19 Result(s)
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Milan N. Stojanovic
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Article
Carbon-nanotube field-effect transistors for resolving single-molecule aptamer–ligand binding kinetics
Small molecules such as neurotransmitters are critical for biochemical functions in living systems. While conventional ultraviolet–visible spectroscopy and mass spectrometry lack portability and are unsuitable...
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Article
Microfluidic isolation of aptamers with affinity towards multiple myeloma monoclonal immunoglobulins
Multiple myeloma (MM) is a bone marrow cancer of resident plasma cells that affects 125,000 patients in the U.S. with about 30,000 new cases per year. Its signature is the clonal proliferation of a single plas...
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Chapter
Implementing Molecular Logic Gates, Circuits, and Cascades Using DNAzymes
The programmable nature of DNA chemistry makes it an attractive framework for the implementation of unconventional computing systems. Our early work in this area was among the first to use oligonucleotide-base...
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Article
Open AccessIntegrated Microfluidic Isolation of Aptamers Using Electrophoretic Oligonucleotide Manipulation
We present a microfluidic approach to integrated isolation of DNA aptamers via systematic evolution of ligands by exponential enrichment (SELEX). The approach employs a microbead-based protocol for the process...
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Article
Recognition and sensing of low-epitope targets via ternary complexes with oligonucleotides and synthetic receptors
Oligonucleotide-based receptors or aptamers can interact with small molecules, but the ability to achieve high-affinity and specificity of these interactions depends strongly on functional groups or epitopes d...
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Chapter
The Effects of Multivalency and Kinetics in Nanoscale Search by Molecular Spiders
Molecular spiders are nanoscale walkers made with catalytic DNA legs attached to a rigid body. They move over a surface of DNA substrates, cleaving them and leaving behind product DNA strands, which they are a...
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Article
Autonomous molecular cascades for evaluation of cell surfaces
Molecular automata are mixtures of molecules that undergo precisely defined structural changes in response to sequential interactions with inputs1,2,3,4. Previously studied nucleic acid-based automata include gam...
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Chapter and Conference Paper
Computing Game Strategies
We revisit the problem of constructing strategies for simple position games. We derive a general, executable formalism for describing game rules and desired strategy properties. We present the outcomes for sev...
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Protocol
Development of Trainable Deoxyribozyme-Based Game Playing Automaton
Molecular automata are self-operating machines serially exchanging information with their environment while changing their configurations. Molecular protoautomata are devices trained in a series of sessions wi...
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Article
Training a molecular automaton to play a game
Research at the interface between chemistry and cybernetics has led to reports of ‘programmable molecules’, but what does it mean to say ‘we programmed a set of solution-phase molecules to do X’? A survey of r...
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Article
Molecular robots guided by prescriptive landscapes
Programming the behaviour of molecules in time and space is a big challenge in nanotechnology. Traditional robots can be given a memory in which to store internal representations of their goals and environment...
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Chapter
Nucleic Acids for Computation
Nucleic acids have many features that are ideal for molecular computation. Using nucleic acids, we have constructed a full set of molecular logic gates, with modular stem-loop-controlled deoxyribozymes as swit...
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Article
DNA-based Nanosystems
DNA-based nanosystems have emerged as an interdisciplinary field that draws on computer science, biochemistry, material science, and engineering. Although the field is still in its infancy, fundamental methodo...
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Article
Study of thiazole orange in aptamer-based dye-displacement assays
We screened a series of RNA and DNA aptamers for their ability to serve in the dye displacement assays in which analytes compete with TO dye. We conclude that, while the performance of the TO dye displacement ...
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Protocol
Solution-Phase Molecular-Scale Computation With Deoxyribozyme-Based Logic Gates and Fluorescent Readouts
Recent development of solution-phase molecular-scale Boolean calculations using deoxyribozymes is potentially an important step toward the development of autonomous therapeutic and diagnostic devices. Here, th...
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Chapter
Bottom-up Approach to Complex Molecular Behavior
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Article
Boolean calculations made easy (for ribozymes)
A new algorithm facilitates the design of ribozymes that encode logical operations.
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Chapter and Conference Paper
Building the Components for a Biomolecular Computer
We propose a new method for amorphous bio-compatible computing using deoxyribozyme logic gates [1] in which oligonucleotides act as enzymes on other oligonucleotides, yielding oligonucleotide products. Moreove...
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Article
A deoxyribozyme-based molecular automaton
We describe a molecular automaton, called MAYA, which encodes a version of the game of tic-tac-toe and interactively competes against a human opponent. The automaton is a Boolean network of deoxyribozymes that...
