NDLI: Biophysically Inspired Rational Design of Structured Chimeric Substrates for DNAzyme Cascade Engineering

Content Provider	PubMed Central
Author	Lakin, Matthew R. Brown, Carl W. Horwitz, Eli K. Fanning, M. Leigh West, Hannah E. Stefanovic, Darko Graves, Steven W.
Editor	Mukund, Thattai
Copyright Year	2014
Abstract	The development of large-scale molecular computational networks is a promising approach to implementing logical decision making at the nanoscale, analogous to cellular signaling and regulatory cascades. DNA strands with catalytic activity (DNAzymes) are one means of systematically constructing molecular computation networks with inherent signal amplification. Linking multiple DNAzymes into a computational circuit requires the design of substrate molecules that allow a signal to be passed from one DNAzyme to another through programmed biochemical interactions. In this paper, we chronicle an iterative design process guided by biophysical and kinetic constraints on the desired reaction pathways and use the resulting substrate design to implement heterogeneous DNAzyme signaling cascades. A key aspect of our design process is the use of secondary structure in the substrate molecule to sequester a downstream effector sequence prior to cleavage by an upstream DNAzyme. Our goal was to develop a concrete substrate molecule design to achieve efficient signal propagation with maximal activation and minimal leakage. We have previously employed the resulting design to develop high-performance DNAzyme-based signaling systems with applications in pathogen detection and autonomous theranostics.
Related Links	http://dx.doi.org/10.1371/journal.pone.0110986
Starting Page	110986
File Format	PDF
ISSN	19326203
e-ISSN	19326203
Journal	PLoS ONE
Issue Number	10
Volume Number	9
Language	English
Publisher	Public Library of Science
Publisher Date	2014-10-01
Access Restriction	Open
Rights Holder	Public Library of Science
Subject Keyword	Biochemistry, Genetics and Molecular Biology(all) Agricultural and Biological Sciences(all) Medicine(all) Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Multidisciplinary

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

Biophysically Realistic Filament Bending Dynamics in Agent-Based Biological Simulation

Virus-Inspired Design Principles of Nanoparticle-Based Bioagents

Rational Design of T Cell Receptors with Enhanced Sensitivity for Antigen

Label-Free Detection of Cu2+ and Hg2+ Ions Using Reconstructed Cu2+-Specific DNAzyme and G-quadruplex DNAzyme

Host Defense Mechanism-Based Rational Design of Live Vaccine

Sample Selection for Training Cascade Detectors

Improving a Natural CaMKII Inhibitor by Random and Rational Design

Rational Design of Temperature-Sensitive Alleles Using Computational Structure Prediction

Stereospecificity of Oligonucleotide Interactions Revisited: No Evidence for Heterochiral Hybridization and Ribozyme/DNAzyme Activity

Biophysically Inspired Rational Design of Structured Chimeric Substrates for DNAzyme Cascade Engineering

Similar Documents

Biophysically Realistic Filament Bending Dynamics in Agent-Based Biological Simulation

Virus-Inspired Design Principles of Nanoparticle-Based Bioagents

Rational Design of T Cell Receptors with Enhanced Sensitivity for Antigen

Label-Free Detection of Cu2+ and Hg2+ Ions Using Reconstructed Cu2+-Specific DNAzyme and G-quadruplex DNAzyme

Host Defense Mechanism-Based Rational Design of Live Vaccine

Sample Selection for Training Cascade Detectors

Improving a Natural CaMKII Inhibitor by Random and Rational Design

Rational Design of Temperature-Sensitive Alleles Using Computational Structure Prediction

Stereospecificity of Oligonucleotide Interactions Revisited: No Evidence for Heterochiral Hybridization and Ribozyme/DNAzyme Activity

Biophysically Inspired Rational Design of Structured Chimeric Substrates for DNAzyme Cascade Engineering