DNA topology and topoisomerases

Abstract

DNA is essentially an extremely long double-stranded rope in which the two strands are wound about one another. As a result, topological properties of the genetic material, including DNA underwinding and overwinding, knotting, and tangling profoundly influence virtually every major nucleic acid process. Despite the importance of DNA topology, it is a conceptionally difficult subject to teach because it requires students to visualize three-dimensional relationships. This article will familiarize the reader with the concept of DNA topology and offer practical approaches and demonstrations to teaching this ''knotty'' subject in the classroom. Furthermore, it will discuss topoisomerases, the enzymes that regulate the topological state of DNA in the cell. These ubiquitous enzymes perform a number of critical cellular functions by generating transient breaks in the double helix. During this catalytic event, topoisomerases maintain genomic stability by forming covalent phosphotyrosyl bonds between active site residues and the newly generated DNA termini. Topoisomerases are essential for cell survival. However, because they cleave the genetic material, these enzymes also have the potential to fragment the genome. This latter feature of topoisomerases is exploited by some of the most widely prescribed anticancer and antibacterial drugs currently in clinical use. Finally, in addition to curing cancer, topoisomerase action also has been linked to the induction of specific types of leukemia.Keywords: nucleic acid structure, function, and processing, nucleic acid enzymology, molecular biology, medical biochemistry.Although the genetic information encoded in DNA is embodied in a one-dimensional array of bases, it is the three-dimensional structure of the genetic material that controls how this information is replicated, expressed, and recombined in the cell [1][2][3][4][5]. Because DNA is double-stranded and compressed into a crowded cellular environment, some of the most important three-dimensional relationships in the double helix are topological in nature.How is the concept of topology applied to the genetic material? As long as the ends of DNA are fixed in space, topological relationships are defined as those that can be altered only by breaking one or both strands of the double helix. For all practical purposes, we always can consider the ends of cellular DNA to be anchored and unable to rotate [3][4][5][6]. This is because there is a high frictional energy associated with the extreme length of chromosomes, plasmids and bacterial chromosomes often are circular (and therefore have no ends), and chromosomal DNA is tethered to membranes in bacteria and to the chromosome scaffold in eukaryotes [3][4][5][6]. Topological relationships in DNA include underwinding and overwinding, knotting, and tangling.DNA topology should be an integral component of biochemistry and molecular biology curricula for a number of reasons, including:

A Guide to Magnetic Tweezers and Their Applications

“…However, DNA behavior under tension somewhat differs from that in bulk measurements, when it is unconstrained, an aspect that must be taken into account during experimental design. We provide below a brief synopsis of DNA topology while more detailed reading is available in numerous excellent reviews [55,59,60].…”

Bacillus anthracis GrlA V96A Topoisomerase IV, a Quinolone Resistance Mutation That Does Not Affect the Water-Metal Ion Bridge

“…Q uinolone resistance has been increasing steadily since the 1990s and is threatening the clinical efficacy of this class of broad-spectrum antibacterials (1-3). The most common form of quinolone resistance is target mediated and results from specific point mutations in gyrase and topoisomerase IV (1, 3-6).Gyrase and topoisomerase IV are type II topoisomerases, and both are encoded by nearly all bacterial species (3,5,(7)(8)(9)(10)(11)(12)(13)(14). These enzymes alter DNA topology by passing an intact double helix through a transient break that they generate in a separate segment of DNA (3,7,8,(10)(11)(12)(13)15).…”

“…Both are heterotetramers, consisting of two A subunits (GyrA in gyrase and GrlA in topoisomerase IV) and two B subunits (GyrB in gyrase and GrlB in topoisomerase IV). The A subunits contain the active site tyrosine residues involved in DNA cleavage and ligation, and the B subunits bind ATP, which is required for overall catalytic activity (3,5,7,8,10,11,13,15). Quinolones, including ciprofloxacin, take advantage of DNA cleavage mediated by type II topoisomerases and kill bacteria by increasing the levels of enzyme-generated strand breaks (1, 3-6, 16).…”

“…These enzymes alter DNA topology by passing an intact double helix through a transient break that they generate in a separate segment of DNA (3,7,8,(10)(11)(12)(13)15). Both are heterotetramers, consisting of two A subunits (GyrA in gyrase and GrlA in topoisomerase IV) and two B subunits (GyrB in gyrase and GrlB in topoisomerase IV).…”

“…Quinolones, including ciprofloxacin, take advantage of DNA cleavage mediated by type II topoisomerases and kill bacteria by increasing the levels of enzyme-generated strand breaks (1,(3)(4)(5)(6)16). Gyrase and topoisomerase IV are essential for cell survival (3,7,8,(10)(11)(12)(13), and both appear to be physiological targets for quinolone antibacterials (3,4,(17)(18)(19)(20)(21).…”