AN OVERVIEW OF DNA COMPUTING

THE NEED FOR QUICKER INFORMATION PROCESSING AND DENSER DATA STORAGE IS ACCELERATING
THE DEVELOPMENT OF NEW COMPUTATION PARADIGMS. BECAUSE OF ITS PREDICTABLE BASE PAIRS
AND NANOSCALE SIZE FOR PROGRAMMABLE AND HIGH-THROUGHPUT CODING AS WELL AS
COMPUTING, DNA, AS AN ESSENTIAL BIOMOLECULE THAT CONVEYS GENETIC INFORMATION, HAS
DEMONSTRATED TREMENDOUS POTENTIAL IN INFORMATION PROCESSING AND STORAGE. IN ADDITION
TO CONTROLLING GENE EXPRESSION AND KEEPING TRACK OF CELLULAR BIOCHEMICAL PROCESSES, DNA
ALSO PLAYS CRUCIAL ROLES IN BIOLOGICAL TASKS. NEW AREAS OF DNA COMPUTING IN BIOLOGY AND
BIOMEDICINE ARE CREATED WHEN THESE SKILLS ARE COMBINED. HERE, THE MOST RECENT AND
SIGNIFICANT ADVANCEMENTS IN DNA-BASED COMPUTING FOR BIOMEDICAL APPLICATIONS ARE
DISCUSSED, WITH A FOCUS ON BIOSENSING RELATED TO DIAGNOSTICS. A DISCUSSION IS ALSO HAD
ABOUT THE CONCEPTION AND APPLICATION OF DNA COMPUTING SYSTEMS AT ALL DEVELOPMENT
STAGES. THE GOAL IS TO ESTABLISH DNA COMPUTING AS A CREDIBLE TOOL FOR SOPHISTICATED
DIAGNOSTICS.

IN PLACE OF STANDARD ELECTRONIC COMPUTING, A NEW FIELD OF UNCONVENTIONAL COMPUTING

CALLED DNA COMPUTING MAKES USE OF HARDWARE RELATED TO MOLECULAR BIOLOGY,
BIOCHEMISTRY, AND DNA. THE THEORY, TESTS, AND APPLICATIONS OF DNA COMPUTING ARE THE
SUBJECT OF THIS RESEARCH AND DEVELOPMENT. A CONTEMPORARY BRANCH OF STUDY CALLED DNA
COMPUTING ACKNOWLEDGES THAT BIOMOLECULES ARE ESSENTIAL COMPONENTS OF ELECTRONIC
DEVICES. THIS HAS CONNECTIONS TO CHEMISTRY, SOFTWARE ENGINEERING, CELL GENETICS, PHYSICS,
AND ARITHMETIC, AMONG OTHER FIELDS. INSTEAD OF USING TRADITIONAL SILICON CHIPS,
COMPUTING IS DONE WITH ORGANIC MOLECULES. ALTHOUGH IT HAS A CONCEPTUAL HISTORY DATING
BACK TO THE EARLY 1950S, THE PRINCIPLE OF COMPUTING WITH MOLECULES WAS NOT SCIENTIFICALLY
UNDERSTOOD UNTIL 1994, WHEN LEONARD ADLEMAN USED CONVENTIONAL MOLECULAR BIOLOGY
TECHNIQUES IN THE LAB TO DEMONSTRATE THE SOLUTION TO A SMALL PORTION OF A VERY WELL-
KNOWN COMBINATORIAL PROBLEM. SINCE THE PUBLICATION OF THIS PAPER, INTEREST IN DNA
COMPUTING HAS GROWN SUBSTANTIALLY, AND THE TOPIC IS CURRENTLY ONE OF THE MOST WELL-
ESTABLISHED. LEONARD ADLEMAN DEMONSTRATED THE USE OF MOLECULES TO SOLVE A STATISTICAL
ISSUE. FOR THE NEXT GENERATION OF COMPUTER CHIPS THEY NEED, SCIENTISTS HAVE FOUND A NEW
SUBSTANCE. SIMILAR TO YOUR BODY, LIVING ORGANISMS INCLUDE HUNDREDS OF THOUSANDS OF
NATURALLY POWERFUL COMPUTERS. DNA (DEOXYRIBONUCLEIC ACID) MOLECULES, WHICH MAKE UP
OUR GENES, ARE CAPABLE OF PRODUCING DATA THAT IS MANY TIMES MORE ABUNDANT THAN THE
MOST ADVANCED HUMAN-MADE COMPUTING SYSTEMS. THIS ENTHUSIASM WAS CAUSED BY THE
AFFORDABILITY, RELATIVE EASE OF PRODUCTION, AND ADAPTABILITY OF DNA MOLECULES. THERE IS NO
UPPER LIMIT TO THE CAPACITY THAT DNA COMPUTATION CAN POTENTIALLY HAVE AS POWER IS
INCREASED AND MORE AND MORE COMPOUNDS ARE ADDED TO THE EQUATION, BUT UNLIKE SILICON
TRANSISTORS, WHICH CAN ONLY CONDUCT ONE LOGICAL ITEM AT A TIME, THESE DNA STRUCTURES
CAN POTENTIALLY CONDUCT AS MANY OPERATIONS AT A TIME AS ARE NECESSARY TO SOLVE A
PROBLEM AND DO EVERYTHING AT ONCE. THE POSSIBILITY OF USING DNA TO STORE DATA HAS LONG
BEEN RECOGNIZED BY SCIENTISTS. DNA COMPUTERS USE A TOTALLY DIFFERENT METHOD TO ADDRESS
PROBLEMS THAN CONVENTIONAL SYSTEMS. WHEN THEY REACH A T-JUNCTION, MODERN ELECTRONIC
PROCESSORS MUST CHOOSE WHICH PATH TO TAKE, BUT A DNA COMPUTER DOESN'T HAVE TO MAKE A
DECISION BECAUSE IT REPLICATES ITSELF BY TRAVELING IN BOTH DIRECTIONS SIMULTANEOUSLY.
ALREADY, DNA MOLECULES HAVE BEEN USED TO TACKLE CHALLENGING MATHEMATICAL PROBLEMS.
ALTHOUGH THEY ARE STILL IN THE RESEARCH AND DEVELOPMENT STAGES, DNA COMPUTERS WILL BE
ABLE TO STORE BILLIONS OF TIMES MORE DATA THAN YOUR CURRENT COMPUTER. IN THE COMING
TEN YEARS, GENETIC MATERIAL WILL BE USED BY THE RESEARCHERS TO BUILD NANO-COMPUTERS THAT
COULD DISPLACE SILICON-BASED DEVICES. THE FIRST DNA COMPUTER PROTOTYPE WAS UNVEILED IN
1994 BY LEONARD ADLEMAN. A 100-MICROLITER SOLUTION OF DNA WAS CONTAINED IN THE TT-100
TEST TUBE. AN INSTANCE OF THE DIRECTED HAMILTONIAN ROUTE PROBLEM WAS SUCCESSFULLY
RESOLVED BY HIM. THE TRAVELING SALESMAN ISSUE WAS USED TO IMPLEMENT THE HAMILTONIAN
PATH ISSUE IN ADLEMAN'S EXPERIMENT. IN ORDER TO ACHIEVE THIS, VARIOUS DNA FRAGMENTS WERE
MADE, EACH OF WHICH STOOD IN FOR A REQUIRED METROPOLIS. ALL OF THESE PIECES HAVE THE
ABILITY TO CONNECT TO THE OTHER PIECES THAT WERE MADE. IN A TEST TUBE, THESE DNA
FRAGMENTS WERE CREATED AND COMBINED. THE LITTLE FRAGMENTS, WHICH REPRESENT THE MANY
TRAVEL ROUTES, COMBINE TO PRODUCE LARGER ONES IN A MATTER OF SECONDS. THE DNA SEGMENTS
REPRESENTING THE LONGER ROUTES WERE REMOVED USING A CHEMICAL PROCESS. THE EXPERIMENT
LASTED A WEEK IN ALL, AND THE SOLUTION IS IN THE REMAINS. HOWEVER, EXISTING TECHNICAL
CONSTRAINTS MAKE IT IMPOSSIBLE TO EVALUATE THE OUTCOMES. THE EXPERIMENT IS THEREFORE
NOT APPROPRIATE FOR THE APPLICATION, BUT IT STILL SERVES AS A PROOF OF CONCEPT.

CAPABILITIES

DNA COMPUTING IS A TYPE OF PARALLEL COMPUTING SINCE IT MAKES USE OF THE NUMEROUS DNA
MOLECULES TO TEST SEVERAL OPTIONS CONCURRENTLY. FOR SOME SPECIALIZED SITUATIONS, DNA
COMPUTERS ARE QUICKER AND MORE COMPACT THAN ANY OTHER COMPUTER EVER CREATED.
FURTHERMORE, IT HAS BEEN PROVEN THAT A DNA COMPUTER CAN DO SPECIFIC MATHEMATICAL
OPERATIONS. COMPATIBILITY THEORY, THE STUDY OF WHICH PROBLEMS ARE COMPUTATIONALLY
SOLVABLE USING VARIOUS MODELS OF COMPUTATION, DOES NOT REVEAL THAT DNA COMPUTING
OFFERS ANY NEW CAPABILITIES. FOR INSTANCE, IF THE AMOUNT OF SPACE NEEDED TO SOLVE A
PROBLEM RISES EXPONENTIALLY WITH ITS SIZE ON VON NEUMANN MACHINES (EXPSPACE ISSUES), IT
CONTINUES TO DO SO ON DNA MACHINES. THE AMOUNT OF DNA NEEDED IS TOO MUCH FOR
PRACTICAL USE IN REALLY BIG EXPSPACE PROBLEMS.

THE DNA COMPUTER’S EXPERIMENTS AND SUCCESSES

IN ORDER TO DISTINGUISH INFECTED CELLS FROM CERTAIN VERY HEALTHY CELLS, SCIENTISTS HAVE
DEVELOPED A NEW TYPE OF DNA DEVICE THAT WORKS IN LIVING BEINGS. THIS DISCOVERY MAY PAVE
THE WAY FOR A DIFFERENT APPROACH. A PROCESS KNOWN AS RNA INTERFERENCE (RNAI), IN WHICH
TINY RNA MOLECULES PREVENT A GENE FROM PRODUCING PROTEIN, POWERS THE DEVICE. THE
SUCCESS OF THE ADLEMAN DNA COMPUTER DEMONSTRATES THE POTENTIAL OF DNA AS A TOOL FOR
SOLVING CHALLENGING MATHEMATICAL PROBLEMS. HOWEVER, IN TERMS OF EFFICIENCY, THIS FIRST
DNA MACHINE IS FAR FROM BECOMING A THREAT TO SILICON-BASED COMPUTERS. USING SIX-BIT
INPUTS TO EFFICIENTLY RUN THEIR OWN PROGRAM, COMPUTER SCIENTISTS FROM DAVIS AND
CALTECH UNIVERSITY IN CALIFORNIA HAVE DEVELOPED DNA MOLECULES THAT CAN SELF-ASSEMBLE
INTO FRAMEWORKS. WHEN BIOPROCESSOR TECHNOLOGY ADVANCES TO THE POINT WHERE IT CAN
RUN MORE COMPLEX ALGORITHMS, MICROSOFT WILL ALSO PROVIDE A PROGRAMMING LANGUAGE
FOR DNA COMPUTING THAT WILL HELP MAKE DNA COMPUTING FUNCTIONAL. ADDITIONALLY,
MICROSOFT WANTS TO SIGNIFICANTLY EXPAND DNA STORAGE SPACE FOR ITS CLOUD COMPUTING BY
2020 AND INTEGRATE DNA COMPUTING INTO ITS CLOUD SERVICES. THE ADLEMAN DNA MACHINE
QUICKLY GENERATED A RANGE OF POTENTIAL SOLUTIONS, BUT IT TOOK ADLEMAN DAYS TO NARROW
THE CHOICES. THE GOAL OF THE FIELD OF DNA COMPUTING IS TO CREATE A SYSTEM THAT CAN
FUNCTION WITHOUT HUMAN INVOLVEMENT. IT WILL TAKE SOME TIME FOR THE DNA COMPUTER
COMPONENTS TO DEVELOP INTO A WORKABLE, PRACTICAL DNA DEVICE, INCLUDING LOGIC GATES AND
BIOCHIPS. ACCORDING TO SCIENTISTS, IF SUCH A COMPUTER WERE EVER CREATED, IT WOULD BE MORE
PORTABLE, DEPENDABLE, AND POWERFUL THAN COMPUTERS USED TODAY.

DNA-BASED COMPUTERS HAVE ADVANTAGES.

BY ASSIGNING DNA STRANDS TO THE CITIES ON A MAP AND TO THE CONNECTIONS BETWEEN THE
CITIES, THE PROCESS BEGINS WITH THE USE OF DNA. THE INTERACTIONS BETWEEN THE CITY STRANDS
ARE TO BE LINKED, FORMING STRANDS THAT FORM ROUTES BETWEEN THE DIFFERENT CITIES. THEN,
THE STRANDS ARE SET UP SO THAT ONLY THE RIGHT NUMBER OF CITIES ARE CONNECTED. THOUSANDS
OF THOUSANDS OF TASKS CAN BE COMPLETED SIMULTANEOUSLY. DUE TO THEIR MASSIVELY PARALLEL
PROCESSING CAPABILITIES, DNA COMPUTERS MAY BE ABLE TO FIND SOLUTIONS TO PROBLEMS THAT
WOULD OTHERWISE BE INTRACTABLE. THEY MAY ALSO BE ABLE TO SPEED UP LARGE-SCALE,
POLYNOMIAL-TIME PROBLEMS THAT ARE FREQUENTLY EMPLOYED TO BOOST THE EFFICIENCY OF A FEW
PROCEDURES. THE DNA IS TRANSPORTED THROUGH FILTRATION; EACH FILTER ONLY GATHERS DNA
THAT INCLUDES A SPECIFIC SECTION BECAUSE THERE IS "STILL THE RISK THAT A FEW OF THE STRANDS
WOULD INCLUDE THE SAME CITY TWICE." (EACH SECTION REPRESENTING A REGION). THE FACT THAT
THIS APPROACH TO DNA RUNS IN "PARALLEL" AND ANALYZES ALL POTENTIAL OUTCOMES
SIMULTANEOUSLY IS ANOTHER BENEFIT. AS A RESULT, IT MAKES IT POSSIBLE TO UNDERTAKE
NUMEROUS SIMULTANEOUS INQUIRIES AND GENERATE A COMPLETE SET OF POTENTIAL SOLUTIONS.
DNA CAN SUPPORT ENORMOUS AMOUNTS OF WORKING MEMORY BY PACKING MORE INFORMATION
PER CUBIC CENTIMETER THAN A TRILLION CDS, ACCORDING TO RESEARCH. THE ENERGY EFFICIENCY OF
THE DNA MACHINE IS SUBSTANTIALLY GREATER THAN A THOUSAND TIMES THAT OF A COMPUTER, AND
IT ALSO CONSUMES VERY LITTLE POWER, EVEN IF IT IS MOUNTED INSIDE A CELL. EVEN THOUGH THEY
ARE STILL IN THEIR INFANCY, DNA-BASED TECHNOLOGIES CAN STORE BILLIONS OF TIMES MORE DATA
THAN A HOME COMPUTER. ALL ALTERNATE ROUTES THROUGH THE CITIES ARE REFLECTED IN THE DNA
STRANDS THAT THE FILTERS MANAGE TO SURVIVE.

THE DNA COMPUTING OF THE FUTURE

DNA COMPUTING IS PARTICULARLY EXCITING BECAUSE IT COMBINES THE WORK OF CHEMISTS,

BIOLOGISTS, MATHEMATICIANS, AND SOFTWARE ENGINEERS TO IDENTIFY AND MIMIC CRUCIAL
BIOLOGICAL PROCESSES AND ALGORITHMS THAT TAKE PLACE INSIDE CELLS. LINEAR CALCULATIONS ARE
CARRIED OUT BY CONVENTIONAL MACHINES. (THAT IS, ASSUME TASKS ONE AT A TIME.) HOWEVER, THE
PARALLEL COMPUTATIONAL ABILITY OF DNA MIGHT SOLVE MATHEMATICAL PROBLEMS IN HOURS THAT
WOULD TAKE ELECTRICAL COMPUTERS MANY YEARS. DESPITE THE FACT THAT THE DNA MACHINE IS
STILL IN ITS EARLY STAGES OF RESEARCH, SEVERAL APPLICATIONS ARE ALREADY IN USE. (OR
UNDERACTIVE TECHNOLOGIES).

IN TERMS OF TECHNOLOGY, THE DATA ENCRYPTION STANDARD, OR DES, HAS PREVIOUSLY BEEN
CRACKED USING TRADITIONAL DNA COMPUTING METHODS. THE DNA MODELS ARE MUCH MORE
FLEXIBLE, EFFICIENT, AND COST-EFFECTIVE, EVEN IF THIS ACTIVITY HAS ALREADY BEEN COMPLETED
USING CONVENTIONAL METHODS IN A LOT LESS TIME THAN SUGGESTED BY DNA APPROACHES. ISRAELI
SCIENTISTS HAVE CREATED A MACHINE MADE OF ENZYMES AND DNA.