Academic literature on the topic 'Hybridized induced polymorphism'

During development of a novel detection method for the UDP-glucuronosyl transferase 1A1 (UGT1A1)*28, the fluorescence intensity of a dye conjugated to cytosine (C) at the end of a DNA strand decreased upon hybridization with guanine (G). This phenomenon is referred to as photoinduced electron transfer (PeT). Using this phenomenon, we devised a method for the naked-eye detection of UGT1A1*28 (thymine-adenine (TA)-repeat polymorphism). Fluorescently labeled single-stranded DNA (ssDNA) oligonucleotides (probes) were designed and hybridized with complementary strand DNAs (target DNAs). Base pair formation at the blunt end between fluorescently labeled C (probe side) and G (target side), induced dramatic fluorescence quenching. Additionally, when the labeled-CG pair formed near the TA-repeat sequence, different TA-repeat numbers were discriminated. However, obtaining enough target DNA for this probe by typical polymerase chain reaction (PCR) was difficult. To enable the practical use of the probe, producing sufficient target DNA remains problematic.

4111 Introduction: A frequent polymorphism of the type I transforming growth factor beta receptor (TGFBR1) is TGFBR1*6A (6A), which has a deletion of 3 CGC triplets coding for alanine within a 9-alanine (9A) repeat of TGFBR1 exon 1. 6A may act as a tumor susceptibility allele through switching TGF-beta growth inhibitory signals into growth stimulatory signals and also appears to be acquired in some cases by primary colon cancers and their liver metastases. Our aim in this study was to compare the gene expression profiles of colorectal tumors bearing the 6A and the more common 9A genotypes to discover pathways that might be differentially induced by the 6A polymorphism. Methods: 28 colorectal tumors with matched synchronous metastases and 23 non-metastatic colorectal tumors were analyzed for TGFBR1 exon 1 genotype by a PCR-based assay. Nine metastatic and 10 non-metastatic tumors were analyzed by gene expression microarrays. Following microdissection of paraffin-embedded specimens, RNA was isolated, amplified, labeled, and hybridized to Affymetrix U133 Plus 2.0 GeneChips. Results: Among the 28 primary metastatic tumors, 19 were 9A (68%), 8 were 9A/6A heterozygotes (29%) and 1 was a 6A homozygote (3%). There was 100% genotype correspondence with the matched metastases. Among the 23 non-metastatic tumors, 18 were 9A (78%), 3 were heterozygotes (13%) and 2 were 6A/6A (9%). Microarray analysis showed 578 differentially expressed genes in the metastatic tumors and 467 in the non-metastatic tumors between the 6A and 9A genotypes (p<0.01). Significant pathway deregulation between 9A and 6A genotypes included estrogen receptor signaling and histidine metabolism in the non-metastatic tumors and B cell receptor, GM-CSF, SAPK/JNK and IL-4 signaling in the metastatic tumors. Conclusion: Microarray analysis shows differentially expressed genes in the 6A genotype compared to 9A, with different deregulated pathways in metastatic and non-metastatic tumors. This alludes to 6A-specific downstream signaling effects, which may contribute to tumor development and progression. No significant financial relationships to disclose.

Abstract Very few mutations derived from Mutator maize lines have been studied at the molecular level. The variety of Mu elements that can induce mutations, the relative frequency of mutant induction by insertion of a given class of Mu elements or by a Mu-induced genomic rearrangement, a possible intragenic insertion site specificity, and the molecular nature of reversion events are all unknown in the Mutator system. To address these questions, we have isolated several partially or fully inactivated bronze alleles from Mutator maize lines and structurally characterized them by gel blot hybridization of genomic DNA. The mutations were induced in three parental Bronze alleles which differ by polymorphisms flanking the coding region. Each of the 14 inactivated bronze mutants characterized was found to contain an insert which cross-hybridized with the transposable element Mu1. Detailed maps of 11 of these alleles revealed a 1.4-kb insert with restriction sites characteristic of Mu1. These Mu1 insertions were found dispersed throughout both of the Bronze exons and in either orientation relative to Bronze transcription. Stable and somatically unstable (mutable) mutant alleles differed with respect to the covalent modification of restriction sites within the inserted Mu1 element. Several germinal revertants of one mutable bronze allele, bzMum4, were isolated. These all were associated with excision of the Mu1 element from the affected locus.

Abstract Background: For most patients with MDS, the disease-associated molecular abnormalities are unknown, which contributes to diagnostic uncertainty and has limited development of effective therapies. Chromosomal deletions such as del(5q) or monosomy 7 are more common than translocations in MDS, but balanced translocations are more likely to be pathobiologically informative. Here we report cloning of an MDS-associated translocation that revealed a novel recurrent molecular abnormality. Methods: We first studied a 71-year old man who presented with MDS and t(6;9)(p21.3;q34) as an isolated chromosomal abnormality in 18 of 20 metaphases. FISH assays for DEK/CAN and ABL rearrangements were unrevealing. We generated somatic hybrid murine/human cell lines from a buffy coat; microdissected and amplified derivative chromosomes; and hybridized to 6p/9q custom comparative genomic hybridization (CGH) arrays. The CGH results considerably narrowed the 6p and 9q breakpoints, which were then amplified by long-range PCR and sequenced to define the rearrangement. Results: The IER3 gene (Immediate Early Response 3; also known as IEX-1) at 6p21.3 was found to be separated from its upstream regulatory elements in this rearrangement and translocated to a transcript-poor region of 9q. RT-PCR confirmed marked downregulation of IER3 expression in the patient compared to healthy controls. IER3 is a plausible candidate for involvement in MDS because of its known role in regulating death receptor-induced apoptosis, interaction with NF-κb pathways, and its importance in response to genotoxic stresses such as ionizing irradiation. We then identified archival bone marrow cell pellets from 204 additional patients with various clonal hematological disorders and chromosomal rearrangements involving 6p21 or 6p22 (i.e., translocations, inversions, deletions, or additions), and designed a splitsignal FISH probe set to assay IER3. FISH results were abnormal in 8 additional patients (9/205 pts total abnormal, 4.4%): 3 split signals and 6 amplifications (one patient had both abnormalities); all 8 patients had MDS and 6p rearrangements as part of a more complex karyotype. FISH studies in MDS patients without 6p rearrangements are ongoing. RTPCR in MDS patients without 6p rearrangements demonstrated down-regulation of IER3 by &gt;2-fold in 38% of patients (67% lower-risk) and up-regulation in 12% of patients (50% higher-risk) when compared to the mean for healthy controls. Direct sequencing of the IER3 coding region and the promoter region in 30 patients without 6p rearrangements revealed no point mutations, but the prevalence of non-synonymous single nucleotide polymorphism rs3094124 (p.A127P) was higher than expected in patients (variant in 28.3 % of MDS alleles vs. 8.6% of 116 HAP-CEU controls, p=0.0015). IER3−/− mice are known to have hypertension, cardiac hypertrophy, and epithelial proliferation, but are not anemic (Sommer SL et al J Appl Physiol 2006). We performed methylcellulose hematopoietic colony growth assays using bone marrow mononuclear cells from IER3−/− mice and wildtype controls, and noted no differences in BFU-E, CFU-E, and CFU-GM growth under unstressed conditions. Studies of IER3 expression induction under stressed conditions in primary MDS cells are ongoing. Conclusion: IER3 rearrangements represent a novel clonally-restricted recurrent genetic abnormality in MDS. Dysregulation of IER3 expression is common in MDS, even in patients without 6p rearrangements. This is the first time IER3 has been linked to human disease. Clarification of the role of IER3 in MDS is likely to yield new insights into MDS pathobiology.

Abstract Background The level of distorted erythrocytes due to polymerization of hemoglobin S in sickle cell disease (SCD) (Science 1949;110:543) is a major determinant of the severity of hemolysis and microvascular occlusion (Lancet 2010;376:2018). Erythropoietin (EPO) is elevated in SCD due to hemolytic anemia and a related increase in hypoxia-inducible factors (HIFs) (Eur J Haematol 2007;78:183). Hydroxyurea (HU) is widely used in the treatment of SCD. HU inhibits ribonucleotide reductase (Semin Oncol 1992;19(3 Suppl 9):1-10) and promotes γ globin synthesis thereby increasing HbF-containing erythrocytes (F cells) while suppressing sickle β hemoglobin production (J Clin Invest 1984;74:652 and 2003;111:231). Increased level of F cells reduces hemolysis and ameliorates clinical complications in SCD. We and others have observed an increase in serum EPO level with HU treatment in SCD despite an increase in the hemoglobin concentration, and we hypothesized that this may be due to the known increased affinity of hemoglobin F for oxygen and related tissue hypoxia (Blood 2009;114:4639). Methods Messenger RNA from peripheral blood mononuclear cells (PBMCs) was profiled using Affymetrix Human Exon 1.0 ST Array. Hypoxic transcriptional alteration was defined in 15 Chuvash polycythemia (CP) patients vs. 17 control individuals. CP leads to constitutive up-regulation of HIFs in the absence of anemia or hypoxia. Transcriptional alteration in SCD was determined in 13 HbSS subjects without HU treatment vs. 16 control individuals, and that induced by HU treatment was determined in 19 HbSS subjects with vs. 13 without HU treatment. For meta-analysis on serum EPO concentration, genomic DNA isolated from PBMCs was hybridized to the Illumina Human 610-Quad SNP array. Genotypes were imputed to 1000 genomes project phase 1 data. A linear regression model was applied adjusting for age, gender, hemoglobin concentration, and HU treatment. Results Gene expression changes by HbSS highly correlated with those associated with homozygous VHLR200W (Pearson's r=0.79, Figure 1A). At 5% false discovery rate (FDR), expression levels of 377 genes were altered in both VHLR200W homozygotes and HbSS by >1.2 fold. For these hypoxic genes, the correlation of expression changes between HbSS and homozygous VHLR200W reached r=0.97 (Figure 1B). In contrast to our hypothesis, HU treatment in general suppressed expression changes induced by HbSS (r=-0.85, Figure 1C), especially for the hypoxic genes (r=-0.95, Figure 1D). In VHLR200W homozygotes, 62 of the hypoxic genes correlated with plasma EPO levels (adjusted P<0.05, n=42). These EPO-correlated genes were the most strongly up-regulated hypoxic genes in HbSS (red points in Figure 1B) and also the most strongly suppressed by HU treatment (red points in Figure 1D). Consistent with previous observations, we found that EPO was elevated by HU treatment in two SCD cohorts, and this persisted after adjusting for covariates including hemoglobin concentration which reflects hypoxic as well as inflammatory and hemolytic responses: Walk-PHaSST (β=0.49, P=2.5×10-15, n=586) and PUSH children (β=0.34, P=2.5×10-7, n=387). This observation suggests that biological signals independent of hypoxic regulation may contribute to EPO production under HU treatment. In a meta-analysis for the Walk-PHaSST and PUSH children cohorts, SNP rs60684937, located within the first intron of MAP2K6, an upstream regulator of HIF signaling (Mole Cell Biol 2005; 25:4853), was significantly associated with EPO levels at genome-wide significance (combined P=3.5×10-8). The C allele of the SNP decreased EPO levels in both Walk-PHaSST (β=-0.30, n=388) and PUSH children (β=-0.24, n=249) cohorts. This association was validated in an additional 89 SCD patients from the Howard cohort (β=-0.39, P=0.011). Further investigations are needed to determine whether the causal polymorphism affects protein function or gene regulation of the nearby genes. Discussion Our study demonstrates a prominent release from hypoxic transcriptional responses by HU treatment in SCD despite an increase in serum EPO, a defining characteristic of an up-regulated hypoxic response. Our study hypothesizes that hypoxia-independent signals trigger EPO production in the setting of HU therapy and it identifies a potential genetic determinant in this alternative pathway. Figure 1. Figure 1. Disclosures No relevant conflicts of interest to declare.

Barley yellow dwarf virus (BYDV) resistance has been transferred to wheat from a group 7 chromosome of Thinopyrum (Agropyron) intermedium. The source of the resistance gene was the L1 disomic addition line, which carries the 7Ai-1 chromosome. The resistance locus is on the long arm of this chromosome. BYDV resistant recombinant lines were identified after three or more generations of selection against a group 7 Th. intermedium short arm marker (red coleoptile) and selection for the presence of BYDV resistance. One recombinant line produced by ph. mutant induced homoeologous pairing and 14 recombinant lines induced by cell culture have been identified. Resistance in seven of the cell culture induced recombinants has been inherited via pollen according to Mendelian segregation ratios for up to eight generations. Meiotic analysis of heterozygotes indicates that the alien chromatin in the cell culture induced recombinants is small enough to allow regular meiotic behaviour. The ph-induced recombinant was less regular in meiosis. A probe, pEleAcc2, originally isolated from Th. elongatum and that hybridizes to dispersed repeated DNA sequences, was utilised to detect Th. intermedium chromatin, which confers resistance to BYDV, in wheat backgrounds. Quantification of these hybridization signals indicated that the translocations involved a portion of alien chromatin that was smaller than the complete long arm of 7Ai-1. Restriction fragment length polymorphism analysis confirmed the loss of the short arm of 7Ai-1 and indicated the retention of segments of the long arm of 7Ai-1. Two 7Ai-1L DNA markers always assorted with the BYDV resistance. A third 7Ai-IL DNA marker was also present in seven of eight recombinants. In all recombinants except TC7, the 7Ai-1L markers replaced the 7DL markers. None of the wheat group 7 markers was missing from TC7. It is concluded that all the resistant lines are the result of recombination with wheat chromosome 7D, except line TC7, which is the result of recombination with an unidentified nongroup 7 chromosome.Key words: Triticum, Agropyron, alien genes, translocation, somatic recombination, luteovirus.

Abstract There is a high background risk of venous thrombotic events (VTE) in patients with Multiple Myeloma (MM) and this is significantly increased following treatment with Thalidomide. The risk may be mediated by the production of a prothrombotic state, via an angiopathic mechanism, or alternatively it may arise from the release of prothrombotic factors from dying myeloma cells targeted by the treatment. No unifying evidence of a prothrombotic state has been demonstrated to date and it remains important to understand the mechanism underlying VTEs in order to prevent them effectively. Inherited genetic variants in the form of SNPs can affect the behaviour of clotting factors. These SNPs are functional and well characterised in the coagulation system and we have used them to analyse the mechanism underlying thalidomide induced VTE. As part of the Bank On A Cure TM project we have carried out an analysis of SNPs in 11 genes: GPIIA, ITGA, MTHFR, MTR, PPARG2, TFP1, VCAM, factor V, HABP2, prothrombin and THDB in a case series of 90 patients treated with thalidomide, with and without DVTs. This study showed a significant association with MTHFR and factor V polymorphisms. In order to validate and extend these initial observations we carried out an analysis of a second nested case control study using 131 Myeloma patients from within the MRC Myeloma IX trial, comprising 47 cases with a VTE and 94 age and sex matched controls exposed to the same treatment. We used a SNPlex panel containing 16 functional venous thrombosis associated SNPs, all of these functional polymorphisms have reported mechanisms and biology. We looked at polymorphisms in the genes: fibrinogen A (Ala331Thr), B (-455G&gt;A, Lys478Arg) and G polypeptides (His140Tyr); Coagulation factors V(Arg534Gln), VIII (Glu1260Asp), IX(Ala194Thr), XI (Phe339Cys) and XII(-4G&gt;T); PROCR(Gly219Ser); prothrombin(19911A&gt;G ,20210G&gt;A); MTHFR(Glu429Ala, Ala222Val); Serpine1(-844G&gt;A) and TFPI(Met292Val). We have typed our selected SNPs using the SNPlex™ Genotyping System, which is based on the oligonucleotide ligation/PCR assay with a universal fluorescently labeled ZipChute™ probe detection. The probes are hybridized to complementary ZipCode™ sequences that are part of genotype-specific amplicons. Probes are eluted and detected on a Applied Biosystems 3130x DNA Analyser. This approach is an attractive alternative to existing genotyping methodologies, as it requires only three unlabeled probes per SNP, and consumes very little gDNA. The data analysis on the polymorphisms frequencies is ongoing to examine associations of thalidomide treatment with VTE events and will be presented. These datasets will allow a better definition of the pathogenesis of thalidomide related VTE, so that we can intervene therapeutically in a rational fashion.

Abstract Objective: A chromosomal translocation plays an important role on the leukemia-generation from the normal hematopoietic cells. Various kinds of translocation-patterns and -partners have been reported; however, a typical translocation has been reported like AML-1 and MTG8 in acute myelogenous leukemia (AML) (M2), and PML and RARα in AML (M3). This implies that some common mechanism exists on the chromosomal double strand breaks and the generation of translocations. We make a hypothesis that, when normal immature cells come into a maturation process, a specific event may occur on DNA level to induce irreversible changes toward cell-death. And a target region for the irreversible change may be the near site to chromosomal translocations. We compared the digested fragment-size for restriction-endonucleases using southern blotting among hematopoietic cell lines, normal bone marrow immature progenitor cells and normal blood mature neutrophils. Materials and Methods: Bone marrows and bloods were obtained from informed healthy persons, and mononuclear cells were prepared after Ficoll-Paque sedimentation method, and neutrophil-rich fractions were prepared with density gravity centrifugation and hypotonic RBC lyses method. Various kinds of human cell lines, cultured in DMEM with 10% FCS, were also prepared. High molecular weight DNA was extracted from these cells, and they were digested with several kinds of restriction endonucleases. After electrophoresis, the digested DNA was transferred to a nitrocellulose membrane, and southern blot-hybridization was examined. The probe used was AML-1, MTG-8, PML, and RARα, in which the 5′ and 3′ breakpoint regions observed in chromosomal translocations were selected, respectively. Results and Discussion: No changes on the blotted fragment-size were observed among in the cultured cell lines, bone marrow immature mononuclear cells, and blood mononuclear cells; however, when 5′-PML probe was hybridized after DNA was digested with HindIII, the observed blot size was changed between normal immature myeloid progenitor cells and normal blood mature neutrophilic granulocytes. This change was not due to the personal polymorphism. These observations indicate that when myeloid cells become mature to neutrophilic granulocytes, some change occurs at DNA level. PML works on the maintenance of nucleobody for cell division, and it is very important to determine whether PML gene is maintained in neutrophilic granulocytes. We now prepare a genomic library from blood neutrophils to isolate the target clone, and determine DNA sequence near at the HindIII site to identify the modification of DNA during maturation of myeloid cells.

Cytogenetic studies in Triticum monococcum (2n = 2x = 14) are nonexistent. To initiate such investigations in this species, a series of primary trisomics was generated from autotriploids derived from crosses between induced autotetraploids and diploids. All trisomics differed phenotypically from their diploid progenitors. Only two of the seven possible primary trisomic types produced distinct morphological features on the basis of which they could be distinguished. The chromosomes in the karyotype were morphologically very similar and could not be unequivocally identified using standard techniques. Therefore, C-banding was used to identify the chromosomes and trisomics of this species. Ag–NOR staining and in situ hybridization, using rDNA probes, were used to substantiate these identifications. A comparison of the C-banding patterns of the chromosomes of T. monococcum with those of the A genome in Triticum aestivum permitted identification of five of its chromosomes, viz., 1A, 2A, 3A, 5A, and 7A. The two remaining chromosomes possessed C-banding patterns that were not equivalent to those of any of the chromosomes in the A genome of the polyploid wheats. When one of these undesignated chromosomes from T. monococcum var. boeoticum was substituted for chromosome 4A of Triticum turgidum, it compensated well phenotypically and therefore genetically for the loss of this chromosome in the recipient species. Because this T. monococcum chromosome appeared to be homoeologous to the group 4 chromosomes of polyploid wheats, it was designated 4A. By the process of elimination the second undesignated chromosome in T. monococcum must be 6A. Analysis of the trisomics obtained led to the following conclusions. (i) Trisomics for chromosome 3A were not found among the trisomic lines analyzed cytologically. (ii) Primary trisomics for chromosomes 2A, 4A, 6A, and 7A were positively identified. (iii) Trisomics for the SAT chromosomes 1A and 5A were positively identified in some cases and not in others because of polymorphism in the telomeric C-band of the short arm of chromosome 1A. (iv) Trisomics for chromosome 7A were identified on the basis of their distinct phenotype, viz., the small narrow heads and small narrow leaves. Because rRNA hybridizes lightly to nucleolus organizer regions on chromosome 1A and heavily to nucleolus organizer regions on chromosome 5A, our results indicate that trisomics in line 50 carry chromosome 1A in triple dose and trisomics in lines 28 and 51 carry chromosome 5A in triplicate. Variable hybridization of the rDNA probe to nucleolus organizer regions on chromosomes in triple dose in lines 7, 20, and 28 precluded the identification of the extra chromosome in these lines. Cytogenetic methods for unequivocally identifying trisomics for chromosomes 1A and 5A are discussed. Thus six of the series of primary trisomics have been identified. Telotrisomic lines are also being produced.Key words: Triticum monococcum, trisomics, C-banding, Ag-NOR staining, in situ hybridization, rDNA probes, plant morphology.

Abstract The expression profile of a number of genes in the rat mesocecum linked to sickle (SS) red blood cell (RBC) adhesion was examined by microarray analysis. The abnormal adherence of SS RBC to the vascular endothelium has been proposed to play an important role in vaso-occlusion in a double capacity; first, by actual physical blockage of the post capillary venules and, second, by inducing the expression of pleiotropic genes that could lead to further modification of the SS phenotype. The goals of these experiments were to identify these pleiotropic genes expressed upon adhesion of SS RBC, to understand how they contribute to the SS phenotype and, to identify potential targets for therapy. The rat mesocecum preparation was prepared as described (Kaul et al, Blood95:368, 2000) and platelet activating factor (PAF) was used to induce endothelial adhesion receptors to accentuate human SS RBC binding. Rat cecum/ mesocecum RNA was prepared by Qiagen RNeasy mini-kit and fluorescent labeled cDNA hybridized to 32K oligonucleotide microarrays followed by analysis using Gene Pix Pro 4.1. The effect of SS RBC perfusion on PAF-treated tissues vs untreated tissues was compared to PAF-only tissues vs untreated tissues using hierarchical clustering. SS RBC adhesion was analyzed as a function of venular diameter and was significantly different (p&lt;0.00001) in the PAF treated tissues as revealed by a significantly higher Y-intercept (work quoted above). Of the 533 transcripts that were up-regulated and 353 transcripts that were down-regulated more than 2 fold, 68 were up-regulated and 32 were down-regulated more than 4-fold; of this subset, 91 transcripts were compared by Cluster analysis. Many of the up-regulated genes detected in the PAF treated SS RBC adherent tissues were associated with inflammation such as phospholipase A2, group IIA; glutathione peroxidase 2; sialyltransferase 4C; and integrin beta 4. Interestingly, a number of proteasome subunits and ubiquitin D were also highly up-regulated; these genes were only present in the SS RBC perfused PAF treated mesocecum and could then be considered potential targets for specific therapies e.g. proteasome inhibitors. Recent studies also indicate that the ubiquitin system controls NF-kappaB pathways that, in turn, control integrin expression that can increase cell adhesion. The genes that were down-regulated included apolipoprotein B; cytochrome P450 Cyp4b1; cyclin G associated kinase; and metallothionein 2 (MT2). The down-regulation of MT2 is interesting because it is known to be highly regulated in response to the plasma zinc concentration; due to the chronic inflammatory/oxidative condition present in SS disease, zinc may be depleted and feedback negatively on MT2 synthesis. SS RBC adhesion however, not just PAF treatment, is necessary for MT2 downregulation and may, paradoxically, increase zinc availability since MT expression and zinc depletion are inversely correlated. Overall, the results suggest that SS RBC adhesion regulates a number of mesocecum genes involved in the inflammatory response, regulation of oxidative damage, increased intracellular protein degradation, decreased vesicular transport and regulation of zinc ion concentration. These pleiotropic genes are candidates for epistatic (modifier) genes if found to be polymorphic in different individuals and ethnicities. Enhancing or interfering with these specific genes or metabolic pathways may open up new therapeutic strategies for SS disease.

The thesis entitled “High-Resolution Charge Density Studies on Electronic Nature of Weak Interactions and Correlation of Molecular Conformation with Packing in Solid State” consist of five chapters. Chapter 1 is a brief introduction to the methodologies and techniques utilized in modelling electron densities and the topics relevant to the work. The subsequent four chapters are divided into two parts-Part A and Part B. Part A has two chapters that discusses the electronic nature of unexplored weak intermolecular interactionspnicogen bonding in nitrogen atom and hydrophobic interactions between methyl groups in molecular crystals. Part B also contains two chapters that investigates the symbiotic relation of molecular conformation and packing in solid state in two unique cases-hybridized induced polymorphism observed in sulfa drug acetazolamide and unusual asymmetry observed in overcrowded Octachloronaphthalene molecule Part A: Electronic Nature of Weak Interactions Chapter 2 discusses the electron density features of pnicogen bond between nitrogen as an electrophile and chlorine as a nucleophile from experimental and theoretical charge density analyses of 2-amino-5-nitropyridine and chloroacetic acid complex. The charge transfer nature of pnicogen bonding due to overlap between donor lone pair orbitals of Cl atom and antibonding N-C sigma star orbital has been demonstrated from gas phase NBO calculations. Presence of sigma hole on N atom is further confirmed from 3D deformation maps and electrostatic maps. Topological description from AIM analysis and energy estimation based on EML method proves this interaction to be weak in nature and comparable to the strength of carbon bonding, type II F•••F halogen bonding. Detailed Cambridge Structural Database (CSD) analysis reveals that planar N atoms have the maximum propensity to participate as electrophile in pnicogen bonding. Chapter 3 reports the frequent occurrence of methyl•••methyl hydrophobic interactions in the solid-state from CSD study with a detailed analysis of these interactions in a series of cocrystals of biologically active molecules such as caffeine, theophylline and tetramethylpyrazine using experimental X-ray charge density analysis, variable-temperature crystallography and solidstate NMR. The visualization of accurate electron density distribution in the interaction region reveals that they are stabilized by the minimized electrostatic repulsion and maximized dispersion forces. This chapter further proves methyl•••methyl HI as a group•••group interaction with a pronounced torsional vibration for the hydrophobic methyl groups which leads to a significant entropic contribution towards its stability. A characteristic C-13 ssNMR up-field chemical shift was found to be associated with these methyl•••methyl interactions in the crystal state. Part B: Correlation of Molecular Conformation with Packing Chapter 4 discusses a new type of polymorphism called hybridized induced polymorphism in connection with the unusual phenomenon of the formation of kinetic form as against the thermodynamic form on slow cooling of boiling aqueous solution of diuretic drug Acetazolamide. Experimental charge density analysis aided with ab initio calculations have investigated the local electron density at the amino region of both polymorphs. A series of crystallization experiments of AZM in aqueous medium were conducted. The boiling solution was ramped down at different rates of cooling; rapid cooling in liquid nitrogen, ambient cooling to room temperature, controlled cooling at (10°C/hr, 7°C/hr and 5°C/hr) to room temperature. PXRD analysis reveals the kinetic form occurs only when the cooling rate is quite slow (7°C/hr and 5°C/hr). The occurrence of both polymorphs from aqueous solution of AZM under different crystallization conditions is rationalized in terms of hybridization induced polymorphism. Chapter 5 investigates electron density distribution in an overcrowded aromatic molecule, Octachloronaphthalene (OCN) by charge density analysis to unravel several unexplored factors responsible for steric hindrance. The topological features of the enigmatic peri interactions contributing to steric overcrowding are qualified and quantified from experimental and theoretical charge density studies. A new facet in the fundamental understanding of peri interactions is revealed by NCI (Non-Covalent Interaction) analysis. The potential role of these interactions in deforming the molecular geometry and subsequent effect on aromaticity are substantiated from NICS (Nuclear Independent Chemical Shift) and QTAIM (Quantum Theory of Atoms in Molecules) calculations. The eye-catching dissimilarity in the out-of-plane twisting of OCN renders the molecule in an asymmetric geometry in the crystalline phase as compared to symmetric geometry in the optimized solvated phase. This is uniquely characterised by their molecular electrostatic potential (MESP) respectively and is explained in terms of conflict between two opposing forces- peri interactions and symbiotic intermolecular Cl•••Cl and Cl••• contacts.