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Dive into the research topics where Anthony G. Frutos is active.

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Featured researches published by Anthony G. Frutos.


Nature | 2000

DNA computing on surfaces

Qinghua Liu; Liman Wang; Anthony G. Frutos; Anne Condon; Robert M. Corn; Lloyd M. Smith

DNA computing was proposed as a means of solving a class of intractable computational problems in which the computing time can grow exponentially with problem size (the ‘NP-complete’ or non-deterministic polynomial time complete problems). The principle of the technique has been demonstrated experimentally for a simple example of the hamiltonian path problem (in this case, finding an airline flight path between several cities, such that each city is visited only once). DNA computational approaches to the solution of other problems have also been investigated. One technique involves the immobilization and manipulation of combinatorial mixtures of DNA on a support. A set of DNA molecules encoding all candidate solutions to the computational problem of interest is synthesized and attached to the surface. Successive cycles of hybridization operations and exonuclease digestion are used to identify and eliminate those members of the set that are not solutions. Upon completion of all the multi-step cycles, the solution to the computational problem is identified using a polymerase chain reaction to amplify the remaining molecules, which are then hybridized to an addressed array. The advantages of this approach are its scalability and potential to be automated (the use of solid-phase formats simplifies the complex repetitive chemical processes, as has been demonstrated in DNA and protein synthesis). Here we report the use of this method to solve a NP-complete problem. We consider a small example of the satisfiability problem (SAT), in which the values of a set of boolean variables satisfying certain logical constraints are determined.


Proceedings of the National Academy of Sciences of the United States of America | 2003

Rare earth-doped glass microbarcodes

Matthew John Dejneka; Alexander Mikhailovich Streltsov; Santona Pal; Anthony G. Frutos; Christy Lynn Powell; Kevin Joseph Yost; Po Ki Yuen; Uwe R. Müller; Joydeep Lahiri

The development of ultraminiaturized identification tags has applications in fields ranging from advanced biotechnology to security. This paper describes micrometer-sized glass barcodes containing a pattern of different fluorescent materials that are easily identified by using a UV lamp and an optical microscope. A model DNA hybridization assay using these “microbarcodes” is described. Rare earth-doped glasses were chosen because of their narrow emission bands, high quantum efficiencies, noninterference with common fluorescent labels, and inertness to most organic and aqueous solvents. These properties and the large number (>1 million) of possible combinations of these microbarcodes make them attractive for use in multiplexed bioassays and general encoding.


Journal of Computational Biology | 1998

A Surface-Based Approach to DNA Computation

Lloyd M. Smith; Robert M. Corn; Anne Condon; Max G. Lagally; Anthony G. Frutos; Qinghua Liu; Andrew J. Thiel

A scalable approach to DNA-based computations is described. Complex combinatorial mixtures of DNA molecules encoding all possible answers to a computational problem are synthesized and attached to the surface of a solid support. This set of molecules is queried in successive MARK (hybridization) and DESTROY (enzymatic digestion) operations. Determination of the sequence of the DNA molecules remaining on the surface after completion of these operations yields the answer to the computational problem. Experimental demonstrations of aspects of the strategy are presented.


BioSystems | 1999

Progress toward demonstration of a surface based DNA computation: a one word approach to solve a model satisfiability problem

Qinghua Liu; Anthony G. Frutos; Liman Wang; Andrew J. Thiel; Susan D. Gillmor; C.Todd Strother; Anne Condon; Robert M. Corn; Max G. Lagally; Lloyd M. Smith

A multi-base encoding strategy is used in a one word approach to surface-based DNA computation. In this designed DNA model system, a set of 16 oligonucleotides, each a 16mer, is used with the format 5-FFFFvvvvvvvvFFFF-3 in which 4-8 bits of data are stored in eight central variable (v) base locations, and the remaining fixed (F) base locations are used as a word label. The detailed implementations are reported here. In order to achieve perfect discrimination between each oligonucleotide, the efficiency and specificity of hybridization discrimination of the set of 16 oligonucleotides were examined by carrying out the hybridization of each individual fluorescently tagged complement to an array of 16 addressed immobilized oligonucleotides. A series of preliminary hybridization experiments are presented and further studies about hybridization, enzymatic destruction, read out and demonstrations of a SAT problem are forthcoming.


BioSystems | 1999

Surface-based DNA computing operations: DESTROY and READOUT

Liman Wang; Qinghua Liu; Anthony G. Frutos; Susan D. Gillmor; Andrew J. Thiel; Todd Strother; Anne Condon; Robert M. Corn; Max G. Lagally; Lloyd M. Smith

DNA computing on surfaces is where complex combinatorial mixtures of DNA molecules are immobilized on a substrate and subsets are tagged and enzymatically modified (DESTROY) in repeated cycles of the DNA computation. A restriction enzyme has been chosen for the surface DESTROY operation. For the READOUT operation, both cycle sequencing and PCR amplification followed by addressed array hybridization were studied to determine the DNA sequences after the computations.


Journal of Computational Biology | 1998

DNA computing on surfaces: encoding information at the single base level.

Qinghua Liu; Anthony G. Frutos; Andrew J. Thiel; Robert M. Corn; Lloyd M. Smith

The feasibility of encoding a bit (0 or 1) of information for DNA-based computations at the single nucleotide level is evaluated, particularly with regard to the efficiency and specificity of hybridization discrimination. Hybridization experiments are performed on addressed arrays of 32 (2(5)) distinct oligonucleotides immobilized on chemically modified glass and gold surfaces with information encoded in a binary (base 2) format. Similar results are obtained on both glass and gold surfaces and the results are generally consistent with thermodynamic calculations of matched and mismatched duplex stabilities. It is found that under the conditions required to obtain single nucleotide specificity in the hybridization process, hybridization efficiency is low, compromising the utility of single nucleotide encoding for DNA computing applications in the absence of some additional mechanism for increasing specificity. Several methods are suggested to provide such increased discrimination.


Analytical Chemistry | 1997

Surface plasmon resonance imaging measurements of DNA hybridization adsorption and streptavidin/DNA multilayer formation at chemically modified gold surfaces

Claire E. Jordan; Anthony G. Frutos; and Andrew J. Thiel; Robert M. Corn


Nucleic Acids Research | 1997

Demonstration of a word design strategy for DNA computing on surfaces

Anthony G. Frutos; Qinghua Liu; Andrew J. Thiel; Anne Marie W. Sanner; Anne Condon; Lloyd M. Smith; Robert M. Corn


Analytical Chemistry | 1997

In Situ Surface Plasmon Resonance Imaging Detection of DNA Hybridization to Oligonucleotide Arrays on Gold Surfaces

Andrew J. Thiel; Anthony G. Frutos; Claire E. Jordan; and Robert M. Corn; Lloyd M. Smith


Analytical Chemistry | 1999

Near-Infrared Surface Plasmon Resonance Measurements of Ultrathin Films. 1. Angle Shift and SPR Imaging Experiments

Bryce P. Nelson; Anthony G. Frutos; and Jennifer M. Brockman; Robert M. Corn

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Robert M. Corn

University of California

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Lloyd M. Smith

University of Wisconsin-Madison

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Andrew J. Thiel

University of Wisconsin-Madison

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Qinghua Liu

University of Wisconsin-Madison

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Anne Condon

University of British Columbia

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Liman Wang

University of Wisconsin-Madison

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Max G. Lagally

University of Wisconsin-Madison

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Susan D. Gillmor

George Washington University

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