Marked difference in conformational fluctuation between giant DNA molecules in circular and linear forms

Abstract

We performed monomolecular observations on linear and circular giant DNAs (208 kbp) in an aqueous solution by the use of fluorescence microscopy. The results showed that the degree of conformational fluctuation in circular DNA was ca. 40% less than that in linear DNA, although the long-axis length of circular DNA was only 10% smaller than that of linear DNA. Additionally, the relaxation time of a circular chain was shorter than that of a linear chain by at least one order of magnitude. The essential features of this marked difference between linear and circular DNAs were reproduced by numerical simulations on a ribbon-like macromolecule as a coarse-grained model of a long semiflexible, double-helical DNA molecule. In addition, we calculated the radius of gyration of an interacting chain in a circular form on the basis of the mean field model, which provides a better understanding of the present experimental trend than a traditional theoretical equation.

Conformational and Dynamic Properties of Short DNA Minicircles in Aqueous Solution from Atomistic Molecular Dynamics Simulations

“…The ratio σ­( R g )/ R g expresses the relative magnitude of conformational fluctuations of the radius-of-gyration tensor and contrasting trends are observed between the circular and linear DNA duplexes studied: while the relative extent of conformational fluctuations is attenuated with increasing size in circular DNA, the opposite holds for linear DNA, with conformational fluctuations increasing significantly (see also Figure and Figure S5). This marked difference in the conformational fluctuations between circular and linear DNA has also been reported for giant DNA (208 kbp) in aqueous solution by use of fluorescence microscopy . The same qualitative trend holds for giant DNA molecules, where a much larger degree of conformational fluctuations is observed for linear (approximately 40% more) than circular DNA.…”

“…This marked difference in the conformational fluctuations between circular and linear DNA has also been reported for giant DNA (208 kbp) in aqueous solution by use of fluorescence microscopy. 79 The same qualitative trend holds for giant DNA molecules, where a much larger degree of conformational fluctuations is observed for linear (approximately 40% more) than circular DNA. It appears that with increasing molecular length, the accompanying increase in backbone flexibility is translated to smaller σ(R g ) values for circular DNA as compares to linear DNA, due to the constraint of ring closure.…”

Fibril Assembly and Gelation of Macromolecules with Amphiphilic Repeating Units

“…Note, at given a PS , the N clust is always lower for linear macromolecules. Larger N clust (Figure 4a) with narrower distribution over aggregation numbers (Figure 3) in the solutions with cyclic homopolymers compared to linear analogues could be the result of the more compact size of the cyclic chains 56 and, hence, the smaller solvation number. However, the full mechanism behind described phenomena can be more sophisticated.…”

Escape dynamics of active ring polymers in a cylindrical nanochannel

“…Different from linear polymers, ring polymers, such as bacterial chromosomes, 31 do not have free ends, which leads to their unique dynamic characteristics. 5,32 Topology plays a crucial role in various biophysical contexts where DNA is constrained, 33 e.g., the DNA strands of the phage can escape from the capsid to infect the bacterial cells, 13,34 the segregation of the compacted circular genome of some bacteria 35 and the compression and ejection of the knotted DNA of a virus. 12,36 Recently, active polymers linked by active particles have gradually entered into the research field of polymers.…”