Integration of chemically modified nucleotides with DNA strand displacement reactions for applications in living systems

2021 ◽  
Author(s):  
Adam M. Kabza ◽  
Nandini Kundu ◽  
Wenrui Zhong ◽  
Jonathan T. Sczepanski
Keyword(s):  
Living Systems ◽  
Strand Displacement ◽  
Modified Nucleotides ◽  
Chemically Modified ◽  
Dna Strand Displacement ◽  
Displacement Reactions ◽  
Dna Strand

Biocomputing based on DNA strand displacement reactions

ChemPhysChem ◽  
2021 ◽  
Author(s):  
Hui Lv ◽  
Qian Li ◽  
Jiye Shi ◽  
Fei Wang ◽  
Chunhai Fan
Keyword(s):  
Strand Displacement ◽  
Dna Strand Displacement ◽  
Displacement Reactions ◽  
Dna Strand

Connecting localized DNA strand displacement reactions

Nanoscale ◽  
2015 ◽  
Vol 7 (30) ◽  
pp. 12970-12978 ◽  
Author(s):  
Ismael Mullor Ruiz ◽  
Jean-Michel Arbona ◽  
Amitkumar Lad ◽  
Oscar Mendoza ◽  
Jean-Pierre Aimé ◽  
...  
Keyword(s):  
Dna Origami ◽  
Strand Displacement ◽  
Dna Strand Displacement ◽  
Displacement Reactions ◽  
Dna Strand

Design and characterization of a DNA-based localized amplification circuit which, upon tethering on a DNA origami platform, greatly accelerates the catalytic response.

The fast detection of streptavidin based on the initial reaction rate of the binding-induced DNA strand-displacement reaction

2016 ◽  
Vol 8 (37) ◽  
pp. 6701-6704 ◽  
Author(s):  
Chenxi Li ◽  
Ruoyun Lin ◽  
Tian Li ◽  
Feng Liu ◽  
Na Li
Keyword(s):  
Small Molecules ◽  
Reaction Rate ◽  
Initial Reaction Rate ◽  
Initial Reaction ◽  
Strand Displacement ◽  
Fast Detection ◽  
Dna Strand Displacement ◽  
Displacement Reactions ◽  
Dna Strand ◽  
Strand Displacement Reaction

Binding-induced DNA strand-displacement reactions diversify the applications beyond nucleic acids and small molecules.

scholarly journals Configuring robust DNA strand displacement reactions for in situ molecular analyses

2011 ◽  
Vol 40 (7) ◽  
pp. 3289-3298 ◽  
Author(s):  
Dzifa Y. Duose ◽  
Ryan M. Schweller ◽  
Jan Zimak ◽  
Arthur R. Rogers ◽  
Walter N. Hittelman ◽  
...  
Keyword(s):  
Strand Displacement ◽  
Molecular Analyses ◽  
Dna Strand Displacement ◽  
Displacement Reactions ◽  
Dna Strand

scholarly journals Meta-DNA: synthetic biology via DNA nanostructures and hybridization reactions

2012 ◽  
Vol 9 (72) ◽  
pp. 1637-1653 ◽  
Author(s):  
Harish Chandran ◽  
Nikhil Gopalkrishnan ◽  
Bernard Yurke ◽  
John Reif
Keyword(s):  
Formal Model ◽  
Heat Denaturation ◽  
Dna Nanostructures ◽  
Strand Displacement ◽  
Dna Strand Displacement ◽  
Wide Range ◽  
Displacement Reactions ◽  
Repeated Applications ◽  
Polymerase Chain ◽  
Dna Strand

Can a wide range of complex biochemical behaviour arise from repeated applications of a highly reduced class of interactions? In particular, can the range of DNA manipulations achieved by protein enzymes be simulated via simple DNA hybridization chemistry? In this work, we develop a biochemical system which we call meta-DNA (abbreviated as mDNA), based on strands of DNA as the only component molecules. Various enzymatic manipulations of these mDNA molecules are simulated via toehold-mediated DNA strand displacement reactions. We provide a formal model to describe the required properties and operations of our mDNA, and show that our proposed DNA nanostructures and hybridization reactions provide these properties and functionality. Our meta-nucleotides are designed to form flexible linear assemblies (single-stranded mDNA ( ss mDNA)) analogous to single-stranded DNA. We describe various isothermal hybridization reactions that manipulate our mDNA in powerful ways analogous to DNA–DNA reactions and the action of various enzymes on DNA. These operations on mDNA include (i) hybridization of ss mDNA into a double-stranded mDNA ( ds mDNA) and heat denaturation of a ds mDNA into its component ss mDNA, (ii) strand displacement of one ss mDNA by another, (iii) restriction cuts on the backbones of ss mDNA and ds mDNA, (iv) polymerization reactions that extend ss mDNA on a template to form a complete ds mDNA, (v) synthesis of mDNA sequences via mDNA polymerase chain reaction, (vi) isothermal denaturation of a ds mDNA into its component ss mDNA, and (vii) an isothermal replicator reaction that exponentially amplifies ss mDNA strands and may be modified to allow for mutations.

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