NDLI: Activatable tiles for compact robust programmable molecular assembly and other applications

Please wait, while we are loading the content...

Activatable tiles for compact robust programmable molecular assembly and other applications

Content Provider	Springer Nature Link
Author	Majumder, Urmi Garg, Sudhanshu LaBean, Thomas H. Reif, John H.
Copyright Year	2015
Abstract	Algorithmic DNA self-assembly is capable of forming complex patterns and shapes, that have been shown theoretically, and experimentally. Its experimental demonstrations, although improving over recent years, have been limited by significant assembly errors. Since 2003 there have been several designs of error-resilient tile sets but all of these existing error-resilient tile systems assumed directional growth of the tiling assembly. This is a very strong assumption because experiments show that tile self-assembly does not necessarily behave in such a fashion, since they may also grow in the reverse of the intended direction. The assumption of directional growth of the tiling assembly also underlies the growth model in theoretical assembly models such as the TAM. What is needed is a means for enforce this directionality constraint, which will allow us to reduce assembly errors. In this paper we describe a protection/deprotection strategy to strictly enforce the direction of tiling assembly growth so that the assembly process is robust against errors. Initially, we start with (1) a single “activated” tile with output pads that can bind with other tiles, along with (2) a set of “deactivated” tiles, meaning that the tile’s output pads are protected and cannot bind with other tiles. After other tiles bind to a “deactivated” tile’s input pads, the tile transitions to an active state and its output pads are exposed, allowing further growth. When these are activated in a desired order, we can enforce a directional assembly at the same scale as the original one. Such a system can be built with minimal modifications of existing DNA tile nanostructures. We propose a new type of tiles called activatable tiles and its role in compact proofreading. Activatable tiles can be thought of as a particular case of the more recent signal tile assembly model, where signals transmit binding/unbinding instructions across tiles on binding to one or more input sites. We describe abstract and kinetic models of activatable tile assembly and show that the error rate can be decreased significantly with respect to Winfree’s original kinetic tile assembly model without considerable decrease in assembly growth speed. We prove that an activatable tile set is an instance of a compact, error-resilient and self-healing tile-set. We describe a DNA design of activatable tiles and a mechanism of deprotection using DNA polymerization and strand displacement. We also perform detailed stepwise simulations using a DNA Tile simulator Xgrow, and show that the activatable tiles mechanism can reduce error rates in self assembly. We conclude with a brief discussion on some applications of activatable tiles beyond computational tiling, both as (1) a novel system for concentration of molecules, and (2) a catalyst in sequentially triggered chemical reactions .
Starting Page	611
Ending Page	634
Page Count	24
File Format	PDF
ISSN	15677818
Journal	Natural Computing
Volume Number	15
Issue Number	4
e-ISSN	15729796
Language	English
Publisher	Springer Netherlands
Publisher Date	2015-11-25
Publisher Place	Dordrecht
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	DNA self-assembly Error correction Tile assembly model Strand displacement Programmable molecular machines Deprotection systems Concentration systems Reaction catalyzation Theory of Computation Evolutionary Biology Processor Architectures Artificial Intelligence (incl. Robotics) Complex Systems
Content Type	Text
Resource Type	Article
Subject	Computer Science Applications

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

Activatable Tiles: Compact, Robust Programmable Assembly and other Applications

Activatable Tiles: Compact, Robust Programmable Assembly and Other Applications (2007)

Reflections on tiles (in self-assembly)

Activatable tiles: compact, ro- bust programmable assembly and other applications’, dna computing (2007).

The effect of malformed tiles on tile assemblies within the kinetic tile assembly model

Isothermal reactivating Whiplash PCR for locally programmable molecular computation

Activatable tiles: Compact, robust programmable assembly and other applications (2008)

An introduction to tile-based self-assembly and a survey of recent results

Signal transmission across tile assemblies: 3D static tiles simulate active self-assembly by 2D signal-passing tiles

Activatable tiles for compact robust programmable molecular assembly and other applications

Similar Documents

Activatable Tiles: Compact, Robust Programmable Assembly and other Applications

Activatable Tiles: Compact, Robust Programmable Assembly and Other Applications (2007)

Reflections on tiles (in self-assembly)

Activatable tiles: compact, ro- bust programmable assembly and other applications’, dna computing (2007).

The effect of malformed tiles on tile assemblies within the kinetic tile assembly model

Isothermal reactivating Whiplash PCR for locally programmable molecular computation

Activatable tiles: Compact, robust programmable assembly and other applications (2008)

An introduction to tile-based self-assembly and a survey of recent results

Signal transmission across tile assemblies: 3D static tiles simulate active self-assembly by 2D signal-passing tiles

Activatable tiles for compact robust programmable molecular assembly and other applications