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Use Style: Paper Title South Asian Journal of Engineering and Technology Vol.2, No.20 (2016) 1–6 DNA Logic Gates to Design a 4*4 bit Carry Select Adder Circuit Seeja V M Daniel Raj A Bannari Amman Institute of Technology Bannari Amman Institute of Technology Sathyamangalam, Erode Sathyamangalam, Erode seejavm@gmail.com danielraja@bitsathy.ac.in Abstract—The DNA molecule is indubitably the most economic limits. And also that has produced small, faster powerful medium known for DNA’s ability to code, store chips, beyond an certain limit, the number of silicon atoms in information as a means of data storage. But till now, DNA the insulating layer of a transistor is no longer sufficient to molecule has found little use in computing applications. For prevent the leakage of electron that causes the circuit to shorten initiating computing application with DNA molecule, it requires [1]. For overcome these limitations the scientists and to design DNA transistors which can be utilized to design basic technologists are looking for new materials, innovative gates to implement Boolean logic. Interestingly some recent structures and revolutionary ideas to realize reliable transistor researches have shown that it’s very much possible to design a like action in such tiny space [2].Most novel materials three terminal transistor like device architecture by controlling available today are at the first step, where researchers are the flow of RNA polymerase along DNA with specific integrases. trying to understand their properties and characteristics of Along with that, very recently, fundamental experimental designs for realizing various basic Boolean logic functions have been transistors fabricated using them. demonstrated successfully with DNA molecule. Present work Presently throughout the world several groups of scientists, adopted, modified and extended such DNA logic gate concept to researchers and technologists are trying to store, retrieve and execute design simulation of a 4*4 bit Carry select adder circuit. process signals using bio-chemical reactions with newer The timing diagram for input and sum output has been simulated biological materials [3-5]. In such context, with research it has and results have been presented. With present research, it has been proven that, the blueprint for life DNA, can also become been established that such DNA logic gate concept can be the templates for making a new generation of transistors, logic extended to complex circuits. At the same time, it has been also gates and subsequent computer chips [6]. In last decades lots of predicted that with the development of proper mathematical model for DNA transistor, a circuit simulator can be designed for research articles have been reported on experimental designing and simulating bioelectronics circuit in near future. realization of transistor like action and logic operation with DNAs [7-9]. Recently, Drew Endy et. al. at Stanford Keywords— DNA, RNA, Transistors, Logic Gates, Carry select University in California have designed a transistor like device adder Simulation that controls the movement of an enzyme called RNA polymerase along a strand of DNA with bacteriophage serine integrases [10]. They have also experimentally created logic I. INTRODUCTION gates that allow both information storage and logical The world of electronics starts with a material called operations with multiple transcriptors [10]. Such remarkable “semiconductor” which can be induced to conduct or stop the break through can be utilized to realize biochip and subsequent flow of electrons or holes. Si has been the dominant electronics biological computers which can be used to study and th material since the latter half of the 20 century. It must be clear reprogram living systems, monitor environments and improve that the successful development of Si devices took years and cellular therapeutics [9-10]. Till now most of the research decades. In conventional electronic circuits transistors are activities related to DNA logic gate realization are concentrated implemented to process, store and transfer signal or data with into intense experimental activities. But, along with such the flow of electrons or holes. Where as two or more transistors experimental ventures theoretical simulation is also important together form a logic gate, which allows a computer to manage to understand the operation and functionality of higher order mathematical operations. From the beginning to till date, the circuits with such DNA based logic gates. Under the present main aim of the electronics industry is to produce more work, based on DNA logic gates, a 4*4 bit Carry select adder powerful chips. In that process, designers have scale transistors has been logically realized with MATLAB Simulink. The input in size to produce smaller, faster, power efficient chip at lower and sum output for the DNA Carry select adder has been price [1]. The net result of this transistor scaling action is simulated and verified with timing diagrams. Such simulation because the transistor to reach the physical, technical and work will not only justify the applicability of such DNA logic 1 South Asian Journal of Engineering and Technology Vol.2, No.20 (2016) 1–6 gates in complex circuit realization, it will also lead a step forward towards practical implementation of Bio-computers. Same time extension of present research with the development of proper mathematical model of DNA transistor will initiate the development of circuit simulator with DNA logic gates. II. LOGICAL MODELING The RNA polymerase is an enzyme that also known as DNA dependent RNA polymerase and it produces primary transcript RNA chains using DNA genes as templates, a process called transcription [11].This produced primary transcript RNA can be reconfigured with a transistor like three terminal device model which can be named as transcriptor[10] The RNA synthesis follows after the attachment of RNA polymerase to a specific site, “promoter”, on the template DNA strand and the synthesis process continues until a termination sequence (“terminator”) is reached [12]. The flow of RNA polymerase along DNA strands between input and output induces an current called transcriptional current. The gate like control will be realized with independent chemical control signals (defined as “integrase”) which will regulate the flow of RNA polymerase to realize Boolean logic operation (“fig. 1”) [10]. Fig. 2. Logic control of RNA polymerase flow with integrase. Symbols: TE: Transcription Elements, RTE: Recombination sites for TE Fig. 1. Schematic for equivalent logic representation Under the present work, “Carry select adder”, a functional digital circuit built with two basic unit devices As shown in the “fig. 2”, the logic element will use (Full adders and multiplexer logic circuits), has been asymmetric transcription terminators as reversible check designed [13]. valves. A transcription terminator will be accommodating two Carry select adder (CSlA) circuit architecture consists opposing DNA recombination sites named as Transcription of independent generation of sum and carry i.e Cin=1 and Elements (TEs, represented with dark green and dark blue solid Cin=0 are executed parallelly. Depending upon Cin. The triangles) which will normally disrupt RNA polymerase flow. The input integrase which is recombinases (genetic external multiplexers select the carry to be propagated to recombination enzymes) will catalyze unidirectional inversion next stage. Further, based on the carry input, the sum will of DNA within opposing recombination sites [10]. This will be selected. The Simulink model of CSlA is shown below. modify TEs (represented with partially dark green-blue and The Carry select adder adds two four-bit binary numbers partially dark blue-green solid triangles) and invert of the and the outputs will be produced as the sum of the two transcription terminator to provide of DNA recombination sites four bit input as shown in “fig. 3”. and will allow RNA polymerase flow. Every opposing recombination sites (TEs) will be recognized by independent integrases which will provide independent control over the orientation or presence of one or more terminators. 2 South Asian Journal of Engineering and Technology Vol.2, No.20 (2016) 1–6 Fig. 3. Schematic for logical carry select adder circuit Fig. 5. Schematic for logical DNA EXOR showing transcription continuation with presence of integrase 1 (=1). So to realize a Carry select adder circuit with DNA logic, the basic DNA EXOR, AND and OR gates have to be designed first. Then with the basic logic gates the half adder [13], full B. Implementing AND Logic adder and multiplexer circuits also designed. A transcriptor AND logic element requires two asymmetric transcription terminators with two pairs of opposing A. Implementing EXOR Logic recombination sites (Transcription Elements) associated with As shown in Fig. 4, a transcriptor EXOR logic element each transcription terminator, as shown in Fig. 5. The requires one asymmetric transcription terminator with two transcription current will flow only when both the intergaces pairs of opposing recombination sites (TEs) recognized by will present but no transcription current flow if only one independent integrases. When none of the integrase is present, integrase is present as shown in “fig 6”. the terminator will block the transcription as shown in fig 4. Fig. 6. Schematic for logical representation of AND showing blocked Fig. 4. Schematic for logical DNA EXOR showing blocked transcription with transcription with presence of intergace
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