When a sample with twice the equilibrium concentration of catenanes was treated with topo iv and atp at a range of enzyme. This can either protect or destabilize the dnas structure. Models and numbers boulder lectures on soft matter physics july 2012 yitzhak rabin r. The monomers are linked by phosphodiester bonds between the 3 carbon of one deoxyribose molecule and the 5 carbon of another. Plasmids can be invaluable tools to define the dynamic.
Of all published articles, the following were the most read within the past 12 months. Bates, anthony maxwell book your preferred reading. Theriot, physical biology of the cell garland, 2009. Two topological levels are inherent in closed circular cc dna. There are further complexities beyond the double helix, including supercoiling, knotting and catenation, that are less widely appreciated and understood but which are critical to its function. Fundamentals sergei m mirkin,university of illinois at chicago, illinois, usa topological characteristics of dna and specifically dna supercoiling influence all major dna transactions in living cells. Unraveling the tangled complexity of dna mathematical. Adenine is always opposite thymine, and cytosine is always oppostie guanine. Dna topology, 2005, 198 pages, andrew d bates, anthony.
Clipping is a handy way to collect important slides you want to go back to later. Dna being long, stiff, and helical means that there is potential for longrange communication between sites but also longrange interference between processes. Each strand of dna shown at the left is a right handed helix. Bates, anthony maxwell dna topology oxford biosciences, by andrew d. Andy bates is at the school of biological sciences at the university of liverpool. Frankkamenetskii center for advanced biotechnology, department of biomical engineering, boston university, boston.
Its orientation, width, width between nucleotides, length and number of nucleotides per helical turn is constant. An enzyme located throughout the nucleoplasm that destroys any unstable dna rna fragments. Dna topology 2in the dna helix than one would expect given the natural pitch of dna in solution 10. A coil of dna coils over itself like twisting a phone cord. Dna topology this page intentionally left blank dna topology andrew d bates school of biological sciences, universi. In focus provides clear, concise explanations of these concepts in their biological contexts, making it a valuable text for students of molecular biology. The physical tightnesslooseness of the dna strands. The linking number lk of a circular dna can only be changed by breaking a phosphodiester bond in one of the two strands, allowing the intact strand to pass through the broken strand and then rejoining the broken strand. Dna topoisomerases catalyse the interconversion of different topological forms of dna, including relaxed and supercoiled, knotted and unknotted, and catenated linked and unlinked dna circles. Dna supercoiling induces the formation of unusual secondary structure by specific dna repeats which can also affect dna functioning. This book explains the concepts of dna topology and. This book is certainly aimed at specialists, whom it will not diappoint with its.
The double helix structure discovered by watson and crick 50 years ago is now very familiar and its importance for dna function is widely appreciated. Our email service will alert you when new material is added to this companion web site. Dna in this state generally forms compensatory negative supercoils, and underwound segments are commonly referred to as negatively supercoiled. The rise of the helix is the same as that of a normal carpenters wood screw shown at center. Almost all biological processes involving dnasuch as replication, recombination, and transcriptionhave effects on, and are affected by, the topological state of the dna. Jul 18, 2014 bates ad, maxwell a 2005 dna topology.
Molecular biology course, delivered by joe loparo on september 10, 2014. Dna structure and topology sep 10, 2014 ericminikel boston, ma bcmp200 these are my notes from lecture 04 of harvards bcmp 200. Now customize the name of a clipboard to store your clips. The reason supercoiling can be harmful if a supercoil causes an important piece of dna to snap off under tension. Dna as the genetic material is a topic of intense interest in the 21st century with the familiar and iconic watsoncrick double helix having a vital importance for its function. The ability of type ii dna topoisomerases to perturb the equilibrium distributions of dna topoisomers is a consequence of their ability to hydrolyse atp. Bates, anthony maxwell dna topology oxford biosciences by andrew d. Dna topology is the study of geometrical and topological properties of dna loops and circular dna molecules. For example, a balloon is a perfect prop to describe how physical relationships can be maintained while an object is stretched or distorted fig. Despite the importance of dna topology, it is a conceptionally difficult subject to teach. When you turn the screw driver in the clockwise direction right handed sense, the screw is driven forward into a wooden board.
Bates and maxwell 14 have provided an excellent indepth treatment of dna topology. Generally helpful in destroying loose dna that can cause harm. Of particular interest are the entanglement of biopolymers and dna protein interactions eg sumners 47, bauer et al 5, colloms et al, grainge et al 24, kilbride et. First, the double helix as a whole can form knots of different types, or form the trivial knot to be unknotted. Dna topoisomerases structure, function, and mechanism.
Dna topology starts with a basic account of dna structure before going on to cover dna supercoiling, the definitions and physical meanings of linking number, twist, and writhe, and the free energy associated with supercoiling. Dna as the genetic material is a topic of intense interest in the 21st century, with the. Tangle analysis of difference topology experiments. Dna topology is a critical factor in essentially all in vivo chromosomal processes, including dna replication, rna transcription, homologous recombination, sitespecific recombination, dna repair, and integration of the abundant and mechanistically distinct forms of transposable elements. Bates, anthony maxwell pdf, epub ebook d0wnl0ad dna as the genetic material is a topic of intense interest in the 21st century with the familiar and iconic watsoncrick double helix having a vital importance for its function. In the case of dna, the use of doublestranded ropes and simple analogies. Mar 24, 2005 dna topology provides a solid basis for understanding the physical properties of dna and its topology, and how this molecule actively participates in many cellular processes.
Dna topology is the study of geometrical and topological properties of circular dna. It is a conceptionally difficult subject to teach, because it requires students to visualize threedimensional relationships that are not always easy to portray using twodimensional slides or chalkboards. Topology is an esoteric field of mathematics that deals with relationships that are not altered by elastic deformation. Dna topology, knot theory, linking number, mathematical manipulatives, supercoil. Enzymes that manipulate the geometry and topology of cellular dna perform many important cellular processes including segregation of daughter chromosomes, gene regulation, dna. May 25, 2016 an exploration of the complicated world of dna topology. The final chapters deal with the topoisomerases, the enzymes that control dna topology, and, most importantly, with the biological significance of the topological aspects of dna structure. Or is the best vendor unique your selection to fulfil your spare time. Unraveling the dna at one position changes the superhelicity. A sliding mechanism of topoisomerase action has been proposed to account for this phenomenon.
This book explains these topological aspects of dna structure. Find all the books, read about the author, and more. Dna ratios, the steadystate fraction of catenanes in the sample was as much as 16fold lower than the value at equilibrium in the absence of enzyme, and this same fraction was obtained when the initial substrate was a mixture of unlinked circles at the same concentrations. Topological characteristics of dna and specifically dna supercoiling influence all major dna transactions in living cells. Professor tony maxwell is head of the department of biological chemistry at the john innes centre, norwich. Theo chem elsevier journal of molecular structure theochem 336 1995 235243 dna topology maxim d.
Although some of these concepts are quite complex, they are presented in an accessible way, drawing on interesting and relevant examples. Bates and anthony maxwell the ability of type ii dna topoisomerases to perturb the equilibrium distributions of dna topoisomers is a consequence of their ability to hydrolyse atp. All of these features were described by watson and crick. Anthony maxwell the existence and biological importance of deformations of the double helix structure of dna have become known and are generally termed topology. It is fundamental to all dna transactions, though often ignored. Everyday low prices and free delivery on eligible orders. Besides reverse gyrase, archaea contain other type i dna topoisomerases.
Regulation of dna replication initiation by chromosome. Dna as the genetic material is a topic of intense interest in the 21st century, with the genomes of many organisms having been sequenced. From a more biological viewpoint, we rec ommend maxwell and bates dna topology 65, and mobile dna for more on recombination. Buy dna topology oxford biosciences new by andrew d. Nucleic acid structure refers to the structure of nucleic acids such as dna and rna. Dna topology is one of the hardest concepts in molecular biology. This book aims to explain these ideas simply, but rigorously, to allow a wider appreciation of dna topology. When a linear dna is free in solution it assumes a pitch which contains 10. The current mechanistic model for type ii enzymes involves the binding of two segments of dna. An exploration of the complicated world of dna topology. Dna is a doublestranded macromolecule in which each strand is a polymer of deoxyribonucleotide monomers. As we shall see in this chapter, there are in fact variations on common themes of structure that arise from the unique physical, chemical, and topological properties of the polynucleotide chain.
It is a conceptionally difficult subject to teach, because it requires students to visualize three. Plasmids can be invaluable tools to define the dynamic mechanisms of proteins that shape dna, organize. Nucleic acid structure is often divided into four different levels. Bates ad, berger jm, maxwell a 2011 the ancestral role of atp hydrolysis in type ii topoisomerases. Classroom aides for illustrating key concepts of dna topology and topoisomerases are presented throughout the article. Apr 02, 2012 it describes about the twist and writhe indna and about the linking number. Right handed supercoiling negative supercoiling underwinding b.
Dna topology provides a solid basis for understanding the physical properties of dna and its topology, and how this molecule actively participates in many cellular processes. There are further complexities beyond the double helix, including supercoilin. Dna structure dna is composed of polynucleotide chains the most important feature of dna is that it is usually composed of two polynucleotide chainstwisted around each other in the form of a. Secondly, the two complementary strands are interlinked in ccdna, which results in a biologically very important phenomenon of dna supercoiling. When you turn the screw driver in the clockwise direction right handed sense, the. The ability of type ii dna topoisomerases to perturb the equilibrium. Auto suggestions are available once you type at least 3 letters.
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