Project Description for the students in the NYU/CCNY SESMI REU during the Summer 2007
Mohammed Bader
Project Title:
Effects of Various Alkanethiols on Calcium
Oxalate Crystallization
REU
Faculty Advisor:
Dr. Michael Ward
Research Synopsis:
Kidney stones pose a major health problem,
affecting greater than 10% of the U.S. population.
Kidney stones are crystal aggregates primarily
composed of calcium oxalate monohydrate. The less
prevalent dihydrate compound is also found in
kidney stones, although it is a benign form which
does not as readily aggregate (and thereby passes
through the urine without forming stones). There
are four primary processes involved in stone
formation: nucleation, crystal growth, aggregation,
and attachment. The effects of varying surface
compositions on crystal formation will be examined.
Several distinct alkanethiol self-assembled
monolayer (SAM) surfaces will be formed on gold
surfaces (gold is used due to its strong
interaction with sulfur from the thiols). Mixed
monolayers (containing varying concentrations of
methyl-terminated and carboxylate-terminated
alkanethiols) will also be constructed. Different
head groups and chain lengths affect monolayer
assembly and surface properties such as wettability
and adhesion. The mixed monolayer surfaces will be
characterized based on water contact angle measured
with a goniometer. This will provide a qualitative
understanding of surface wettability with respect
to relative concentrations (of the constituent
alkanethiols). Calcium oxalate nucleation and
growth rates will then be measured and compared for
the various monolayer surfaces.
Stamping methods will be utilized to create
patterned, more ordered arrays of different
monolayers (to allow for more meaningful
statistical comparisons of nucleation and growth
rates). Crystals will be characterized according to
x-ray structure, atomic force microscopy and
optical microscopy images.
Amber Bowen
Project Title:
Colloidal Research
REU Faculty Advisor: Dr. David Pine
Research Synopsis:
My research will concentrate on selective and controllable aggregation of microspheres through DNA conjugation via alteration of the molecular surface layer. Single stranded DNA is covalently bonded to the microsphere surface, and acts like Velcro becuase the strand is sequence selective. This directed three-dimentional self assembly of microstructures and nanostructures is important in the research of fabrication of new materials, and could potentially be utilized for making full photonic bandgap crystals.
First, some results from previous experiments need to be refined. We will want to optimize the process of DNA conjugation, identify the possible creation of an anhydride bond and the effect of treatment with ammonia as these processes have been seen to vary the effects of nonspecific binding between the microspheres. We will want to identify if the carboxylated microspheres become more stable in dilution and reduce the need of a surfactant by dendritic branching on the surface. We will also want to know the approximate number of DNA bonds between attached beads to help us reduce the sharpness of the dispersion transition, which will assist in the annealing process.
Microsphere polymerization research done in Professor Pine’s lab investigates various microsphere forms that may be used with varying results. I hope to repeat the successful DNA bead experiments with the “patchy particles” made in Dave Pine’s lab. The first experiment is to do the DNA experiments with plain beads which have been swollen with toluene and treated with F108 (because the clusters are made this way). These experiments will use the fluorescent DNA in order to quantify DNA surface density and hybridization efficiency with FACS (fluorescent-activated cell sorting). We hope to get the “palindrome” DNA working so we can start working with a system that self hybridizes.
Once we can show that impurities can be corrected and controlled, we will be able to anneal the aggregates in hopes of showing the same affects as annealing crystal structures. We can then change the geometry of the particles in taking closer steps to creating a template for a tetrahedral photonic bandgap crystal.
REU Faculty Advisor: Dr. David Pine
Research Synopsis:
My research will concentrate on selective and controllable aggregation of microspheres through DNA conjugation via alteration of the molecular surface layer. Single stranded DNA is covalently bonded to the microsphere surface, and acts like Velcro becuase the strand is sequence selective. This directed three-dimentional self assembly of microstructures and nanostructures is important in the research of fabrication of new materials, and could potentially be utilized for making full photonic bandgap crystals.
First, some results from previous experiments need to be refined. We will want to optimize the process of DNA conjugation, identify the possible creation of an anhydride bond and the effect of treatment with ammonia as these processes have been seen to vary the effects of nonspecific binding between the microspheres. We will want to identify if the carboxylated microspheres become more stable in dilution and reduce the need of a surfactant by dendritic branching on the surface. We will also want to know the approximate number of DNA bonds between attached beads to help us reduce the sharpness of the dispersion transition, which will assist in the annealing process.
Microsphere polymerization research done in Professor Pine’s lab investigates various microsphere forms that may be used with varying results. I hope to repeat the successful DNA bead experiments with the “patchy particles” made in Dave Pine’s lab. The first experiment is to do the DNA experiments with plain beads which have been swollen with toluene and treated with F108 (because the clusters are made this way). These experiments will use the fluorescent DNA in order to quantify DNA surface density and hybridization efficiency with FACS (fluorescent-activated cell sorting). We hope to get the “palindrome” DNA working so we can start working with a system that self hybridizes.
Once we can show that impurities can be corrected and controlled, we will be able to anneal the aggregates in hopes of showing the same affects as annealing crystal structures. We can then change the geometry of the particles in taking closer steps to creating a template for a tetrahedral photonic bandgap crystal.
Shafiqah Faust
Project Title:
Suspension Fluid
Mechanics
REU Faculty Advisor: Dr. Jeff Morris
Research Synopsis:
This summer the goal of my research is to vary the concentration of the particles in a suspension until the fluid no longer flows through a channel contraction: this is jamming. This will be completed by looking experimentally probing the flow using velocity measurement for the different concentrations. After the jamming stage, a fluid tends to act as its own filter, and we would like to know the properties of this filter, and what conditions lead to the jamming, and why. Studying the particle suspensions under various conditions will allow us to see how the behavior changes as the the jamming is approached. The experimental results will be compared against a flow model the group has previously developed, but which has no jamming information included, as a start toward including jamming within this model.
REU Faculty Advisor: Dr. Jeff Morris
Research Synopsis:
This summer the goal of my research is to vary the concentration of the particles in a suspension until the fluid no longer flows through a channel contraction: this is jamming. This will be completed by looking experimentally probing the flow using velocity measurement for the different concentrations. After the jamming stage, a fluid tends to act as its own filter, and we would like to know the properties of this filter, and what conditions lead to the jamming, and why. Studying the particle suspensions under various conditions will allow us to see how the behavior changes as the the jamming is approached. The experimental results will be compared against a flow model the group has previously developed, but which has no jamming information included, as a start toward including jamming within this model.
Rachel Ferguson
Project Title:
Confined Crystallization
REU Faculty Advisor: Alexander Couzis
Research Synopsis:
The regulated crystallization of nanometer scale particles with controlled structures is an important process for many different scientific areas, including pharmaceuticals and nanotechnology. However, the process to produce a specific crystalline structure in large quantities can be complicated and expensive. Current research into confined crystallization has focused on new techniques that can be used to crystallize specific polymorphs onto templates, which can control particle size and development.
In order to control the nucleation and development of crystals, the interfacial tension that determines crystallization must be manipulated. The interfacial tension can be controlled by creating self-assembling monolayers, or SAMs, to be used as templates for crystallization. The SAM becomes the interface for crystallization, and therefore conditions affecting nucleation and crystal growth can be manipulated. Another interesting research area comes from the development of mixed monolayers, using multiple surfactants to create differing monolayer heights. The differences in the monolayer create small nano-islands. If the surfactants are correctly chosen, nucleation will occur only on the nano-islands and will be structurally guided to form only the desired polymorph. Manipulation of the template, surfactant ratios, and size and distribution of the islands can all affect nucleation and polymorph development. The nano-islands can also isolate individual crystals and prevent the agglomeration that typically increases particle size.
The research being directed by Alexander Couzis and Michael Ward is mainly exploring the crystallization of calcium oxalate, a core component in kidney stones. Calcium oxalate crystallizes into one of two forms, a monohydrate and a dihydrate, but only the monohydrate causes kidney stone formation. It is not known what causes one hydrate to form over the other, and research into this area may eventually lead to treatments for or prevention of kidney stone disease.
For this research, I will be producing SAMs using silicon wafers and silanes with varying terminal functionalities. By changing the terminal functionalities, which are the sites where crystallization on the monolayer will occur, we should be able to affect the nucleation and growth processes. I will begin my research using amino, carboxyl, and polyethylene glycol functionalities. After producing the monolayers, I will be studying the crystallization of calcium oxalate onto the SAMs. Ideally, the use of polyethylene glycol should inhibit crystal formation in an aqueous environment, while the carboxyl and amino functionalities will mimic the attraction of negatively and positively charged ions, respectively, to the oppositely charged oxalate or calcium ions. I will also be working with mixed monolayers and studying the use of nano-islands in crystal development. By creating monolayers using polyethylene glycol and amino or carboxyl functionalities as the nano-island surfaces, the calcium oxalate should crystallize only in the nano-islands, and direct comparisons between then carboxyl and amino affects can be drawn.
REU Faculty Advisor: Alexander Couzis
Research Synopsis:
The regulated crystallization of nanometer scale particles with controlled structures is an important process for many different scientific areas, including pharmaceuticals and nanotechnology. However, the process to produce a specific crystalline structure in large quantities can be complicated and expensive. Current research into confined crystallization has focused on new techniques that can be used to crystallize specific polymorphs onto templates, which can control particle size and development.
In order to control the nucleation and development of crystals, the interfacial tension that determines crystallization must be manipulated. The interfacial tension can be controlled by creating self-assembling monolayers, or SAMs, to be used as templates for crystallization. The SAM becomes the interface for crystallization, and therefore conditions affecting nucleation and crystal growth can be manipulated. Another interesting research area comes from the development of mixed monolayers, using multiple surfactants to create differing monolayer heights. The differences in the monolayer create small nano-islands. If the surfactants are correctly chosen, nucleation will occur only on the nano-islands and will be structurally guided to form only the desired polymorph. Manipulation of the template, surfactant ratios, and size and distribution of the islands can all affect nucleation and polymorph development. The nano-islands can also isolate individual crystals and prevent the agglomeration that typically increases particle size.
The research being directed by Alexander Couzis and Michael Ward is mainly exploring the crystallization of calcium oxalate, a core component in kidney stones. Calcium oxalate crystallizes into one of two forms, a monohydrate and a dihydrate, but only the monohydrate causes kidney stone formation. It is not known what causes one hydrate to form over the other, and research into this area may eventually lead to treatments for or prevention of kidney stone disease.
For this research, I will be producing SAMs using silicon wafers and silanes with varying terminal functionalities. By changing the terminal functionalities, which are the sites where crystallization on the monolayer will occur, we should be able to affect the nucleation and growth processes. I will begin my research using amino, carboxyl, and polyethylene glycol functionalities. After producing the monolayers, I will be studying the crystallization of calcium oxalate onto the SAMs. Ideally, the use of polyethylene glycol should inhibit crystal formation in an aqueous environment, while the carboxyl and amino functionalities will mimic the attraction of negatively and positively charged ions, respectively, to the oppositely charged oxalate or calcium ions. I will also be working with mixed monolayers and studying the use of nano-islands in crystal development. By creating monolayers using polyethylene glycol and amino or carboxyl functionalities as the nano-island surfaces, the calcium oxalate should crystallize only in the nano-islands, and direct comparisons between then carboxyl and amino affects can be drawn.
Elad Firnberg
Project Title:
Barcoded Lipobeads
REU Faculty Advisor: Dr. Charles Maldarelli
Research Synopsis:
This research project will focus on the formation of quantum dot (QD) encoded polystyrene microbeads, 10-100 µm in diameter. Different methods will be investigated to obtain the desirable bead size and narrow size distribution. The microbeads will be encoded with a luminescent spectral barcode comprised of quantum dots emitting at different wavelengths or colors. Different combinations of QDs give each microbead a unique identifiable signature.
In addition to the QDs, magnetic iron oxide nanoparticles will also be inserted into the microbeads in order to help spread apart the QDs within the spheres. This is because the solubility of the QDs in polystyrene is low, so that they are pushed out into pockets in the sphere and form aggregate clumps. This tendency results in Förster resonance energy transfer (FRET) between colors, affecting the emitted spectrum and therefore the barcode.
Confocal laser scanning microscopy will be used to image the beads and observe the QD distribution and emission spectrum. The placement of the encoded beads in a microarray will be investigated using a magnetic surface. The encoded microbeads will ultimately serve as carriers of molecular receptors in microarrays, used to identify binding affinity with a ligand, such as a protein molecule. This technology has great potential to aid in the discovery of the role of many cell surface receptor proteins in an efficient and timely manner. Additionally, it will lead to the development of novel drugs targeting specific receptor molecules.
REU Faculty Advisor: Dr. Charles Maldarelli
Research Synopsis:
This research project will focus on the formation of quantum dot (QD) encoded polystyrene microbeads, 10-100 µm in diameter. Different methods will be investigated to obtain the desirable bead size and narrow size distribution. The microbeads will be encoded with a luminescent spectral barcode comprised of quantum dots emitting at different wavelengths or colors. Different combinations of QDs give each microbead a unique identifiable signature.
In addition to the QDs, magnetic iron oxide nanoparticles will also be inserted into the microbeads in order to help spread apart the QDs within the spheres. This is because the solubility of the QDs in polystyrene is low, so that they are pushed out into pockets in the sphere and form aggregate clumps. This tendency results in Förster resonance energy transfer (FRET) between colors, affecting the emitted spectrum and therefore the barcode.
Confocal laser scanning microscopy will be used to image the beads and observe the QD distribution and emission spectrum. The placement of the encoded beads in a microarray will be investigated using a magnetic surface. The encoded microbeads will ultimately serve as carriers of molecular receptors in microarrays, used to identify binding affinity with a ligand, such as a protein molecule. This technology has great potential to aid in the discovery of the role of many cell surface receptor proteins in an efficient and timely manner. Additionally, it will lead to the development of novel drugs targeting specific receptor molecules.
Jonathan Hitt
Project Title:
Self-assembled peptide DNA scaffolds
complexes
REU Faculty Advisor: Dr. Raymond Tu
Research Synopsis:
This summer I will focus my efforts on the design and synthesis of peptide-based self assemblies. These bottom-up systems will be composed of a hierarchical structure involving the binding of designed peptide dimers, in ordered arrays, to DNA scaffold complexes. The initial steps will utilize a methodology called solid phase peptide
synthesis (SPPS). SPPS will be accomplished through iterative additions of amino acids to form several dimerization motifs followed by purification using a vacuum filtration method. The peptides' characteristic structures will be catalogued after being analyzed with spectroscopic techniques, such as circular dichroism spectropolarimetry. Later, in this study, I hope to test the reactivities of my peptides with various DNA scaffold binding sites; this will be monitored while controlling the dimerization of the peptide, a prerequisite for binding. The specific binding of the peptide dimers to the ordered DNA array will be characterized with atomic force microscopy and crystallographic diffraction techniques.
REU Faculty Advisor: Dr. Raymond Tu
Research Synopsis:
This summer I will focus my efforts on the design and synthesis of peptide-based self assemblies. These bottom-up systems will be composed of a hierarchical structure involving the binding of designed peptide dimers, in ordered arrays, to DNA scaffold complexes. The initial steps will utilize a methodology called solid phase peptide
synthesis (SPPS). SPPS will be accomplished through iterative additions of amino acids to form several dimerization motifs followed by purification using a vacuum filtration method. The peptides' characteristic structures will be catalogued after being analyzed with spectroscopic techniques, such as circular dichroism spectropolarimetry. Later, in this study, I hope to test the reactivities of my peptides with various DNA scaffold binding sites; this will be monitored while controlling the dimerization of the peptide, a prerequisite for binding. The specific binding of the peptide dimers to the ordered DNA array will be characterized with atomic force microscopy and crystallographic diffraction techniques.
Scott McIsaac
Project
Title: Protein
Folding
REU Faculty Advisor: Dr. Jasna Brujic
Research Description:
Protein folding remains one of the basic unsolved problems in biology, and recently, techniques have been developed to study conformation at the single-protein level. To this end, I will help set up an atomic force microscope (AFM), which is one of the state-of-the-art techniques for this type of experimentation, at Dr. Brujic's lab at NYU. I will then take data with the AFM to study unfolding time distributions of proteins as a function of force.
REU Faculty Advisor: Dr. Jasna Brujic
Research Description:
Protein folding remains one of the basic unsolved problems in biology, and recently, techniques have been developed to study conformation at the single-protein level. To this end, I will help set up an atomic force microscope (AFM), which is one of the state-of-the-art techniques for this type of experimentation, at Dr. Brujic's lab at NYU. I will then take data with the AFM to study unfolding time distributions of proteins as a function of force.
Kathryn Myers
Project Title:
Heterogeneous
Nucleation of Calcium
Oxalate
REU
Faculty Advisor: Dr. Michael Ward (NYU) and Dr.
Alexander Couzis (CCNY)
Research
Synopsis:
Heterogeneous crystallization, a process resulting in the formation of crystals on a given surface, occurs as a multi-step process. In the first step, molecules or ions assemble into a pre-nucleation aggregate whose structure mimics that of a mature crystal. After the initial aggregate is formed, it matures to form a crystal nucleus which will remain stable only if it has reached a “critical size,” whereby a sustainable nucleus has formed that allows for crystal growth. Heterogeneous nucleation, which toccurs on a surface rather than in solution, is energetically more favorable than homogeneous nucleation. Surfaces provide interfacial interactions resulting in increased rates of nucleation as well as a smaller critical nucleus. More simply, the four steps of crystal formation are nucleation, growth, aggregation, and attachment of aggregates to epithelial cells.
Kidney stones, which are aggregates of small crystals containing primarily calcium oxalate monohydrate (COM), and small amounts of embedded proteins, form through the nucleation process described above. Kidney stones affect over 10% of the US population, causing intense discomfort and possible renal failure. Although the mechanism of stone formation is not entirely understood, studies have been conducted using atomic force microscopy to investigate the adhesion characteristics of different crystal faces of COM to calcium oxalate. Further investigation of the nucleation and growth of these crystals must be conducted, however, to design new pharmaceuticals that could disperse formed aggregates or block crystal aggregation entirely.
Calcium oxalate monohydrate forms crystals more readily than calcium oxalate dihydrate (COD). We would like to examine how surface composition affects the rate of crystal formation between these two species of calcium oxalate. Crystal formation on epithelial cells is affected by functional groups such as carboxylates found in aspartic acid. We would like to determine how exposed intracellular proteins containing various functionalities affect crystal nucleation.
Intact phospholipid bilayer liposomes bound to silicon oxide wafers will be used to simulate cell membranes where nucleation occurs. Kidney stones form primarily on damaged cell membranes, where functional groups become exposed to the surrounding aqueous media. The surface of the membrane can be both decorated with different peptide sequences or reinforced with cholesterol to stiffen the nucleation surface. To mimic the human body, all experiments will be carried out at approximately 36.6 C. We can observe with AFM how calcium oxalate attaches to cell membranes.
Heterogeneous crystallization, a process resulting in the formation of crystals on a given surface, occurs as a multi-step process. In the first step, molecules or ions assemble into a pre-nucleation aggregate whose structure mimics that of a mature crystal. After the initial aggregate is formed, it matures to form a crystal nucleus which will remain stable only if it has reached a “critical size,” whereby a sustainable nucleus has formed that allows for crystal growth. Heterogeneous nucleation, which toccurs on a surface rather than in solution, is energetically more favorable than homogeneous nucleation. Surfaces provide interfacial interactions resulting in increased rates of nucleation as well as a smaller critical nucleus. More simply, the four steps of crystal formation are nucleation, growth, aggregation, and attachment of aggregates to epithelial cells.
Kidney stones, which are aggregates of small crystals containing primarily calcium oxalate monohydrate (COM), and small amounts of embedded proteins, form through the nucleation process described above. Kidney stones affect over 10% of the US population, causing intense discomfort and possible renal failure. Although the mechanism of stone formation is not entirely understood, studies have been conducted using atomic force microscopy to investigate the adhesion characteristics of different crystal faces of COM to calcium oxalate. Further investigation of the nucleation and growth of these crystals must be conducted, however, to design new pharmaceuticals that could disperse formed aggregates or block crystal aggregation entirely.
Calcium oxalate monohydrate forms crystals more readily than calcium oxalate dihydrate (COD). We would like to examine how surface composition affects the rate of crystal formation between these two species of calcium oxalate. Crystal formation on epithelial cells is affected by functional groups such as carboxylates found in aspartic acid. We would like to determine how exposed intracellular proteins containing various functionalities affect crystal nucleation.
Intact phospholipid bilayer liposomes bound to silicon oxide wafers will be used to simulate cell membranes where nucleation occurs. Kidney stones form primarily on damaged cell membranes, where functional groups become exposed to the surrounding aqueous media. The surface of the membrane can be both decorated with different peptide sequences or reinforced with cholesterol to stiffen the nucleation surface. To mimic the human body, all experiments will be carried out at approximately 36.6 C. We can observe with AFM how calcium oxalate attaches to cell membranes.
Porter Williams
Project
Title: Nylon-DNA
Polymers
REU Faculty Advisor: Professor Nadrian Seeman and Professor James Canary
Research Synopsis:
The SESMI REU Summer 2007 Research on the topic of Nylon-DNA Polymers will be following the previous work of Professor Nadrian Seeman and Professor James Canary. The goal of this project is to use DNA as a template to build nylon polymers with specific properties that cannot be obtained using classical polymer synthesis techniques. This was accomplished through the “preparation of 2’-β-substituted phosphoramidites, synthesis of oligonucleotides with appended amine and carboxylate groups, and coupling of the pendent groups to form oligopeptide strands covalently linked at each base pair to give a nylon/DNA ladder polymer” (Zhu, Lukeman, Canary, & Seeman, 2003). The use of DNA as a template will give the opportunity to specifically design optical, electrical, stereochemical, or specific shapes that are desired of the polymer being created (Zhu et al.). In the case of this summer, the polyamide will be monodispersed, all the molecules having the same mass, which is something that cannot be prepared with current methods. The assembly of molecules using nanometer precision also gives the opportunity to create polyamides with unique shape, such as the trefoil knot which is extremely uncommon. DNA structures that will be utilized include a quadruple branched junction that must use 1:1:1:1 stoichiomtry and non-symmetry in order to properly form (Kallenbach, Ma, & Seeman, 1983). A Jy junction of DNA with two complementary sticky ends will also be used allowing the formation of a cyclic structure which can be isolated using radioactive 32P to identify the cyclic strands after the ligation of the helical DNA using Exonuclease III of E. Coli (Ma, Kallenbach, Sheardy, Petrillo, & Seeman, 1986). Finally, a two dimensional DNA crystal will be created using specific patterns that are designed at the nanometer scale (Winfree, Liu, Wenzler, & Seeman, 1998). DNA is purified using Polyacrylamide gel electrophoresis. Positive confirmation of the purified DNA is found using atomic force microscopy.
References
REU Faculty Advisor: Professor Nadrian Seeman and Professor James Canary
Research Synopsis:
The SESMI REU Summer 2007 Research on the topic of Nylon-DNA Polymers will be following the previous work of Professor Nadrian Seeman and Professor James Canary. The goal of this project is to use DNA as a template to build nylon polymers with specific properties that cannot be obtained using classical polymer synthesis techniques. This was accomplished through the “preparation of 2’-β-substituted phosphoramidites, synthesis of oligonucleotides with appended amine and carboxylate groups, and coupling of the pendent groups to form oligopeptide strands covalently linked at each base pair to give a nylon/DNA ladder polymer” (Zhu, Lukeman, Canary, & Seeman, 2003). The use of DNA as a template will give the opportunity to specifically design optical, electrical, stereochemical, or specific shapes that are desired of the polymer being created (Zhu et al.). In the case of this summer, the polyamide will be monodispersed, all the molecules having the same mass, which is something that cannot be prepared with current methods. The assembly of molecules using nanometer precision also gives the opportunity to create polyamides with unique shape, such as the trefoil knot which is extremely uncommon. DNA structures that will be utilized include a quadruple branched junction that must use 1:1:1:1 stoichiomtry and non-symmetry in order to properly form (Kallenbach, Ma, & Seeman, 1983). A Jy junction of DNA with two complementary sticky ends will also be used allowing the formation of a cyclic structure which can be isolated using radioactive 32P to identify the cyclic strands after the ligation of the helical DNA using Exonuclease III of E. Coli (Ma, Kallenbach, Sheardy, Petrillo, & Seeman, 1986). Finally, a two dimensional DNA crystal will be created using specific patterns that are designed at the nanometer scale (Winfree, Liu, Wenzler, & Seeman, 1998). DNA is purified using Polyacrylamide gel electrophoresis. Positive confirmation of the purified DNA is found using atomic force microscopy.
References
- Kallenbach, Neville R.; Ma, Rong-Ine; Seeman, Nadrian C. “An Immobile Nucleic Acid Junction Constructed from Oligonucleotides,” Nature, 1983, 305(27), 829-31.
- Ma, Rong-Ine; Kallenbach, Neville R.; Sheardy, Richard D; Petrillo, Mary L; Seeman, Nadrian C. “Three-arm Nucleic Acid Junctions are Flexible,” Nature, 1986, 14(24), 9745-53.
- Seeman, Nadrian C. “Nanotechnology and the Double Helix,” Scientific American, Inc., Jun. 2004, 65-75.
- Winfree, Erik; Liu, Furong; Wenzler, Lisa A.; Seeman, Nadrian C. “Design and Self-Assembly of Two-Dimensional DNA Crystals,” Nature, 1998, 394, 539-44.
- Zhu, Lei; Lukeman, Philip S.; Canary, James W.; Seeman, Nadrian C. “Nylon/DNA: Single-Stranded DNA with a Covalently Stitched Nylon Lining,” Journal of the American Chemical Society, 2003, 125(34), 10178-79.
Lauren Martini
Project
Title: Organic Polymers
REU Faculty Advisor: Professor James W. Canary
Research Synopsis:
Much of the work done in Professor James Canary’s lab is centered on nanotechnology. Nanotechnology focuses on research development at the atomic, molecular, or macromolecular level to create structures, devices, and systems that have novel properties and functions due to their small size. Various building blocks are being explored to assemble nanoscale devices and materials, among which DNA stands out as an excellent candidate. Previous work in Professor Ned Seeman’s lab has shown that single-stranded DNA can be ligated to form DNA structures with unique topological properties such as a cube device, a truncated octahedron, a trefoil knot, and even molecular Borromean rings made from DNA. This work is possible because opposite strands of DNA have complimentary relationships, with interactions that enable the combination of molecules in a desired, specific fashion. This characteristic permits us to produce molecules with predictable topological properties. A potential application would be the production of two-dimensional molecular chain-mail out of circular DNA on a macroscopic scale that could serve as a strong and lightweight synthetic material. Even though DNA is a wonderful building block, it is sensitive to air and electromagnetic radiation and therefore does not offer the same practical advantages enjoyed by organic polymers such as nylon.
The project in Professor Canary’s lab uses the topological structures made of DNA as templates for the synthesis of a new material by translating DNA nanotechnology into nylon nanotechnology. From unmodified RNA, 2’-β-substituted phosphoramidites are synthesized with modified pendant chains protected by amino or carboxyl groups. Automated DNA synthesis is used to form an oligonucleotide chain. The alternating amine and carboxylate groups on neighboring nucleic acids are coupled by condensation to form a nylon ladder polymer on the oligonucleic acid template. Finally the nylon-polymer is cleaved from its template by reductive desulfurization. The desired result of this four-step process is a nylon-polymer with a topology identical to its oligonucleic acid template.
To date, this technology has only been used to produce single-strand nylon polymers due to the fact that only 2’-modified phosphoramidites containing uridine and cytidine have been synthesized. Once the 2’-modified nucleosides containing all four nucleobases are synthesized, nylon nanostructures may be produced with the same unique topological properties as the DNA produced in Professor Seeman’s lab. My work for this summer will focus on the synthesis of the 2’-modified nucleoside containing adenine
REU Faculty Advisor: Professor James W. Canary
Research Synopsis:
Much of the work done in Professor James Canary’s lab is centered on nanotechnology. Nanotechnology focuses on research development at the atomic, molecular, or macromolecular level to create structures, devices, and systems that have novel properties and functions due to their small size. Various building blocks are being explored to assemble nanoscale devices and materials, among which DNA stands out as an excellent candidate. Previous work in Professor Ned Seeman’s lab has shown that single-stranded DNA can be ligated to form DNA structures with unique topological properties such as a cube device, a truncated octahedron, a trefoil knot, and even molecular Borromean rings made from DNA. This work is possible because opposite strands of DNA have complimentary relationships, with interactions that enable the combination of molecules in a desired, specific fashion. This characteristic permits us to produce molecules with predictable topological properties. A potential application would be the production of two-dimensional molecular chain-mail out of circular DNA on a macroscopic scale that could serve as a strong and lightweight synthetic material. Even though DNA is a wonderful building block, it is sensitive to air and electromagnetic radiation and therefore does not offer the same practical advantages enjoyed by organic polymers such as nylon.
The project in Professor Canary’s lab uses the topological structures made of DNA as templates for the synthesis of a new material by translating DNA nanotechnology into nylon nanotechnology. From unmodified RNA, 2’-β-substituted phosphoramidites are synthesized with modified pendant chains protected by amino or carboxyl groups. Automated DNA synthesis is used to form an oligonucleotide chain. The alternating amine and carboxylate groups on neighboring nucleic acids are coupled by condensation to form a nylon ladder polymer on the oligonucleic acid template. Finally the nylon-polymer is cleaved from its template by reductive desulfurization. The desired result of this four-step process is a nylon-polymer with a topology identical to its oligonucleic acid template.
To date, this technology has only been used to produce single-strand nylon polymers due to the fact that only 2’-modified phosphoramidites containing uridine and cytidine have been synthesized. Once the 2’-modified nucleosides containing all four nucleobases are synthesized, nylon nanostructures may be produced with the same unique topological properties as the DNA produced in Professor Seeman’s lab. My work for this summer will focus on the synthesis of the 2’-modified nucleoside containing adenine