines. Bien que les deux domaines puissent lier l’ADNsb, il fut démontré qu’une différence majeure existe au niveau de leur affinité pour ce type d’ADN. En effet, le domaine «hinge» possède une affinité plus forte pour l’ADNsb que la tête ATPase. De plus, cette dernière est incapable de lier l’ADNdb alors que le domaine «hinge» le peut. L’identification des sites de liaison à l’ADN sur Smc5 et Smc6 permettra de créer de nouveaux mutants possédant un défaut dans la liaison à l’ADN. Ainsi, l’étude du complexe Smc5-6 durant la réparation de l’ADN in vivo sera facilité. / The Smc5-6 complex is part of the SMC (Structural Maintenance of Chromosomes) family and is involved in the maintenance of genome integrity. This complex is required for the replication and repair of DNA. Unfortunately, the DNA substrates recognized by the Smc5-6 complex are still unknown. To address this gap, I used a biochemical approach to purify and functionally characterize the core of the Smc5-6 complex represented by the two SMC proteins. Subsequently, I wanted to understand which part(s) of Smc5 or Smc6 mediate their binding to DNA. I show here that Smc5 and Smc6 bind to all types of DNA tested. Despite this ability to associate with several types of nucleic acids, they have a clear preference for single-stranded DNA (ssDNA). The ability of Smc5 and Smc6 to link DNA independently of each other suggests that both SMC proteins have the potential to target the Smc5-6 complex to its DNA substrates in vivo. Furthermore, the minimal length of ssDNA required for the binding of Smc5 or Smc6 is between 45 to 75 nucleotides. This length of ssDNA is shorter than the size of ssDNA intermediates created during DNA repair or replication reactions. In addition to having a preference for ssDNA, the binding of both SMC proteins to this type of DNA is stronger than their binding to double-stranded DNA (dsDNA). Finally, the molecular dissection of SMC proteins into functional domains revealed that there are two independent DNA-binding sites on each molecule of Smc5 or Smc6. The first region is located in the hinge domain, while the second region is located in the ATPase head of the protein. The affinity and selectivity of independent domains towards DNA substrates suggest a functional differentiation between the two DNA-binding sites of SMC molecules. Indeed, the hinge domain has a greater affinity for ssDNA than the ATPase head. In terms of selectivity, the hinge domain is capable of binding to dsDNA whereas the ATPase head cannot. Taken together, our identification of the DNA-binding domains on Smc5 and Smc6 will enable the creation of new mutants with a defect in their DNA-binding activity. Thus, the study of the Smc5-6 complex during DNA repair, in vivo, will be facilitated.

Chez les plantes, le génome plastidique est continuellement exposé à divers stress mutagènes, tels l’oxydation des bases et le blocage des fourches de réplication. Étonnamment, malgré ces menaces, le génome du plastide est reconnu pour être très stable, sa stabilité dépassant même celle du génome nucléaire. Néanmoins, les mécanismes de réparation de l’ADN et du maintien de la stabilité du génome plastidique sont encore peu connus. Afin de mieux comprendre ces processus, nous avons développé une approche, basée sur l’emploi de la ciprofloxacine, qui nous permet d’induire des bris d’ADN double-brins (DSBs) spécifiquement dans le génome des organelles. En criblant, à l’aide de ce composé, une collection de mutants d’Arabidopsis thaliana déficients pour des protéines du nucléoïde du plastide, nous avons identifié 16 gènes vraisemblablement impliqués dans le maintien de la stabilité génomique de cette organelle. Parmi ces gènes, ceux de la famille Whirly jouent un rôle primordial dans la protection du génome plastidique face aux réarrangements dépendants de séquences de microhomologie. Deux autres familles de gènes codant pour des protéines plastidiques, soit celle des polymérases de types-I et celle des recombinases, semblent davantage impliquées dans les mécanismes conservateurs de réparation des DSBs. Les relations épistatiques entre ces gènes et ceux des Whirly ont permis de définir les bases moléculaires des mécanismes de la réparation dépendante de microhomologies (MHMR) dans le plastide. Nous proposons également que ce type de mécanismes servirait en quelque sorte de roue de secours pour les mécanismes conservateurs de réparation. Finalement, un criblage non-biaisé, utilisant une collection de plus de 50,000 lignées mutantes d’Arabidopsis, a été réalisé. Ce criblage a permis d’établir un lien entre la stabilité génomique et le métabolisme des espèces réactives oxygénées (ROS). En effet, la plupart des gènes identifiés lors de ce criblage sont impliqués dans la photosynthèse et la détoxification des ROS. Globalement, notre étude a permis d’élargir notre compréhension des mécanismes du maintien de la stabilité génomique dans le plastide et de mieux comprendre l’importance de ces processus. / The plant plastidial genome is constantly threatened by many mutagenic stresses, such as base oxidation and replication fork stalling. Despite these threats, the plastid genome has long been known to be more stable than the nuclear genome, suggesting that alterations of its structure would have dramatic consequences on plant fitness. At the moment, little is known about the genes and the pathways allowing such conservation of the organelle genome sequences. To gain insight into these mechanisms, we developed an assay which uses ciprofloxacin, a gyrase inhibitor, to generate DNA double-strand breaks (DSBs) exclusively in plant organelles. By screening mutants deficient for proteins composing the plastid nucleoid on ciprofloxacin, we were able to identify 16 candidate genes, most likely involved in the repair of DSBs in plastid. Among these genes, those of the Whirly family of single-stranded DNA binding proteins are shown to be key factors in protecting the genome from error-prone microhomology mediated repair (MHMR). Two other family of proteins, the plastid type-I polymerases and the plastid recombinases, seem to be involved in the conservative repair pathways. The evaluation of the epistatic relationship between those two genes and the Whirly genes led us to define the molecular basis of MHMR and to propose that they might act as a backup system for conservative repair pathways. Finally, a non-biased screen, using 50,000 different insertion lines, allowed the identification of numerous genes that were already associated with ROS homeostasis, suggesting a link between DNA repair and ROS imbalance. Globally, our study shed light on the mechanisms that allow the maintenance of plastid genome, while explaining the importance of such conservation of the plastid genome.

The recent explosion of DNA sequence information has provided compelling evidence for the following facts. (1) Simple repetitive sequences-microsatellites and minisatellites occur commonly in the human genome and (2) these repetitive DNA sequences could play an important role in the regulation of various genetic processes including modulation of gene expression. These sequences exhibit extensive polymorphism in both length and the composition between species and between organisms of the same species and even cells of the same organism. The repetitive DNA sequences also exhibit structural polymorphism depending on the sequence composition. The functional significance of repetitive DNA is a well-established fact. The work done in many laboratories including ours has conclusively documented the functional role played by repetitive sequences in various cellular processes. Structural studies have established the sequence requirement for various non-B DNA structures and the functional significance of these unusual DNA structures is becoming increasingly clear. The structures that were characterised earlier purely from conformation point of view have aroused interest after the recent realisation that these structures could be formed in vivo when cloned in a supercoiled plasmid. The discovery of novel type of dynamic mutations where intragenic amplifications of trinucleotide repeats is associated with phenotypic changes causing many neurodegenerative disorders has provided the most compelling evidence for the importance of simple repeats in the etiology of these disorders. Secondary structures adopted by these simple repeats is a common causative factor in the mechanism of expansion of these repeats. This realisation prompted many investigations into the relationship between the DNA sequence, structure and molecular basis of dynamic mutation. Many experimental evidences have implicated paranemic DNA structures in various biological processes, especially in the regulation of gene expression. Earlier work done in our laboratory on the structure function relationship of repetitive DNA sequences provided experimental evidence for the role of paranemic DNA structure in the regulation of gene expression. It was demonstrated that intramolecular triplex potential sequences within a gene downregulate its expression in vivo (Sarkar and Brahmachari (1992) Nucleic Acids Res., 20, 5713-5718). Similarly the effect of cruciform structure forming sequences on gene expression was also documented. Sequence specific alterations in DNA structures were studied in our laboratory using a variety of biophysical and biochemical techniques. An intramolecular, antiparallel tetraplex structure was proposed for human telomeric repeat sequences (Balagurumoorthy, et al., (1994) J. Biol. Chem., 269, 21858-21869). The telomeric repeats are not only present at the end of chromosomes but they are also present at many interstitial sites in the human genome. Database search reveals that the human telomeric sequences as well as similar sequences with minor variations are present at many locations in the human genome. Telomeric repeats are GC rich sequences with the G rich strand protruding as a 3' end overhang at the end of chromosomes. When human telomeric repeats are cloned in a supercoiled plasmid, the C rich strand adopts a hairpin like conformation where as the G-rich strand extrudes into a quadruplex structure. However, the biological significance of these structures in vivo still remains to be elucidated completely. The role of a putative tetraplex DNA structure in the insulin gene linked polymorphic region of the human insulin gene in vivo in the regulation of expression of the insulin gene has been suggested. In this context, we have addressed the question whether the telomeric repeats when present within a gene affect its expression in vivol If so, what would be the possible mechanism? An attempt has been made to understand the effect of presence of telomeric repeats within a gene on its expression. The details of these studies have been presented in Chapter 2 of this thesis. Contrary to telomeric repeats which provide stability to the chromosomes, recently expansion of a GC rich dodecamer repeat upstream of cystatin B gene (chromosome 21q) has been shown to be the most common mutation associated with Progressive Myoclonus Epilepsy (EPM1) of Unverricht-Lundberg type. Two to three copies of the repeat (CCCCGCCCCGCG)n are present in normal individuals whereas the affected individuals have 30-75 copies of this repeat. The expression of cystatin B gene is reduced in patients in a cell specific manner. The repeat also shows intergenerational variability. The exact mechanism of expansion of this repeat is not known. In the case of trinucleotide repeat expansion, it is shown that the structure adopted by the repeat plays an important role in the mechanism of expansion and that some of the secondary structures adopted by trinucleotide repeats could be inherently mutagenic conformations. In order to understand the mechanism of expansion EPM1 dodecamer repeat, the work reported in this thesis was carried out with the following objectives. • To understand the structure of G rich and C-rich strands of EPM1 repeat. • To understand the variations in the structure with the increase in the length and its possible implications in the mechanism of expansion of EPM 1 repeat. Studies aimed with these objectives are presented in chapters 3, 4 and 5 of the thesis. Chapter 1 provides a general introduction to repetitive DNA, the various structures adopted by repetitive DNA sequences in the genome, the functional significance of the various simple repetitive DNA sequences in the genome has been presented. An account of trinucleotide repeat expansion and associated disorders, non-trinucleotide repeat expansions and associated disorders has been presented. The various non B-DNA structures adopted these repeats and their implications in the mechanism of expansion have been discussed. Chapter 2 describes in frame cloning of human telomeric repeats d(G3T2A)3G3 in the N-terminal region of β-galactosidase gene. The effect of such repeat Sequences on transcription elongation in vivo has been studied using E.coli as a model system. The 3.5 copies of human telomeric repeat sequences were cloned in the sense strand of plasmid pBluescriptllSK+ so as to create plasmid clone pSBQ8 and in the template strand of plasmid pBluescriptHKS+ so as to create clone pSBRQ8. One dimensional chloroquine gel shift assay indicated presence of an unwound structure in pSBQ8 and pSBRQ8. β-galactosidase activity assay suggested downregulation of the gene in vivo. In the case of plasmid pSBQ8 the difference in β-galactosidase activity was approximately 6 fold as compared to the parent plasmid pBluescriptIISK+ whereas in the case of pSBRQ8 the difference in β-galactosidase activity was approximately 8 fold as compared to the control pBluescriptIIKS+. The analysis of β-galactosidase transcript showed that full length transcript was formed in the case of pSBQ8. Full length transcript was not formed in the case of pSBRQ8. We propose that in the case of pSBQ8 the gene expression is inhibited in steps subsequent to transcription elongation. In the case of pSBRQ8, we propose that quadruplex structure may be formed by the template strand at the DNA level thereby blocking transcription elongation step. Chapter 3 describes studies aimed at understanding the structure of G-rich strand (referred to as G strand) of Progressive Myoclonus Epilepsy (EPM1) repeat. The sequence of the G strand of dodecamer EPM1 repeat is d(GGGGCGGGGCGC)n. Oligoucleotides containing one (12mer), two (24mer) and three(36mer) were synthesised. These oligonucleotides are referred to as dG12, dG24 and dG36 respectively. Structural studies were carried out using CD spectroscopy, UV melting, non-denaturing gel electrophoresis and chemical and enzymatic probing. The G strand oligonucleotides showed enhanced gel elecrophoretic mobility in the presence of monovalent cations KCl and NaCl. Oligonucleotide dG12 also showed retarded species on non-denaturing gel in the presence of 70mM KCl indicating intermolecular associations. Oligonucleotides dG24 and dG36 predominantly formed intramolecular structures which migrated anomalously faster than the expected size. The CD spectrum for dG12 showed an intense positive band at 260nm and a negative band at 240nm in the presence of KCl indicative of an intermolecular, parallel G quartet structure. The CD spectra of dG24 and dG36 showed 260nm positive peak, 240nm negative peak along with a positive band around 290nm. This is indicative of folded back structure. These findings support the results of non-denaturing gel electrophoresis of G strand oligonucleotides. The UV melting profiles suggested increase in the stability with the increase in the length. These structures were further characterised by PI nuclease and chemical probing using DMS and DEPC. The structural studies with G-rich strand of EPM1 dodecamer repeat showed that this repeat motif adopts intramolecularly folded structures with increase in the length of the repeat thereby favouring slippage during replication. Chapter 4 deals with the studies aimed at understanding the structure at acidic pH of C-rich strand (referred to as C strand) of Progressive Myoclonus Epilepsy (EPM1) repeat. The sequence of the C strand of dodecamer EPM1 repeat is d(CCCCGCCCCGCG)n. The C rich oligonucleotides are known to form a four stranded structure called i-motif at acidic pH involving intercalated base pairs. The i-motif consists of two parallel stranded, base paired duplexes are arranged in an antiparallel orientation. Since, the base pairs of one base paired duplex intercalate into those of the other duplex, the structure is called as i-motif. We have investigated structure of C strand of EPM1 repeat by circular dichroism (CD), native polyacrylamide gel electrophoresis and UV melting. Oligonucleotide dC12 showed two bands of which the major band was retarded on the native gel (pH 5.0) at low temperature suggesting that dC12 predominantly formed intermolecular structure, Oligonucleotides dC24 and dC36 migrated anomalously faster than the expected size indicating formation of compact, intramolecularly folded structures. Circular dichroism studies indicate that, all the oligonucleotides displayed an intense positive band near 285nm, a negative band around 260nm with a cross over at 270nm, This is a characteristic CD signature for an i-motif structure and reflects the presence of secondary structure due to formation of hydrogen bonded pairs between protonated cytosines. All the C strand oligonucleotides showed hyperchromism at 265nm, which is an isobestic wavelength for C protonation. Studies described in this chapter suggest an intramolecular i-motif structure for dC24 and dC36 and an intermolecular i-motif for oligonucleotide dC12. In addition, it was interesting to note that inspite of the presence of G residues, the stretch of C residues could adopt i-motif structure. Although these structures are formed at an acidic pH, it is indicative of formation of possible intramolecularly folded structure. Many reports have suggested the possibility of cytosine rich sequences adopting i-motif structure even at neutral pH. In order to test this possibility, structural studies were carried out on the C strand EPM1 oligonucleotides at pH 7.2 in the presence of 70mM NaCl. These studies have been described in Chapter 5. The investigations were done using CD spectroscopy, UV melting, native polyacrylamide gel electrophoresis, and chemical probing using hydroxylamine and PI nuclease. These studies indicate that all the C strand oligonucleotides form intramolecular, hairpin structure at physiological pH. All the three C strand oligonucleotides migrated anomalously faster on the native gel indicating the presence of a compact structure. The CD spectra at pH 7.2 showed a blue shift as compared to those at pH 5.0. This indicated absence of base pairs. The hydroxylamine chemical probing suggested presence of G-C Watson-Crick base pairs. The loop residues of the folded back hairpin structures were probed with PI nuclease. The C strand oligonucleotides showed possibility of formation of multiple hairpin structures with the increase in the length of the repeat. The propensity to form hairpin structures suggests a possibility of formation of slip loop structures during the replication process thereby promoting expansion of this repeat. Formation of folded back hairpin like structures is significant in terms of mechanism of expansion of this repeat. Chapter 6 is devoted to concluding remarks highlighting the significance of the experimental results presented in this thesis and their possible biological implications in the light of contemporary research.