DNA knots reveal a chiral organization of DNA in phage capsids

Abstract

Icosahedral bacteriophages pack their double-stranded DNA genomes to near-crystalline density and achieve one of the highest levels of DNA condensation found in nature. Despite numerous studies, some essential properties of the packaging geometry of the DNA inside the phage capsid are still unknown. We present a different approach to the problems of randomness and chirality of the packed DNA. We recently showed that most DNA molecules extracted from bacteriophage P4 are highly knotted because of the cyclization of the linear DNA molecule confined in the phage capsid. Here, we show that these knots provide information about the global arrangement of the DNA inside the capsid. First, we analyze the distribution of the viral DNA knots by high-resolution gel electrophoresis. Next, we perform Monte Carlo computer simulations of random knotting for freely jointed polygons confined to spherical volumes. Comparison of the knot distributions obtained by both techniques produces a topological proof of nonrandom packaging of the viral DNA. Moreover, our simulations show that the scarcity of the achiral knot 41 and the predominance of the torus knot 51 over the twist knot 52 observed in the viral distribution of DNA knots cannot be obtained by confinement alone but must include writhe bias in the conformation sampling. These results indicate that the packaging geometry of the DNA inside the viral capsid is writhe-directed.bacteriophage ͉ DNA condensation ͉ DNA electrophoresis ͉ Monte Carlo simulation ͉ DNA writhe A ll icosahedral bacteriophages with double-stranded DNA genomes are believed to pack their chromosomes in a similar manner (1). During phage morphogenesis, a procapsid is first assembled, and a linear DNA molecule is actively introduced inside it by the connector complex (2, 3). At the end of this process, the DNA and its associated water molecules fill the entire capsid volume, where DNA reaches concentrations of 800 mg͞ml (4). Some animal viruses (5) and lipo-DNA complexes used in gene therapy (6) are postulated to hold similar DNA arrangements as those found in bacteriophages.Although numerous studies have investigated the DNA packing geometry inside phage capsids, some of its properties remain unknown. Biochemical and structural analyses have revealed that DNA is kept in its B form (7-9) and that there are no specific DNA-protein interactions (10, 11) or correlation between DNA sequences and their spatial location inside the capsid, with the exception of the cos ends in some viruses (12). Many studies have found that regions of the packed DNA form domains of parallel fibers, which in some cases have different orientations, suggesting a certain degree of randomness (8,9,13,14). The above observations have led to the proposal of several long-range organization models for DNA inside phage capsids: the ball of string model (13), the coaxial spooling model (8,11,13,14), the spiral-fold model (15), and the folded toroidal model (16). Liquid crystalline models, which take into account properties of DNA at high concen...

Self-assembling knots of controlled topology by designing the geometry of patchy templates

“…3 do not resemble the repertoire of topologies commonly formed by biopolymers such as proteins and DNA, whether in solution or under confinement [34][35][36][37][38][39][40][41] . Arguably, a key element favouring the self-assembly of the knots in Fig.…”

Knotted Globular Ring Polymers: How Topology Affects Statistics and Thermodynamics

“…Clarifying issues related to knots and links in polymer physics has been since long recognized of key importance in a variety of fields, ranging from molecular biology to nanotechnology. [11][12][13][14][15][27][28][29][30][31] So far, for isolated ring polymers, which are the object of the present study, most theoretical and numerical approaches provided informations referring to ensembles with unrestricted topology. This means that information on the frequency of occurrence of different knots is in general not available for models of random ring polymer configurations.…”

“…Besides the translocation processes, of central importance for biology, the study of topological spectra of DNA extracted from viral capsids is a typical context where the knowledge of spectra for specific models of random polymers is very valuable. 11,12,14 Model calculations like those carried out in the present work Figure 1: Example of a collapsed interacting selfavoiding ring with N = 500 steps on the cubic lattice, and its shortened form after the BFACF 39,40 reduction procedure with a low fugacity per step. The latter reveals that the ring holds a 5 2 knot, whose projection with the minimal crossing number n c = 5 is also shown.…”

Untying Knotted DNA with Elongational Flows

“…2−4 At microscopic scales, chromosomal knots are modified by topoisomerases during cell division 5 and are thought to participate in gene regulation. 6 Knots are found in proteins 7,8 and viral capsid DNA,9,10 likely with yet to be fully understood functions. It has been mathematically proven that knots become asymptotically likely as the length of a polymer increases, 11 a fact that explains their ubiquity.…”