Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Chemistry, 1999. / Includes bibliographical references (leaf 36). / by Pankaj Bhatia. / S.M.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 2010. / Vita. Cataloged from PDF version of thesis. / Includes bibliographical references. / Cisplatin, carboplatin, and oxaliplatin are three FDA-approved members of the platinum anticancer drug family. These compounds induce apoptosis in tumor cells by binding to nuclear DNA, forming a variety of adducts, and triggering cellular responses, one of which is the inhibition of transcription. The focus of this thesis is on studying the structure of these adducts, and correlating these effects with inhibition of transcription. Chapter 1 presents (i) a detailed review of the structural investigations of various Pt-DNA adducts and the effects of these lesions on global DNA geometry; (ii) research detailing inhibition of cellular transcription by Pt-DNA adducts; and (iii) a mechanistic analysis of how DNA structural distortions induced by platinum damage may inhibit RNA synthesis in vivo. These hypotheses will be explored in subsequent chapters of the thesis. In Chapter 2, features of the 2.17 A resolution X-ray crystal structure of cisdiammine( pyridine)chloroplatinum(II) (cDPCP) bound in a monofunctional manner to deoxyguanosine in a DNA duplex are discussed and compared to those of a cisplatin-1,2- d(GpG) intrastrand cross-link in double-stranded DNA. The global geometry of cDPCPdamaged DNA is quite different from that of DNA containing a cisplatin 1,2-d(GpG) cross-link. The latter platinated duplex is bent by ~40* toward the major groove at the site of the adduct; however, the monofunctional Pt-dG lesion causes no significant bending of the double helix. Like the cisplatin intrastrand adduct, however, the cDPCP moiety creates a distorted base pair step to the 5' side of the platinum site that may be correlated to its ability to destroy cancer cells. Structural features of monofunctional platinum adducts are analyzed, the results of which suggest that such adducts may provide a new platform for the design and synthesis of Pt anticancer drug candidates. The role of carbonate in the binding of cis-diamminedichloroplatinum(II) to DNA was investigated in Chapter 3 in order to understand the potential involvement of carbonato-cisplatin species in the mechanism of action of platinum anticancer agents. Cisplatin was allowed to react with single-stranded DNA in carbonate, phosphate, and HEPES buffers, and the products were analyzed by enzymatic digestion/mass spectrometry. The data from these experiments demonstrate (1) that carbonate, like other biological nucleophiles, forms relatively inert complexes with platinum that inactivate cisplatin, and (2) that the major cisplatin-DNA adduct formed is a bifunctional cross-link. These results are in accord with previous studies of cisplatin- DNA binding and reveal that the presence of carbonate has no consequence on the nature of the resulting adducts. The 1.77-A resolution X-ray crystal structure of a dodecamer DNA duplex with the sequence 5'-CCTCTGGTCTCC-3' that has been modified to contain a single engineered 1,2-cis- {Pt(NH 3)2}2+-d(GpG) cross-link, the major DNA adduct of cisplatin, is reported in Chapter 4. These data represent a significant improvement in resolution over the previously published 2.6-A structure. The ammine ligands in this structure are clearly resolved, leading to improved visualization of the cross-link geometry with respect to both the platinum center and to the nucleobases, which adopt a higher energy conformation. Also better resolved are the deoxyribose sugar puckers, which allow us to re-examine the global structure of platinum-modified DNA. Another new feature of this model is the location of four octahedral [Mg(H 20)6]2+ ion associated with bases in the DNA major groove and the identification of 124 ordered water molecules that participate in hydrogen bonding interactions with either the nucleic acid or the diammineplatinum(II) moiety. Chapter 5 discusses structural investigations of nucleosomal DNA modified by sitespecific platinum adducts. Nucleosome core particles containing a single 1,3-cis-{Pt(NH 3)2}2+_ d(GpTpG) intrastrand cross-link were synthesized and crystallized, and the X-ray structure was determined at 3.2 A resolution. The cisplatin adduct adopts a conformation facing toward the octamer core, in agreement with previous experiments. DNA in the vicinity of the Pt adduct has a similar helical bend as that observed in the NMR solution structure of free DNA containing the same cross-link, indicating that the rotational positioning power of cisplatin intrastrand crosslinks stems from the propensity to align the bent Pt-DNA structure with the DNA curvature arising from the nucleosome superhelix. Functional consequences of cisplatin binding to nucleosomal DNA are explored in Chapter 6. The effect of a single engineered platinum intrastrand cross-link on ATPindependent nucleosome mobility was investigated in vitro. Both 1,2-d(GpG) and 1,3-d(GpTpG) adducts of cisplatin inhibit translocation of DNA along the histone octamer, with the former Pt lesion providing a larger barrier. In vitro transcription assays with T7 RNA polymerase were conducted to determine whether cisplatin-DNA cross-links inhibit RNA synthesis by preventing access to nucleosomal DNA. Immobilized transcription templates containing a T7 RNAP promoter site, a single engineered cisplatin 1,2-d(GpG) or 1,3-d(GpTpG) intrastrand cross-link, and a phased nucleosome core particle were prepared. Analysis of resulting RNA transcript length revealed that the T7 RNAP elongation complex can overcome the energy barrier to nucleosome sliding caused by platinum intrastrand cross-links, but stalls when it reaches a Pt- DNA adduct placed on the DNA template strand. These results provide further evidence that intrastrand cross-links of cisplatin inhibit transcription by creating a physical barrier that the polymerase cannot pass. Appendices A and B summarize incomplete work that may be of use to future researchers working in this area. Appendix A describes attempts to isolate isomerically pure Pt- DNA probes containing a photoreactive benzophenone moiety, for use in cross-linking experiments that identify proteins that recognize and interact with cisplatin-DNA damage. In Appendix B efforts to obtain an X-ray crystal structure of an 1 Imer duplex DNA containing the 1,3- cis-{Pt(NH 3)2} 2 -d(GpTpG) intrastrand cross-link are reported. Appendix C details HPLC and mass spectrometric methods for purification and analysis of platinated oligonucleotides that were developed in the course of this research. / by Ryan Christopher Todd. / Ph.D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 1993. / Includes bibliographical references (leaves 151-152). / by Joseph Timothy Jarrett. / Ph.D.

Thesis (Ph.D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 2000. / Includes bibliographical references. / This thesis details studies of the chemical reactivity of silicon surfaces and the development of new reactions for manipulating its surface properties by the formation of covalently attached molecular and polymeric films. Silicon is the central material in modern electronic devices, and the ability to tailor its surface, particularly in a hydrogen-terminated form, at a molecular level has been desired. In this research, porous and crystalline silicon were examined as substrates, where the latter material can offer notable interesting luminescent properties. Chapters 2 and 3 discuss the formation of molecular films on hydrogen-terminated silicon surfaces by reactions using alcohols and Grignard and organolithium reagents. In the first reaction, alcohols formed alkoxy films to silicon surfaces via Si-0 bonds after reaction for 1-2 h at 40-90 °C. Alcohols were suggested to react with surface Si-Si bonds to cleave these bonds and produce Si-OR and Si-H species. In the second reaction, molecular films were obtained on silicon by exposing silicon substrates to Grignard and organolithium reagents at room temperature for 1-6 h and a quench with an anhydrous acid. A mechanism is proposed whereby the reagent alkyl anions cleaved surface Si-Si bonds and produced Si-R attachments anchored by Si-C bonds and an equivalent of silyl anions that were later quenched using an acid or an acyl halide. Both reactions caused little surface oxidation, and modified porous silicon samples retained their luminescent properties. Molecular films formed on crystalline silicon supports by these reactions exhibited a surfoce coverage of 50-90 % and moderate packing density. Chapters 4 and 5 describe the use of these thin molecular films for forming polymer films on crystalline silicon supports. In Chapter 4, a pyrrole-terminated molecular film was formed on a hydrogen-terminated silicon substrate using a pyrrole-terminated organolithium reagent. The electrochemical polymerization of pyrrole on the support produced polypyrrole films that were covalently attached to the substrate. The resulting polymer films demonstrated improved physical properties such as smooth and uniform surface morphology and strong adhesion to the substrate over those formed to native hydrogen-terminated silicon surfaces. Similarly, the junctions containing a modified silicon substrate exhibited enhanced electrical characteristics due to efficient charge transfer at the interface over those of an unmodified substrate. In Chapter 5, a norbomene-terminated molecular film was prepared on silicon bearing thin native oxide and used for a surface-initiated ring-opening metathesis polymerization (ROMP) process. In this strategy, a Ru-based ROMP catalyst was immobilized onto the modified silicon surface by reaction with a norbornenyl monolayer. Upon exposure to solutions of various norbornene-based monomers, the attached catalyst produced a series of grafted polymer films with control over thickness and chemical composition of the films. By combining this method with microcontact printing ([mu]CP), the procedure was used to generate patterned polymer films on silicon by simple solution-phase reactions. / by Namyoung Kim. / Ph.D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 2003. / Vita. / Includes bibliographical references. / This thesis describes the syntheses, characterizations, and applications of novel type-II quantum dots and versatile oligomeric phosphine ligands. Type-II band engineered quantum dots (CdTe/CdSe(core/shell) and CdSe/ZnTe(core/shell) heterostructures) are synthesized by chemical means. The optical properties of these type-II quantum dots are studied in parallel with their type-I counterparts. The spatial distributions of carriers are controlled within the type-II quantum dots, which make their properties strongly governed by the band offset of the comprising materials. This allows access to optical transition energies that are not restricted to bandgap energies. The type-II quantum dots can emit at lower energies than the bandgaps of comprising materials. The type-II emission can be tailored by the shell thickness as well as the core size. The enhanced control over the carrier distributions afforded by these type-II materials is useful for many applications such as photovoltaics, and photoconduction devices. A new family of oligomeric alkyl phosphine ligands is synthesized for quantum dots. These oligomeric phosphines show effective binding affinity to quantum dot surfaces. They form thin and secure organic shells that stabilize quantum dots in diverse environments. They maintain high photoluminescence quantum yield of the quantum dots, and enable homogeneous incorporation into various matrices. They present a chemically flexible structure that can be used for further chemistry, such as crosslinking, co-polymerization, and conjugation to biomolecules. Selection of optimal quantum dot wavelengths for biomedical assays and imaging is studied by simple mathematical modeling. / (cont.) Exploiting the design flexibilities of type-II quantum dots and the superior stabilities from oligomeric phosphine ligands, aqueous soluble near-infrared quantum dots for biomedical imaging are obtained. They are optimized for the emission wavelength, absorption cross-section, hydrodynamic size, and photoluminescence quantum yield. Using these quantum dots in small and large animal model systems, sentinel lymph node mapping, a major cancer staging procedure, is successfully performed in real-time using near-infrared light. Oliogomeric phosphine ligands with polymerizable moieties are used to incorporate quantum dots into polymer microspheres. The ligands enable co-polymerization of quantum dots with heterogeneous polymer matrices without phase separations or aggregations. Their potential applications for full color, particle-based displays, and information storage are demonstrated. / by Sungjee Kim. / Ph.D.

Thesis (M.S.)--Massachusetts Institute of Technology, Dept. of Chemistry, 1995. / Includes bibliographical references. / by Chee-Kiang Lim. / M.S.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 2006. / This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections. / Includes bibliographical references (leaves 187-207). / A new methodology for monitoring post-translational modifications of histone H3 in living cells was developed using genetically encoded fluorescent reporters. These reporters were constructed for sensing histone phosphorylation and methylation by fluorescence resonance energy transfer (FRET). These reporters are four-part chimeric proteins with the domains from N- to C-terminus as follows: a cyan fluorescent protein (CFP), a phosphoserine recognition domain (14-3-3 tau) or a methyllysine recognition domain (HP1 or Pc chromodomain), a peptide whose sequence corresponds to the Nterminus of histone H3, and a yellow fluorescent protein. The histone phosphorylation reporter exhibited a 25 % YFP/CFP emission ratio increase upon phosphorylation in vitro by Msk-1 kinase. Site-directed mutagenesis studies suggested that Ser28 phosphorylation gave rise to the reporter FRET response. When tested in living HeLa cells, the reporter exhibited a rapid increase in the emission ratio 5-15 min prior to the nuclear membrane breakdown and the FRET peaked during cell division. Another reporter, in which the 14-3-3 tau and the H3 peptide were swapped, exhibited the FRET response to both Ser10 and Ser28 phosphorylation. Two methylation reporters, K9 and K27, were constructed for sensing H3-lysine9 and H3-lysine27 methylation. / (cont.) The reporters gave 60 % (K9) and 28 % (K27) emission ratio changes after in vitro methylation, catalyzed by the histone methyltransferase vSET. Applying the K9 reporter in cells showed different levels of reporter FRET in fibroblasts either expressing or lacking methyltransferases Suv39h1 and Suv39h2. Site-specific incorporation of biophysical probes onto cell surface proteins is critical for the study of protein trafficking. One general solution to achieve labeling specificity is the use of enzymes for the ligation of probes to a substrate peptide tagged onto a protein of interest. Transglutaminase incorporates amine probes to cell surface proteins expressing a 6- or 7-amino acid consensus sequence (Q-tag). A variety of probes such as biotin cadaverine and fluorescein cadaverine were incorporated to Q-tag-CFP and Q-tag-EGF receptor constructs expressed on the surface of living HeLa and HEK cells. The NF?B p50 transcription factor fused to a Q-tag was labeled with a benzophenone photo-affinity probe in vitro. Upon UV irradiation, elevated levels of p50 homodimerization were observed in the presence of DNA or the interacting protein myotrophin. / by Chi-Wang Lin. / Ph.D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 1988. / Vita. On t.p. "[alpha]" appears as original Greek letter. / Bibliography: leaves 239-255. / by Roy Carl Smith. / Ph.D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 2010. / Vita. Page 208 blank. Cataloged from PDF version of thesis. / Includes bibliographical references. / The design, synthesis and characterization of conjugated macrocycles and polymers are presented in this dissertation. In particular, work involving the exploration of unusual and/or novel aromatic structures for various materials applications is described in detail, along with appropriate discussions of relevant structure-property relationships. A brief general introduction to J-aggregates and conjugated polymers is given in Chapter 1, which represents two major areas that are dealt with throughout this thesis. Besides providing an overview of the basic principles, this introductory chapter will hopefully serve to give insight into the motivation behind the work discussed herein. In Chapter 2, the facile one-step construction of highly functionalized cyclohexa-mphenylene macrocycles from simple monobenzenoid building blocks is presented. This methodology is based on a six-fold Suzuki-Miyaura coupling, and represents an improvement over preceding cyclohexa-m-phenylene preparations. In Chapter 3, the development of novel J-aggregating dibenz[aj]anthracene-based macrocycles are reported. These materials are uniquely non-polar compared to all other known Jaggregates, and are also much more photostable relative to the classic J-aggregating cyanine dyes. A variation on the dibenzanthracene theme was extended to the work described in Chapter 4, which features poly(aryleneethynylene)s containing dibenz[a,h]anthracene repeat units. These polymers have unusual stair-stepped structures that confer unto them spectroscopic properties that are atypical of the more common poly(phenyleneethynylene)s. Chapter 5 details recent efforts aimed at utilizing the J-aggregate design principles discussed in Chapter 3 in our search for new J-aggregate candidates in various conjugated polymers and small molecules (e.g. the dibenz[a,m]rubicenes). / by Julian M.W. Chan. / Ph.D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 1994. / Includes bibliographical references. / by Gregory L. Warren. / Ph.D.