TripDesign: A DNA Triplex Design Approach Based on Interaction Forces

Abstract

A DNA triplex has the advantages of improved nanostructure stability and pH environment responsiveness compared with single-stranded and double-stranded nucleic acids. However, sequence stability and low design efficiency hinder the application of DNA triplexes. Therefore, a DNA triplex design approach (TripDesign) based on interaction forces is proposed. First, we present the stacking force constraint, torsional stress constraint, and G-quadruplex motif constraint and then use an improved memetic algorithm to design triplex sequences under combinatorial constraints. Finally, to quantify the process of triplex formation, we also explore the minimum length of the triplexforming oligos (TFOs) required to form the triplex and the factors that produce depletion in cyclic pH-jump experiments. The experimental results show that the sequences produced by TripDesign have high stability and reversibility, and the proposed approach achieves efficient and automatic sequence design. In addition, this study characterizes multiple basic parameters of DNA triplex formation and promotes the wider application of DNA triplexes in nanotechnology.

Folding Double‐Stranded DNA into Designed Shapes with Triplex‐Forming Oligonucleotides

“…There is room for improvement in the sequence design methodology, as it currently has not involved any refined optimization steps. [ 68 ] Furthermore, there is mounting evidence that scaffolded self‐assembly permits a surprising extent of sequence redundancy, without it affecting the yield. [ 69 ] These boundaries must be explored before we can quantify the size limit of triplex origami structures.…”

Reconfigurable DNA triplex structure for pH responsive logic gates

“…It shows great advantages in optimizing storage methods [10][11][12] and solving non-traditional computing problems. [13][14][15] The DNA logic gate, which has functions like logical analysis, judgment and multi-input recognition, is regarded as the basis of DNA computing. [16][17][18] It has shown great potential practicability in the elds of analytical detection and disease diagnosis.…”

A DNA Finite-State Machine Based on the Programmable Allosteric Strategy of DNAzyme

“…It provides a powerful tool for recording and processing time-related information and has attracted a wide range of attention from researchers. Owing to its high stability, modifiability, and programmability, DNA has promising applications in biosensing [ 8 , 9 , 10 ], disease diagnosis [ 11 , 12 , 13 ], molecular computing [ 14 , 15 , 16 , 17 ], information storage [ 18 , 19 , 20 ], nanomachines [ 21 , 22 ], and quantum computing [ 23 , 24 ]. It is one of the ideal materials for constructing artificial state machines.…”