Thesis (Ph. D.)--Ohio State University, 2007. / Title from first page of PDF file. Includes bibliographical references (p. 239-251).

Chung Ka Wing. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2004. / Includes bibliographical references (leaves 151-162). / Abstracts in English and Chinese. / Contents --- p.i / Acknowledgements --- p.v / Abstract --- p.vi / 論文摘要 --- p.ix / List of Abbreviations --- p.xi / List of Figures --- p.xiii / List of Tables --- p.xv / Chapter Chapter 1 --- Introduction --- p.1 / Chapter 1.1 --- Breast Cancer --- p.2 / Chapter 1.1.1 --- Incidence Rate of Breast Cancer --- p.2 / Chapter 1.1.2 --- Risk Factors Lead to Breast Cancer --- p.5 / Chapter 1.1.3 --- Conventional Treatments --- p.5 / Chapter 1.2 --- Relationship between Breast Cancer and Glucose Transporters --- p.7 / Chapter 1.2.1 --- Importance of Glucose and Fructose --- p.7 / Chapter 1.2.2 --- Facilitative Glucose Transporters (Gluts) and The Relationship with Breast Cancer --- p.7 / Chapter 1.3 --- Antisense Oligonucleotides --- p.13 / Chapter 1.3.1 --- Characteristics of Antisense Oligonucleotides --- p.13 / Chapter 1.3.2 --- Action Mechanism of Antisense Oligonucleotides --- p.15 / Chapter 1.3.3 --- Sequence Selection --- p.19 / Chapter 1.3.4 --- Chemical Modifications of Antisense Oligonucleotides --- p.20 / Chapter 1.3.5 --- Uptake and Delivery Means of Antisense Oligonucleotides --- p.24 / Chapter 1.4 --- Objectives of Present Study --- p.26 / Chapter Chapter 2 --- Materials and Methods --- p.31 / Chapter 2.1 --- Materials --- p.32 / Chapter 2.1.1 --- Cell Lines and Culture Medium --- p.32 / Chapter 2.1.2 --- Buffers and Reagents --- p.33 / Chapter 2.1.3 --- Reagents for Transfection --- p.34 / Chapter 2.1.4 --- Reagents for D-[U14C]-Fructose and 2-Deoxy-D-[l-3H] Glucose Uptake Assay --- p.35 / Chapter 2.1.5 --- Reagents for ATP Assay --- p.35 / Chapter 2.1.6 --- Reagents for RT-PCR --- p.36 / Chapter 2.1.6.1 --- Reagents for RNA Extraction --- p.36 / Chapter 2.1.6.2 --- Reagents for Reverse Transcription --- p.36 / Chapter 2.1.6.3 --- Reagents for Gel Electrophoresis --- p.37 / Chapter 2.1.7 --- Reagents for Real Time-PCR --- p.38 / Chapter 2.1.8 --- Reagents and Chemicals for Western Blotting --- p.39 / Chapter 2.1.8.1 --- Reagents for Protein Extraction --- p.39 / Chapter 2.1.8.2 --- Reagents for SDS-PAGE --- p.39 / Chapter 2.1.9 --- Reagents for Flow Cytometry --- p.42 / Chapter 2.1.10 --- In Vivo Study --- p.43 / Chapter 2.2 --- Methods --- p.44 / Chapter 2.2.1 --- Oligonucleotide Design --- p.44 / Chapter 2.2.2 --- Trypan Blue Exclusion Assay --- p.47 / Chapter 2.2.3 --- Transfection --- p.47 / Chapter 2.2.4 --- MTT Assay --- p.47 / Chapter 2.2.5 --- D-[U14C]-fructose and 2-deoxy-D-[l-3H] Glucose Uptake Assay --- p.48 / Chapter 2.2.6 --- Detection of Intracellular ATP Concentration --- p.49 / Chapter 2.2.7 --- Reverse Transcription-Polymerase Chain Reaction (RT-PCR) --- p.51 / Chapter 2.2.7.1 --- RNA Extraction by TRIzol Reagent --- p.51 / Chapter 2.2.7.2 --- Determination of RNA Concentration --- p.51 / Chapter 2.2.7.3 --- Reverse Transcription --- p.52 / Chapter 2.2.7.4 --- Polymerase Chain Reaction (PCR) --- p.52 / Chapter 2.2.8 --- Real-Time PCR --- p.55 / Chapter 2.2.8.1 --- Analysis of the Real-Time PCR Data --- p.57 / Chapter 2.2.9 --- Western Blot Analysis --- p.58 / Chapter 2.2.9.1 --- Protein Extraction --- p.58 / Chapter 2.2.9.2 --- Protein Concentration Determination --- p.58 / Chapter 2.2.9.3 --- Western Blotting --- p.60 / Chapter 2.2.10 --- Flow Cytometry --- p.62 / Chapter 2.2.10.1 --- Detection of Cell Cycle Pattern with PI --- p.62 / Chapter 2.2.10.2 --- Detection of Apoptosis with Annexin V/PI --- p.62 / Chapter 2.2.11 --- In Vivo Study --- p.63 / Chapter 2.2.11.1 --- Establishment of Tumor-Bearing Animal Model --- p.63 / Chapter 2.2.11.2 --- Treatment Schedule --- p.63 / Chapter 2.2.11.3 --- Toxicity of Antisense Oligonucleotides --- p.64 / Chapter Chapter 3 --- Results --- p.66 / Chapter 3.1 --- In Vitro Study --- p.67 / Chapter 3.1.1 --- Effect of Tamoxifen on MCF-7 cells and MDA-MB-231 cells --- p.67 / Chapter 3.1.2 --- Cytotoxicity of Antisense Oligonucleotides against Glut 5 on MCF-7 cells and MDA-MB-231 cells by MTT Assay --- p.69 / Chapter 3.1.3 --- Effect of Antisense Oligonucleotides against Glut 5 on Fructose and Glucose Uptake of MCF-7 cells and MDA-MB-231 cells by D-[U14C]-Fructose & 2-Deoxy-D-[l-3H] Glucose Uptake Assay --- p.77 / Chapter 3.1.4 --- Effect of Antisense Oligonucleotides against Glut 5 on Intracellular ATP Content of MCF-7 cells and MDA-MB-231 cells by ATP Assay --- p.81 / Chapter 3.1.5 --- Effect of Antisense Oligonucleotides against Glut 5 on Glut 5 RNA Expression of MCF-7 cells and MDA-MB-231 cells by RT-PCR and Real-Time PCR --- p.83 / Chapter 3.1.5.1 --- RT-PCR --- p.83 / Chapter 3.1.5.2 --- Real-Time PCR --- p.87 / Chapter 3.1.6 --- Effect of Antisense Oligonucleotides against Glut 5 on Glut 5 Protein Expression of MCF-7 cells and MDA-MB-231 cells by Western Blot Analysis --- p.89 / Chapter 3.1.7 --- "Effect of Antisense Oligonucleotides against Glut 5 on Change in Cell Cycle Pattern of MCF-7 cells and MDA-MB-231 cells by Flow Cytometry, Using PI Stainning" --- p.93 / Chapter 3.1.8 --- "Effect of Antisense Oligonucleotides against Glut 5 on Induction of Apoptosis of MCF-7 cells and MDA-MB-231 cells by Flow Cytometry, Using Annexin V-FITC Stainning" --- p.98 / Chapter 3.2 --- In Vivo Study --- p.101 / Chapter 3.2.1 --- Animal Model: Nude Mice --- p.101 / Chapter 3.2.2 --- Effect of Antisense Oligonucleotides against Glut 5 on the MCF-7 cells-Bearing Nude Mice --- p.101 / Chapter 3.2.2.1 --- Change of Weight of the Tumor-Bearing Nude Mice --- p.101 / Chapter 3.2.2.2 --- Tumor Growth Rate --- p.105 / Chapter 3.2.2.3 --- Glut 5 RNA Expression by Real-Time PCR --- p.109 / Chapter 3.2.2.4 --- Glut 5 RNA Expression by Western Blotting --- p.111 / Chapter 3.2.3 --- "Assessment of Side Effects of Antisense Oligonucleotides against Glut 5, by Measuring the Plasma Enzyme Level" --- p.113 / Chapter Chapter 4 --- Discussion --- p.118 / Chapter 4.1 --- Antisense Oligonucleotides against Glut 5 on Human Breast Cancer --- p.119 / Chapter 4.1.1 --- Antisense Oligonucleotides Strategy --- p.119 / Chapter 4.1.2 --- Role of Glut 5 in Breast Cancer --- p.123 / Chapter 4.1.3 --- Effects of Tamoxifen on MCF-7 and MDA-MB-231 --- p.126 / Chapter 4.2 --- In Vitro Study of Antisense Oligonucleotides against Glucose Transporter 5 on Breast Cancer Cells --- p.127 / Chapter 4.3 --- In Vivo Study of Antisense Oligonucleotides against Glucose Transporter 5 on Breast Cancer Cells --- p.135 / Chapter 4.3.1 --- Effects of Antisense Oligonucleotides against Glut 5 on Body Weight and Tumor Size --- p.137 / Chapter 4.3.2 --- Expression Level of Glut 5 of the Tumor --- p.138 / Chapter 4.3.3 --- Assessment of Side Effects of Antisense Oligonucleotides against Glut 5，by Measuring the Plasma Enzymes Level --- p.140 / Chapter 4.4 --- Possible Mechanism of Antisense Oligonucleotides against Glut 5 on Breast Cancer --- p.141 / Chapter Chapter 5 --- Future Prospectus and Conclusions --- p.143 / Chapter 5.1 --- Future Prospectus of Antisense Oligonucleotides --- p.144 / Chapter 5.1.1 --- Antisense Oligonucleotides and Treatment of Breast Cancer --- p.144 / Chapter 5.1.2 --- Role of Glut 5 in Breast Cancer --- p.147 / Chapter 5.2 --- Conclusions and Remarks --- p.148 / References --- p.151

The discovery of RNA interference and the increasing understanding of disease genetics have created a new class of potential therapeutics based on oligonucleotides. This therapeutic class includes antisense molecules, small interfering RNA (siRNA), and microRNA modulators such as antagomirs (antisense directed against microRNA) and microRNA mimics, all of which function by altering gene expression at the translational level. While these molecules have the promise of treating a host of diseases from neurological disorders to cancer, a major hurdle is their inability to enter cells on their own, where they may render therapeutic effect. Nanotechnology is the engineering of materials at the nanometer scale and has gained significant interest for nucleic acid delivery due to its biologically relevant length-scale and amenability to multifunctionality. While a number of nanoparticle vehicles have shown promise for oligonucleotide delivery, there remains a lack of understanding of how nanoparticle coating and size affect these delivery processes. This dissertation seeks to elucidate some of these factors by evaluating oligonucleotide delivery efficiencies of a panel of iron oxide nanoparticles with varying cationic coatings and sizes. A panel of uniformly-sized nanoparticles was prepared with surface coatings comprised of various amine groups representing high and low pKas. A separate panel of nanoparticles with sizes of 40, 80, 150, and 200 nm but with the same cationic coating was also prepared. Results indicated that both nanoparticle surface coating and nanoparticle hydrodynamic size affect transfection efficiency. Specific particle coatings and sizes were identified that gave superior performance. The intracellular fate of iron oxide nanoparticles was also tracked by electron microscopy and suggests that they function via the proton sponge effect. The research presented in this dissertation may aid in the rational design of improved nanoparticle delivery vectors for nucleic acid-based therapy.

Theses (Ph. D.)--Marshall University, 2004. / Title from document title page. Includes abstract. Document formatted into pages: contains xiv, 192 p. including illustrations. Bibliography: p. 157-192.

by Judy, Yuet-wa Chan. / Thesis (M.Phil.)--Chinese University of Hong Kong, 1997. / Includes bibliographical references (leaves 107-111). / Acknowledgements --- p.i / Contents --- p.ii-iv / Abstract --- p.v-vii / Abbreviations --- p.ix / List of figures and tables --- p.x-xii / Chapter Chapter One: --- Introduction --- p.1-20 / Chapter 1.1 --- Facilitative Glucose Transporter Family (GLUT) / Chapter 1.2 --- Sequence and characterization of GLUT / Chapter 1.3 --- Overexpression of GLUT 1 in human cancer cells / Chapter 1.4 --- Inhibition of gene expression by antisense nucleic acid / Chapter 1.5 --- Types of antisense nucleic acids / Chapter 1.5.1 --- Nuclear expression of RNA by engineered antisense genes / Chapter 1.5.2 --- Antisense oligonucleotides / Chapter 1.6 --- Use of antisense oligomers in cell culture system / Chapter 1.7 --- Modification of antisense oligonucleotides / Chapter 1.8 --- Length and sequence selection of antisense oligomers / Chapter 1.9 --- Controls for measuring antisense effect / Chapter 1.10 --- Internalization and targeting of oligonucleotides / Chapter 1.11 --- Possible action mechanisms of antisense nucleotides / Chapter 1.12 --- Clinical applications of antisense approach / Chapter 1.13 --- Aim of the project / Chapter Chapter Two: --- Materials and Methods --- p.21-45 / Chapter 2.1 --- Materials / Chapter 2.1.1 --- Cell line and culture medium / Chapter 2.1.1a --- Cell line / Chapter 2.1.1b --- Culture medium / Chapter 2.1.2 --- Reagents and Buffers / Chapter 2.1.2a --- Phosphate-Buffered Saline (PBS) / Chapter 2.1.2b --- 50XTAE Buffer / Chapter 2.1.2c --- Tris-EDTA Buffer / Chapter 2.1.2d --- MTT solution / Chapter 2.1.2e --- Lipofectin Reagent / Chapter 2.1.3 --- Reagents for Northern Analysis / Chapter 2.1.3a --- DEPC-treated water (0.1% DEPC) / Chapter 2.1.3b --- 20X SSC / Chapter 2.1.3c --- 20X SSPE / Chapter 2.1.3d --- 10X Formaldehyde gel-running buffer / Chapter 2.1.3e --- Formaldehyde gel-loading buffer / Chapter 2.1.3f --- Prehybridization buffer / Chapter 2.1.3g --- Hybridization buffer / Chapter 2.2 --- Methods / Chapter 2.2.1 --- Synthesis of oligonucleotides and phosphorothioated oligonucleotides / Chapter 2.2.2 --- Cloning of human GLUT 1 cDNA into pRc/CMV expression vector at sense and antisense orientation / Chapter 2.2.2a --- Primer designed for cloning of sense and antisense GLUT 1 cDNA / Chapter 2.2.2b --- Isolation of sense and antisense GLUT 1 clone by PCR / Chapter 2.2.2c --- Restriction Digestion / Chapter 2.2.2d --- Purification of Restriction Digested DNA / Chapter 2.2.2e --- DNA Ligation / Chapter 2.2.2f --- Preparation of competent bacterial cells for transformation / Chapter 2.2.2g --- Plasmid DNA Transformation / Chapter 2.2.3 --- Large scale preparation of plasmid DNA / Chapter 2.2.4 --- Formation of Lipofectin-encapsulated oligonucleotides / Chapter 2.2.5 --- [32P]-labeled oligonucleotides uptake assay / Chapter 2.2.6 --- Methods to monitor antisense effect / Chapter 2.2.6a --- MTT assay / Chapter 2.2.6b --- Northern Analysis / Chapter (i) --- Preparation of radiolabeled probe / Chapter (ii) --- Isolation of total RNA from HL-60 cells / Chapter (iii) --- Separation of total RNA by eletrophoresis and blotting onto a membrane / Chapter (iv) --- Prehybridization of the Northern blot / Chapter (v) --- Hybridization of the Northern blot / Chapter 2.2.6c --- [3H]-deoxyglucose uptake assay / Chapter Chapter Three: --- Results --- p.46-88 / Chapter 3.1 --- Synthesis of Oligonucleotides / Chapter 3.2 --- Multiple alignment of cDNA sequence of Glucose Transporter isoforms / Chapter 3.3 --- [32P]-labeled oligonucleotide uptake assay / Chapter 3.4 --- Antisense oligonucleotides designed against different regions of GLUT 1 cDNA sequence / Chapter 3.4.1 --- Effects on HL-60 cell proliferation / Chapter 3.4.2 --- Effects on GLUT 1 mRNA level / Chapter 3.5 --- The effects of different oligonucleotide concentrations on HL- 60cell proliferation / Chapter 3.6 --- The effects of modified oligonucleotides on HL-60 cell proliferation / Chapter 3.7 --- The effects of different oligonucleotide lengths on HL-60 cell proliferation / Chapter 3.8 --- [3H]-deoxyglucose uptake assay / Chapter 3.9 --- Cloning of sense and antisense GLUT 1 cDNA into pRc/CMV vector / Chapter 3.10 --- Inhibition of GLUT 1 gene expression by expressed antisense nucleotides / Chapter Chapter Four: --- Discussion --- p.89-106 / Chapter 4.1 --- Importance of GLUT 1 gene / Chapter 4.2 --- HL-60: the target cancer cell line / Chapter 4.3 --- "Importance of ""Antisense Approach""" / Chapter 4.4 --- Optimization of condition for antisense inhibition by oligonucleotides / Chapter 4.4.1 --- Oligonucleotide length / Chapter 4.4.2 --- Oligonucleotide Modification / Chapter 4.4.3 --- Sequence selection / Chapter 4.4.4 --- Uptake efficiency / Chapter 4.5 --- Intracelluar distribution of oligonucleotides / Chapter 4.6 --- Inhibition of GLUT 1 gene expression by expressed antisense nucleotides / Chapter 4.7 --- Mechanisms for antisense inhibition of gene expression / Chapter 4.8 --- Further Directions / References --- p.107-117

The major aims of this thesis were to investigate the influence of i) antisense gene location relative to the target gene locus (?????location effect?????), ii) double-stranded RNA (dsRNA) formation, and iii) over-expression of host-encoded proteins on antisense RNA-mediated gene regulation. To test the location effect hypothesis, strains were generated which contained the target lacZ gene at a fixed location and the antisense lacZ gene at various genomic locations including all arms of the three fission yeast chomosomes and in close proximity to the target gene locus. A long inverse-PCR protocol was developed to rapidly identify the precise site of antisense gene integration in the fission yeast transformants. No significant difference in lacZ suppression was observed when the antisense gene was integrated in close proximity to the target gene locus, compared with other genomic locations, indicating that target and antisense gene co-localisation is not a critical factor for efficient antisense RNA-mediated gene suppression in vivo. Instead, increased lacZ down-regulation correlated with an increase in the steady-state level of antisense RNA, which was dependent on genomic position effects and transgene copy number. In contrast, convergent transcription of an overlapping antisense lacZ gene was found to be very effective at inhibiting lacZ gene expression. DsRNA was also found to be a central component of antisense RNA-mediated gene silencing in fission yeast. It was shown that gene suppression could be enhanced by increasing the intracellular concentration of non-coding lacZ RNA, while expression of a lacZ panhandle RNA also inhibited beta-galactosidase activity. In addition, over-expression of the ATP-dependent RNA-helicase, ded1, was found to specifically enhance antisense RNA-mediated gene silencing. Through a unique overexpression screen, four novel factors were identified which specifically enhanced antisense RNA-mediated gene silencing by up to an additional 50%. The products of these antisense enhancing sequences (aes factors), all have natural associations with nucleic acids which is consistent with other proteins which have previously been identified to be involved in posttranscriptional gene silencing.

The major aims of this thesis were to investigate the influence of i) antisense gene location relative to the target gene locus (?????location effect?????), ii) double-stranded RNA (dsRNA) formation, and iii) over-expression of host-encoded proteins on antisense RNA-mediated gene regulation. To test the location effect hypothesis, strains were generated which contained the target lacZ gene at a fixed location and the antisense lacZ gene at various genomic locations including all arms of the three fission yeast chomosomes and in close proximity to the target gene locus. A long inverse-PCR protocol was developed to rapidly identify the precise site of antisense gene integration in the fission yeast transformants. No significant difference in lacZ suppression was observed when the antisense gene was integrated in close proximity to the target gene locus, compared with other genomic locations, indicating that target and antisense gene co-localisation is not a critical factor for efficient antisense RNA-mediated gene suppression in vivo. Instead, increased lacZ down-regulation correlated with an increase in the steady-state level of antisense RNA, which was dependent on genomic position effects and transgene copy number. In contrast, convergent transcription of an overlapping antisense lacZ gene was found to be very effective at inhibiting lacZ gene expression. DsRNA was also found to be a central component of antisense RNA-mediated gene silencing in fission yeast. It was shown that gene suppression could be enhanced by increasing the intracellular concentration of non-coding lacZ RNA, while expression of a lacZ panhandle RNA also inhibited beta-galactosidase activity. In addition, over-expression of the ATP-dependent RNA-helicase, ded1, was found to specifically enhance antisense RNA-mediated gene silencing. Through a unique overexpression screen, four novel factors were identified which specifically enhanced antisense RNA-mediated gene silencing by up to an additional 50%. The products of these antisense enhancing sequences (aes factors), all have natural associations with nucleic acids which is consistent with other proteins which have previously been identified to be involved in posttranscriptional gene silencing.