DNA Logic Gates

Abstract

A conceptually new logic gate based on DNA has been devised. Methoxybenzodeazaadenine ((MD)A), an artificial nucleobase which we recently developed for efficient hole transport through DNA, formed stable base pairs with T and C. However, a reasonable hole-transport efficiency was observed in the reaction for the duplex containing an (MD)A/T base pair, whereas the hole transport was strongly suppressed in the reaction using a duplex where the base opposite (MD)A was replaced by C. The influence of complementary pyrimidines on the efficiency of hole transport through (MD)A was quite contrary to the selectivity observed for hole transport through G. The orthogonality of the modulation of these hole-transport properties by complementary pyrimidine bases is promising for the design of a new molecular logic gate. The logic gate system was executed by hole transport through short DNA duplexes, which consisted of the "logic gate strand", containing hole-transporting nucleobases, and the "input strand", containing pyrimidines which modulate the hole-transport efficiency of logic bases. A logic gate strand containing multiple (MD)A bases in series provided the basis for a sharp AND logic action. On the other hand, for OR logic and combinational logic, conversion of Boolean expressions to standard sum-of-product (SOP) expressions was indispensable. Three logic gate strands were designed for OR logic according to each product term in the standard SOP expression of OR logic. The hole-transport efficiency observed for the mixed sample of logic gate strands exhibited an OR logic behavior. This approach is generally applicable to the design of other complicated combinational logic circuits such as the full-adder.

Electrical Conductance in Biological Molecules

“…It is a known result that all combinational logic can be reduced to a two level multiinput AND/OR circuit with possible inversion at the inputs. The work in [118] demonstrates a technique using DNA in which logic gate functions can be realized. The method depends on charge transport along a DNA molecule.…”

DNA biomolecular-electronic encoder and decoder devices constructed by multiplex biosensors

“…[16][17][18][19][20][21][22] Winfree, Stojanovic, Willner, Katz and their co-workers have, for example, developed optically reported 'AND' , 'OR' and 'SET-RESET' logic gate operations. 7,[23][24][25][26][27][28][29][30][31] Although the above examples serve as promising proofs of principle (see also refs 27-35), it remains necessary to create complex, multicomponent devices on a single biomolecular platform to achieve increased computational complexity and develop realistic DNAbased information processing systems. In this study, we fabricated and tested encoders and decoders based on a multiplex, DNA-based electrochemical biosensor that uses electronic (electrochemical) signals as its readout.…”

Functionalized DNA Nanostructures for Nanomedicine

“…Since then various other DNA nanomachines have been reported, including DNA tweezers driven by hybridization of complementary strands, [42,43] catalytic DNA, [43,44] G-rich quadruplexes, [45,46] and i-motifs. [47,48] In recent years there has been a great deal of interest in DNA computing, with reports of the construction of a series of DNA logic gates and higher-order DNA circuits [49][50][51][52][53] that produce output signals based on various inputs (usually DNA strands). These DNA nanomachines can be used to detect various targets, such as fragments of DNA or RNA, pH changes, Figure 3.…”

“…[58] The idea was demonstrated again in multi-logic gate DNA circuits in which strand displacement served as the recognition event and the fluorescence of a selected reporter yielded the output signal. [49][50][51][52][53] In combination with other nanomachines, such as i-motifs, molecular beacons and DNA circuits can also detect the presence of different target molecules.…”