File Name: half subtractor and full subtractor writer.zip
First, we will take a look at the logic equations of the circuits and then the syntax for the VHDL code.
The whole system is established by one gate molecule and three input sequences, all made of single-stranded DNA sequences.
As interest in nanotechnology research has grown, nanoscale devices, which can be designed using either a top-down or a bottom-up approach, have been widely studied 1 , 2 , 3. In , Adleman introduced a DNA-based biocomputing system for solving famous mathematic traveling salesman problems 4. This led to additional explorations and experiments demonstrating that DNA sequences can serve as elementary computing devices such as half-adders 5 , 6 , 7 , 8 , half-subtractors 9 , full-adders 10 and full-subtractors Related DNA-based computing experiments have involved smart molecular systems such as majority voting logic circuits 12 , 13 , 14 , 15 , keypad locks 16 and multilevel logic circuits 17 , 18 , In addition to providing these basic computing capabilities, effectively designed DNA molecules show promise for application in other functions such as molecularly targeted cancer therapy 20 , 21 , In designing nanoscale devices, many scientists prefer using DNA molecules over typical synthetic polymers because DNA molecules offer a wealth of favorable conformational characteristics that typical polymers lack.
For example, DNA molecules can have single-stranded sticky ends or can form duplexes and a DNA molecule may possess a hairpin loop, G-quadruplex, or crossover structures. DNAzyme molecules or aptamer—substrate complexes are also options for biomolecular designers Designers combine these types of logic gate to create logic circuits for arithmetic calculations.
For example, the logic circuit of a half-subtractor requires two binary digits: I A the minuend and I B the subtrahend to perform subtraction and the involved outputs are a difference-bit by using an XOR gate and a borrow-bit by using an INHIBIT gate.
The value of the difference-bit is equal to the minuend subtracts the subtrahend, regardless of whether the value is positive or negative; if the minuend is less than the subtrahend, then the borrow-bit value equals 1.
A full-subtractor is a combinational logic circuit that performs subtraction using inputs of three binary digits: one minuend and two subtrahends and considers eight input states: 0,0,0 , 0,1,0 , 1,0,0 , 1,1,0 , 0,0,1 , 0,1,1 , 1,0,1 and 1,1,1.
Similar to a half-subtractor, a full-subtractor outputs values for one difference-bit and one borrow-bit. The full-subtractor proposed herein is designed to be relatively compact and composed of merely four DNA molecules. Three strands are as inputs: I A the minuend , I B the first subtrahend and B in the second subtrahend and one strand as a logic gate to recognize the input strand s and produce two sets of output signals obeying the truth tables of difference- and borrow-bits in a full-subtractor.
The design of the gate strand relies on a molecular beacon, which commonly serves as an optical DNA probe. When a molecular beacon is in a hairpin conformation, its quencher and fluorophore remain in vicinity to each other and the fluorescence signal is thus quenched.
However, when a complementary DNA target is detected, the hairpin opens into a linear form and the fluorophore, now away from the quencher, releases an observable signal. When the gate strand is in hairpin form, the fluorescence signal is off and designated as 0; whereas in linear form, the fluorescence signal of the gate strand is on and designated as 1.
Herein, we used a gold surface to immobilize the molecular beacons and to replace the quenchers, because of the superior quenching capability of the gold surface for certain fluorophores All three inputs are also single-stranded DNA sequences. Based on most designs in related studies 5 , 6 , 7 , 8 , 9 , 10 , 11 , the presence and absence of an input strand at the gate molecule are assigned Boolean values of 1 and 0, respectively. Eight combinations of input strands may be applied to the logic gate, represented by the aforementioned eight input states.
Table 1 shows the DNA sequences used in the proposed full-subtractor. When the gate molecule is in hairpin form, the fluorescein emission is quenched by the nearby gold surface; however, when an input molecule is present, the gate molecule opens into linear form and the fluorescence from fluorescein is observable.
Figure 1 A shows a schematic illustration of the proposed full-subtractor. In a 0,0,0 input state, no input is added and the fluorescein of the gate molecule remains near the gold surface; hence, no fluorescein signal is released. Both the borrow-bit and difference-bit are read as 0, as listed in the truth table in Fig. In the 1,0,0 input state, input strand I A is added, thus changing the gate molecule conformation from hairpin to linear. In the 0,1,0 input state, input strand I B is added, thus disrupting the hairpin conformation of the gate molecule.
In addition to the green fluorescence signal from the gate molecule, a red fluorescence signal from Cy5 on the I B strand is also observable. In the 1,1,0 input state, both the I A and I B strands are added. The borrow-bit and difference-bit values are both read as 0, as indicated in the truth table in Fig.
A A schematic representation of the proposed full-subtractor. The green and red ovals represent the green dye fluorescein and the red dye Cy5 , respectively; the gray rectangle represents BHQ3, a quencher to Cy5. B Truth tables for the eight input states and their matched outputs. C The observed fluorescence intensity corresponding to the eight input states. The right half of Fig. In the 0,0,1 input state, the added B in strand works in the manner of the added I B strand, using the same nucleotide segment to hybridize part of the gate molecule and transform the gate molecule from hairpin to linear form.
In the 1,0,1 input state, the added I A and B in strands have a higher priority to hybridize each other, instead of interacting with the gate molecule similar to the I A and I B interactions in the 1,1,0 input state. Both the Cy5 on the B in strand and the fluorescein on the gate molecule are off not released.
The gate molecule remains in hairpin conformation and the fluorescein signal is quenched by the gold surface. The truth table in Fig. Figure 1 C shows the measured fluorescence intensities, in arbitrary units a. The 0,1,1 input state produces a Cy5 fluorescence intensity that is nearly twice those in the 0,1,0 , 0,0,1 and 1,1,1 input states because in 0,1,1 state there are two Cy5 sources I B and B in , instead of only one Cy5 source either I B or B in in the other three input states.
However, in the 1,1,1 state the Cy5 intensity is similar to those in the 0,1,0 and 0,0,1 states, but lower than that of 0,1,1 state, regardless the presence of I B and B in in 1,1,1. This study presents a simple and elegant design of a full-subtractor using four single-stranded DNA molecules whereas an electronic full-subtractor in silico would require combinational circuits to perform subtraction.
The proposed DNA-based logic operations rely on the interactions among the four DNA strands to switch the gate molecule between hairpin and linear forms and to manipulate the duplex formation of the input strands.
The compactness of the proposed design makes it a promising foundation for future applications and integrations with other DNA-based computing devices, although there is a long road ahead toward integrating the developed molecular systems for practical functions and competition with silicon-based technology. In addition to the arithmetic operations, numerous logic gate systems have been synthesized and employed on the DNA sensor development for medicinal applications 17 , For example, logic gates designed with colorimetric property may have the potential to form intelligent diagnostic devices in response to disease markers.
To summarize, the presented work provides a novel prototype for the future circuit design on nanoscale for complicated arithmetic operations. Furthermore, it is also possible to adopt the design concept demonstrated herein along with other arrangement to blueprint new systems for medicinal usage.
Sodium chloride A. Baker Phillipsburg, NJ. All purchased chemicals were used as received, unless noted otherwise. During all processes including gate immobilization and hybridization, all DNA molecules were covered with aluminum foil to prevent photobleaching. The fluorescence intensities were monitored using a fluorescence spectrophotometer F, Hitachi High-Technologies, Japan , equipped with a solid sample holder.
Figure 2 demonstrates the sensitivity of I A and I B concentrations on the aforementioned gate-coated gold surface. As indicated in Fig. In Fig. A gel electrophoresis experiment was carried out to characterize the hairpin structure of the gate molecule. As shown in Fig. Meanwhile, ethidium bromide staining indicated the gate molecule alone is in hairpin conformation with a stem region to intercalate ethidium bromide.
Agarose gel electrophoresis of reaction products. The gate molecule alone and the three combinations underwent in heating and annealing procedure. How to cite this article : Lin, H. A simple three-input DNA-based system works as a full-subtractor. Simmel, F. A DNA-based molecular device switchable between three distinct mechanical states. Appl Phys Lett 80, — Turberfield, A.
DNA fuel for free-running nanomachines. Phys Rev Lett 90, Shin, J. Rewritable memory by controllable nanopatterning of DNA. Nano Lett 4, — Adleman, L. Molecular computation of solutions to combinatorial problems. Science , — Stojanovic, M. Deoxyribozyme-based half-adder. J Am Chem Soc , — Yang, C. Molecular beacon-based half-adder and half-subtractor.
Chem Comm 48, — Xu, S. Implementation of half adder and half subtractor with a simple and universal DNA-based platform.
NPG Asia Mater 5, e76 An optical deoxyribonucleic acid-based half-subtractor. Chem Comm 49, — Lederman, H. Deoxyribozyme-based three-input logic gates and construction of a molecular full adder.
In this chapter, let us discuss about the basic arithmetic circuits like Binary adder and Binary subtractor. These circuits can be operated with binary values 0 and 1. The most basic arithmetic operation is addition. The circuit, which performs the addition of two binary numbers is known as Binary adder. First, let us implement an adder, which performs the addition of two bits.
Show all documents In addition, transient analysis is performed . The proposed specifications supply a good choice of variable between two types of implementations, even with an analogy problem.
Navendra Rawat, Rakesh Jain. The increasing market of mobile devices and battery operated portable electronic systems has led to the demands for chips that consume smallest possible amount of power and equally having high chip density and high throughput during recent years. The purpose of this design is to develop a subtractor circuit that meets the requirement for minimum power dissipation as well as not growing too much in size but if possible than minimize the size too. These goals are achieved using and comparing different techniques including alternate design for AND function. Keywords: Standby power dissipation, Subtractor, Drain gating, Lector.
The operation of adding two binary numbers is one of the fundamental tasks performed by a digital computer. In the first three operations, each binary addition gives sum as one bit , i. But the fourth addition operation gives a sum that consists of two binary digits. In such result of the addition, lower significant bit is called as the sum bit, whereas the higher significant bit is called as the carry bit. The logic circuits which are designed to perform the addition of two binary numbers are called as binary adder circuits. In this article we are going to look at the binary addition performed by various adder circuits. Logic gates are used to accomplish the arithmetic operation of binary addition in digital circuits.
Half Adder and Full Adder circuits is explained with their truth tables in this article. Design of Full Adder using Half Adder circuit is also shown. Before going into this subject, it is very important to know about Boolean Logic and Logic Gates. An adder is a kind of calculator that is used to add two binary numbers. There are two kinds of adders;.
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