Denaturation of circular DNA: supercoils and overtwist

Large bubble drives circular DNA melting

We investigate the melting transition of non-supercoiled circular DNA of different lengths, employing Brownian dynamics simulations. In the absence of supercoiling, we find that melting of circular DNA is driven by a large bubble, which agrees with the previous predictions of circular DNA melting in the presence of supercoiling. By analyzing sector-wise changes in average base-pair distance, our study reveals that the melting behavior of circular DNA closely resembles that of linear DNA. Additionally, we find a marked difference in the thermal stability of circular DNA over linear DNA at very short length scales, an effect that diminishes as the length of circular DNA increases. The stability of smaller circular DNA is linked to the occurrence of transient small bubbles, characterized by a lower probability of growth.

Exact extreme-value statistics at mixed-order transitions

We study extreme-value statistics for spatially extended models exhibiting mixed-order phase transitions (MOT). These are phase transitions that exhibit features common to both first-order (discontinuity of the order parameter) and second-order (diverging correlation length) transitions. We consider here the truncated inverse distance squared Ising model, which is a prototypical model exhibiting MOT, and study analytically the extreme-value statistics of the domain lengths The lengths of the domains are identically distributed random variables except for the global constraint that their sum equals the total system size L. In addition, the number of such domains is also a fluctuating variable, and not fixed. In the paramagnetic phase, we show that the distribution of the largest domain length l_{max} converges, in the large L limit, to a Gumbel distribution. However, at the critical point (for a certain range of parameters) and in the ferromagnetic phase, we show that the fluctuations of l_{max} are governed by novel distributions, which we compute exactly. Our main analytical results are verified by numerical simulations.

Enhancement of PCR Detection Limit by Single-Tube Restriction Endonuclease-PCR (RE-PCR)

BACKGROUND

Polymerase chain reaction (PCR) is widely used in biological research and diagnostics because of its high sensitivity and specificity. However, the sensitivity of PCR is strongly influenced by topological characteristics of the template. Supercoiled templates are known to inhibit PCR, whereas linearized forms of the same supercoiled templates facilitate PCR.

OBJECTIVES

This study was conducted to compare the PCR efficiency of circular supercoiled DNA templates to their restriction endonuclease (RE)-mediated linearized forms. Additionally, we also evaluated the possibility of RE digestion of the circular supercoiled templates within the complete PCR buffer.

METHODS

Following a systematic approach, we demonstrated that circular supercoiled templates could be efficiently linearized by RE in the complete PCR buffer itself. This allowed linearization of circular supercoiled templates and their subsequent amplification in the PCR buffer in a single-tube format.

RESULTS

Using this extremely simple RE-PCR approach, we documented up to tenfold increases in detection efficiency of PCR with two different circular supercoiled templates of clinical origin, including an international calibration standard.

CONCLUSIONS

This inexpensive and easy approach to increasing PCR sensitivity can be easily adapted to any standard PCR protocol aimed at amplifying circular supercoiled genomes. Apart from its application in the development of sensitive clinical diagnostic PCR assays for a large number of organisms, this method could also prove to be very useful in simplifying the existing protocols for other applications where pre-PCR restriction digestion is required, such as mutation detection, genotyping, and selective template amplification.

Twist-DNA: computing base-pair and bubble opening probabilities in genomic superhelical DNA

SUMMARY

Local opening of the DNA double helix is required in many fundamental biological processes and is, in part, controlled by the degree of superhelicity imposed in vivo by the protein machinery. In particular, positions of superhelically destabilized regions correlate with regulatory sites along the genome. Based on a self-consistent linearization of a thermodynamic model of superhelical DNA introduced by Benham, we have developed a program that predicts the locations of these regions by efficiently computing base-pair and bubble opening probabilities in genomic DNA. The program allows visualization of results in standard genome browsers to compare DNA opening properties with other available datasets.

AVAILABILITY AND IMPLEMENTATION

Source codes freely available for download at http://www.cbp.ens-lyon.fr/doku.php?id=developpement:productions:logiciels:twistdna, implemented in Fortran90 and supported on any Unix-based operating system (Linux, Mac OS X).