Synthesis of a DNA knot containing both positive and negative nodes

Du, Shou Ming; Seeman, Nadrian C.

doi:10.1021/ja00050a053

Cited by 69 publications

(40 citation statements)

References 1 publication

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…These attempts have recently come to fruition with the elegant and complete synthesis of a hydrocarbon knot by Dietrich-Buchecker and Sauvage (6). A distinct synthetic route based on the properties of nucleic acids has been used by Seeman's group to synthesize different types of knots (7).…”

mentioning

confidence: 99%

Probability of DNA knotting and the effective diameter of the DNA double helix.

Rybenkov

Cozzarelli

Vologodskii

1993

Proc. Natl. Acad. Sci. U.S.A.

374

435

View full text Add to dashboard Cite

During the random cyclization of long polymer chains, knots of different types are formed. We investigated experimentally the distribution ofknot types produced by random cyclization of phage P4 DNA via its long cohesive ends. The simplest knots (trefoils) predominated, but more complex knots were also detected. The fraction of knots greatly diminished with decreasing solution Na+ concentration. By comparing these experimental results with computer simulations of knotting probability, we calculated the effective diameter ofthe DNA double helix. This important excluded-volume parameter is a measure of the electrostatic repulsion between segments of DNA molecules. The calculated effective DNA diameter is a sensitive function of electrolyte concentration and is several times larger than the geometric diameter in solutions of low monovalent cation concentration.A classic problem in polymer physics is the probability that the random cyclization of a polymer produces a knot of a particular topology. The issues were formulated more than 30 years ago by Frisch and Wasserman (1) and by Delbruck (2). The initial solution was provided by a Monte Carlo simulation in 1974 (3), and since then several computational analyses of the knotting probability of polymer chains have appeared (reviewed in refs. 4 and 5).Experimental measures of knotting frequency have not been made, however, despite the considerable interest in these forms. Ever since the production oflinked hydrocarbon rings, organic chemists have striven to synthesize knotted molecules. These attempts have recently come to fruition with the elegant and complete synthesis of a hydrocarbon knot by Dietrich-Buchecker and Sauvage (6). A distinct synthetic route based on the properties of nucleic acids has been used by Seeman's group to synthesize different types of knots (7).Knots made of DNA, first identified in 1976 (8), are much easier to synthesize and to analyze than other knotted polymers. Knotted DNA has been identified in numerous in vitro and in vivo experiments (9, 10). The topology of the knots is diagnostic of the mechanism of the enzymes that produce them and of the structure of the DNA substrates (9). The experimental studies of DNA knots have been guided by the development of mathematical methods for analyzing DNA topology (11,12).DNA is thus the most suitable polymer for the experimental investigation of the probability of knotting. The measurement of the probability of knotting duplex DNA is of special interest because it provides an excellent means for determining the effective diameter of DNA. This important parameter characterizes the excluded volume of DNA. The effective diameter of DNA is the diameter of an uncharged polymer chain that mimics the conformational properties of actualThe publication costs of this article were defrayed in part by page charge payment. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. §1734 solely to indicate this fact. electrically charged DNA. Because DNA is a highly charge...

show abstract

mentioning

confidence: 99%

Probability of DNA knotting and the effective diameter of the DNA double helix.

Rybenkov

Cozzarelli

Vologodskii

1993

Proc. Natl. Acad. Sci. U.S.A.

374

435

View full text Add to dashboard Cite

show abstract

“…[8][9][10][11][12][13][14][15][16][17][18][19]). Furthermore, crystal engineers have produced coordination networks that contain knots and links [6].…”

Section: Introductionmentioning

confidence: 99%

Toroidal embeddings of abstractly planar graphs are knotted or linked

Barthel

Buck

2015

J Math Chem

View full text Add to dashboard Cite

show abstract

“…In each case, a complete DNA strand is synthesized, but the final ligation that circularizes the molecule is done enzymatically. We have made trefoil knots from two motifs of B-DNA, [55,56] a figure-eight knot from a strand containing two negative nodes (B-DNA) and two positive nodes (Z-DNA), [57] and a trefoil knot containing positive nodes. [58] The figureeight knot is a topological rubber glove, [59] that is, a structure whose molecular graph can be deformed to its mirror image, but cannot be deformed to a symmetry presentation.…”

Section: Dna Nanostructuresmentioning

confidence: 99%

Nucleic Acid Nanostructures and Topology

Seeman

1998

Angewandte Chemie International Edition

Self Cite

317

View full text Add to dashboard Cite

Three aesthetically pleasing topological target structures resulting from DNA nanotechnology (from top to bottom): a cube, Borromean rings, and a truncated octahedron.These molecules are constructed by applying the assembly methods of biotechnology to stable branched DNA molecules.1. Introduction DNA NanotechnologyThe term ªnanotechnologyº has become a word encountered frequently in chemistry. There are many interpretations to this word, but the most visible goal of nanotechnology is to establish the same level of control over the manipulation and assembly of real molecules and molecular groupings that molecular graphics has over the manipulation and assembly of molecular models. There have been two key inspirations for this approach to very ambitious chemistry: The first was Feynmans famous talk, entitled ªTheres Plenty of Room at the Bottomº.[1] He suggested that it would be possible to make machines that could make replicas of themselves on a somewhat smaller scale; the ultimate application of this procedure would be very tiny factories that could be packed densely. The second inspiration has been our growing knowledge of the ways that biological systems arrange their structural components, primarily by self-assembly on a supramolecular scale; hence, this second approach to nanotechnology is biomimetic. Feynmans approach has engendered the ªtop-downº methodology, best exemplified today by molecular assemblies that have been arranged by using scanning probe microscopes.[2] By contrast, biomimetic nanotechnology is ªbottom-upº, in that individual components are designed to assume particular tertiary structures, and ultimately to self-assemble into quaternary structures and arrays.Top-down nanotechnology is characterized at this stage by elegance and by the ability to deal with substances of largely arbitrary composition. Its key limitation is its lack of parallelism; only small numbers of objects can be assembled at once. The bottom-up approach has a number of drawbacks, but it has the primary advantage of enormous parallelism; even chemistry done with a picomole of material results in more than 100 billion copies of the product species. Biomimetic nanotechnology cannot make use conveniently of intervention by the scanning probe microscopist; hence it has an additional burden, the design of molecules that fold correctly and reliably into their proper shapes. We understand this type of design best in those systems composed of biological macromolecules. This is a very restricted set of species, and their behavior is largely limited to aqueous systems. Nevertheless, we have better control over the folding of nucleic acids and, to a lesser extent, proteins than over most other polymers on the nanoscale. The design of a protein and accurate prediction of protein folding remain key challenges in the area, although striking progress is being made. [3] Nucleic acids are much simpler, and therefore we have a much better grasp of their folding. Here, we will dwell on nucleic acid nanotechnology, primarily DNA nanotechnolo...

show abstract

Synthesis of a DNA knot containing both positive and negative nodes

Cited by 69 publications

References 1 publication

Probability of DNA knotting and the effective diameter of the DNA double helix.

Probability of DNA knotting and the effective diameter of the DNA double helix.

Toroidal embeddings of abstractly planar graphs are knotted or linked

Nucleic Acid Nanostructures and Topology

Contact Info

Product

Resources

About