scholarly journals Functionalizing lipid sponge droplets with DNA

2021 ◽  
Author(s):  
Christy Cho ◽  
Henrike Niederholtmeyer ◽  
Hyeonglim Seo ◽  
Ahanjit Bhattacharya ◽  
Neal K. Devaraj
Keyword(s):  
Nucleic Acids ◽  
Size Dependence ◽  
Construction Materials ◽  
Dna Molecules ◽  
Strand Displacement ◽  
Double Stranded Dna ◽  
Displacement Reactions ◽  
Dna Strands ◽  
Capture And Release ◽  
Sponge Phase

Nucleic acids are among the most versatile molecules for the construction of biomimetic systems because they can serve as information carriers and programmable construction materials. How nucleic acids interact with membranous coacervate compartments such as lipid sponge droplets is not known. Here we systematically characterize the potential of DNA to functionalize lipid sponge droplets and demonstrate a strong size dependence for sequestration into the sponge phase. Double stranded DNA molecules of more than 300 bp are excluded and form a corona on the surface of droplets they are targeted to. Shorter DNA molecules partition efficiently into the lipid sponge phase and can direct DNA-templated reactions to droplets. We demonstrate repeated capture and release of labeled DNA strands by dynamic hybridization and strand displacement reactions that occur inside droplets. Our system opens new opportunities for DNA-encoded functions in lipid sponge droplets such as cargo control and signaling.

The Mechanical Properties of Nucleic Acids

2018 ◽  
pp. 67-104
Author(s):  
David Bensimon ◽  
Vincent Croquette ◽  
Jean-François Allemand ◽  
Xavier Michalet ◽  
Terence Strick
Keyword(s):  
Mechanical Properties ◽  
Nucleic Acids ◽  
Elastic Properties ◽  
Hydrodynamic Interactions ◽  
Elastic Behaviour ◽  
Dna Molecules ◽  
Base Pairing ◽  
Double Stranded Dna ◽  
Stretched Polymers ◽  
Experimental Behaviour

This chapter reviews models which describe the elastic properties of stretched polymers—the Kratky–Porod, Freely Jointed Chain (FJC), and Worm-Like Chain (WLC) models—and the effect of self-avoidance on results derived from these. The models are compared with double-stranded DNA (dsDNA) stretching experiments. Dynamics of a single polymer in the presence (Zimm model) or absence (Rouse model) of hydrodynamic interactions between its segments is described, and results on the dynamics of dsDNA and ssDNA of various lengths are discussed. Theoretical and experimental behaviour of twisted DNA is described, deducing the molecule’s torsional modulus and its coupling between stretching and twisting. After discussing the braiding of two DNA molecules and simulation of the twisting and stretching of DNA molecules, this chapter describes the results of stretching experiments on ssDNA and RNA, where self-avoiding and base-pairing interactions contribute to elastic behaviour.

scholarly journals Strand displacement and duplex invasion into double-stranded DNA by pyrrolidinyl peptide nucleic acids

2015 ◽  
Vol 13 (35) ◽  
pp. 9223-9230 ◽  
Author(s):  
Peggy R. Bohländer ◽  
Tirayut Vilaivan ◽  
Hans-Achim Wagenknecht
Keyword(s):  
Nucleic Acid ◽  
Nucleic Acids ◽  
Peptide Nucleic Acid ◽  
Peptide Nucleic Acids ◽  
Dna Duplexes ◽  
Strand Displacement ◽  
Nucleic Acid Probes ◽  
Double Stranded Dna

Strand displacement and duplex invasion of DNA duplexes by pyrrolidinyl peptide nucleic acid are demonstrated using the concept of wavelength-shifting nucleic acid probes.

scholarly journals Programming colloidal phase transitions with DNA strand displacement

Science ◽  
2015 ◽  
Vol 347 (6222) ◽  
pp. 639-642 ◽  
Author(s):  
W. Benjamin Rogers ◽  
Vinothan N. Manoharan
Keyword(s):  
Crystal Structures ◽  
Three Dimensional ◽  
Strand Displacement ◽  
Dna Strand Displacement ◽  
Displacement Reactions ◽  
Dna Strands ◽  
Reversible Transitions ◽  
Grafted Nanoparticles ◽  
Dna Strand ◽  
Full Temperature

DNA-grafted nanoparticles have been called “programmable atom-equivalents”: Like atoms, they form three-dimensional crystals, but unlike atoms, the particles themselves carry information (the sequences of the grafted strands) that can be used to “program” the equilibrium crystal structures. We show that the programmability of these colloids can be generalized to the full temperature-dependent phase diagram, not just the crystal structures themselves. We add information to the buffer in the form of soluble DNA strands designed to compete with the grafted strands through strand displacement. Using only two displacement reactions, we program phase behavior not found in atomic systems or other DNA-grafted colloids, including arbitrarily wide gas-solid coexistence, reentrant melting, and even reversible transitions between distinct crystal phases.

Synchrony of Digestion of SV40 DNA by Exonuclease III Determined by EM

1975 ◽  
Vol 33 ◽  
pp. 674-675
Author(s):  
Ray Wu ◽  
G. Ruben ◽  
B. Siegel ◽  
P. Spielman ◽  
E. Jay
Keyword(s):  
Dark Field ◽  
Uranyl Acetate ◽  
Enzyme Digestion ◽  
Dna Molecules ◽  
Exonuclease Iii ◽  
Aluminum Films ◽  
Double Stranded Dna ◽  
Before And After ◽  
Exo Iii ◽  
Sv40 Dna

A method for determining long nucleotide sequences of double-stranded DNA is being developed. It involves (a) the synchronous digestion of the DNA from the 3' ends with EL coli exonuclease III (Exo III) followed by (b) resynthesis with labeled nucleotides and DNA polymerase. A crucial factor in the success of this method is the degree to which the enzyme digestion proceeds synchronously under proper conditions of incubation (step a). Dark field EM is used to obtain accurate measurements on the lengths and distribution of the DNA molecules before and after digestion with Exo III, while gel electrophoresis is used in parallel to obtain a mean length for these molecules. It is the measurements on a large enough sample of individual molecules by EM that provides the information on how synchronously the digestion proceeds. For length measurements, the DNA molecules were picked up on 20-30 Å thick carbon-aluminum films, using the aqueous Kleinschmidt technique and stained with 7.5 x 10-5M uranyl acetate in 90% ethanol for 3 minutes.

scholarly journals Kinetics of DNA Strand Displacement Systems with Locked Nucleic Acids

2017 ◽  
Vol 121 (12) ◽  
pp. 2594-2602 ◽  
Author(s):  
Xiaoping Olson ◽  
Shohei Kotani ◽  
Bernard Yurke ◽  
Elton Graugnard ◽  
William L. Hughes
Keyword(s):  
Nucleic Acids ◽  
Strand Displacement ◽  
Dna Strand Displacement ◽  
Locked Nucleic Acids ◽  
Dna Strand ◽  
Kinetics Of

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

Poly-adenine-mediated spherical nucleic acids for strand displacement-based DNA/RNA detection

2019 ◽  
Vol 127 ◽  
pp. 85-91 ◽  
Author(s):  
Lu Wang ◽  
Huan Zhang ◽  
Chenguang Wang ◽  
Yi Xu ◽  
Jing Su ◽  
...  
Keyword(s):  
Nucleic Acids ◽  
Strand Displacement ◽  
Rna Detection ◽  
Displacement Based ◽  
Spherical Nucleic Acids

PROCEDURES FOR LOGIC AND ARITHMETIC OPERATIONS WITH DNA MOLECULES

2004 ◽  
Vol 15 (03) ◽  
pp. 461-474 ◽  
Author(s):  
AKIHIRO FUJIWARA ◽  
KEN'ICHI MATSUMOTO ◽  
WEI CHEN
Keyword(s):  
Truth Table ◽  
Boolean Operation ◽  
Dna Molecules ◽  
Boolean Operations ◽  
Arithmetic Operations ◽  
Input And Output ◽  
Dna Strands ◽  
Logic Operations ◽  
N Additions

In this paper, we consider procedures for logic and arithmetic operations with DNA molecules. We first show a DNA representation of n binary numbers of m bits, and propose a procedure to assign the same values for the representation. The representation enables addressing feature, and the procedure is applicable to n binary numbers of m bits in O(1) steps in parallel. Next, we propose a procedure for logic operations. The procedure enables any boolean operation whose input and output are defined by a truth table, and executes different kinds of boolean operations simultaneously for any pair of n binary numbers of m bits in O(1) lab steps using O(mn) DNA strands. Finally, we propose a procedure for additions of pairs of two binary numbers. The procedure executes O(n) additions of two m-bit binary numbers in O(1) steps using O(mn) DNA strands.

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