Complete Phase Diagram of DNA Unzipping: Eye,<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mi>Y</mml:mi></mml:math>Fork, and Triple Point

Kapri, Rajeev; Bhattacharjee, Somendra M.; Seno, Flavio

doi:10.1103/physrevlett.93.248102

Cited by 55 publications

(87 citation statements)

References 22 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…The recognition of force as a thermodynamic variable for this process has helped in completing the phase transition picture of dsDNA [5]. Even though the nature of the thermal denaturation of DNA remains a puzzle, the force induced unzipping transition is theoretically well-settled [5][6][7][8][9][10][11][12][13][14][15][16][17][18]. In addition, the force induced unzipping transition has emerged as a possible scenario for opening of DNA [19] with the replication Y-fork as the junction of two phase coexistence, the zipped and the unzipped DNA.…”

mentioning

confidence: 99%

See 1 more Smart Citation

Manipulating a single adsorbed DNA for a critical endpoint

Kapri¹,

Bhattacharjee²

2008

Europhys. Lett.

Self Cite

View full text Add to dashboard Cite

Abstract. -We show the existence of a critical endpoint in the phase diagram of unzipping of an adsorbed double-stranded (ds) polymer like DNA. The competition of base pairing, adsorption and stretching by an external force leads to the critical end point. From exact results, the location of the critical end point is determined and its classical nature established.A critical end point (CEP) occurs when a continuous transition line terminates on a first order transition line. It's specialty: even though it is surrounded by three phases, still there is no three phase coexistence, but, instead, a scale-free critical phase coexists with a noncritical phase [1,2]. For comparison, a triple point, also surrounded by three phases, would show three phase coexistence. A CEP is expected to occur in various mixtures and ferroelectrics and in vortex lattice [1][2][3]. We show here that a different way of locating and studying a CEP is through single molecular manipulations of an adsorbed DNA.The melting of DNA is known to be a crucial step in many biological processes [4]. The double stranded DNA(dsDNA) is a bound state of two polymers or strands held together by hydrogen bonds of base pairs. The phenomenon of cooperative breaking of the base-pairings thermally or otherwise is melting. The recognition of force as a thermodynamic variable for this process has helped in completing the phase transition picture of dsDNA [5]. Even though the nature of the thermal denaturation of DNA remains a puzzle, the force induced unzipping transition is theoretically well-settled [5][6][7][8][9][10][11][12][13][14][15][16][17][18]. In addition, the force induced unzipping transition has emerged as a possible scenario for opening of DNA [19] with the replication Y-fork as the junction of two phase coexistence, the zipped and the unzipped DNA. A thermodynamic description of DNA would entail two conjugate ensembles of fixed force and fixed distance. These two ensembles are important in both theoretical and experimental situations [8,[20][21][22]. The Melting and unzipping of DNA are generally considered in the free environment of bulk solutions, but often the presence of interacting surfaces cannot be ignored. In vivo, during replication, DNA gets attached to the membrane but otherwise it remains away ("desorbed") from the membrane. The protein-induced membrane-DNA attachment is used in the replication process and cell division [23]. In gene therapy, targeted delivery is achieved by taking advantage of adsorption-desorption of DNA on cationic liposomes [24,25]. That metallic (e.g., gold), semiconducting (e.g., silicon) or insulating (e.g., mica) surfaces can also adsorb DNA has opened up the possibility of biosensors for fast and precise detection of DNA in samples like hair, blood etc. In all these cases, the surface-DNA interaction depends (and hence tunable) on the nature of the surface, fluctuation of the surface as for fluid membranes, ionic concentration of the environment, nature of hydrophobicity and van der Waal interactions. A wellstu...

show abstract

mentioning

confidence: 99%

“…A thermodynamic description of DNA would entail two conjugate ensembles of fixed force and fixed distance. These two ensembles are important in both theoretical and experimental situations [8,[20][21][22].…”

mentioning

confidence: 99%

Manipulating a single adsorbed DNA for a critical endpoint

Kapri¹,

Bhattacharjee²

2008

Europhys. Lett.

Self Cite

View full text Add to dashboard Cite

show abstract

“…Consequently by using force as a thermodynamic variable, many theoretical and numerical studies were done in establishing a wealth of definite falsifiable predictions [3,5,17,18,19,20]. Among these, a very important role was played by simple models which are amenable to analytical solution or very accurate numerical treatments [3,17,19]. Such models despite their simplicity, have been proved to be quite predictive and provided many important information about the cellular processes.…”

mentioning

confidence: 99%

“…Furthermore, these experiments elucidated the mechanism involved in crucial processes like transcription and replication [1, 2,13,14,15] . Consequently by using force as a thermodynamic variable, many theoretical and numerical studies were done in establishing a wealth of definite falsifiable predictions [3,5,17,18,19,20]. Among these, a very important role was played by simple models which are amenable to analytical solution or very accurate numerical treatments [3,17,19].…”

mentioning

confidence: 99%

See 1 more Smart Citation

Can re-entrance be observed in force-induced transitions?

Kumar

2009

Europhys. Lett.

View full text Add to dashboard Cite

A large conformational change in the reaction co-ordinate and the role of the solvent in the formation of base-pairing are combined to settle a long standing issue i.e. prediction of re-entrance in the force induced transition of DNA. A direct way to observe the re-entrance, i.e a strand goes to the closed state from the open state and again to the open state with temperature, appears difficult to be achieved in the laboratory. An experimental protocol (in direct way) in the constant force ensemble is being proposed for the first time that will enable the observation of the re-entrance behavior in the force-temperature plane. Our exact results for small oligonucleotide that forms a hairpin structure provide the evidence that re-entrance can be observed.

show abstract

Efimov-Like Behaviour in Low-Dimensional Polymer Models

et al. 2016

View full text Add to dashboard Cite

In the quantum Efimov effect, identical bosons form infinitely many bound trimer states at the bound dimer dissociation threshold, with their energy spectrum obeying a universal geometrical scaling law. Inspired by the formal correspondence between the possible trajectories of a quantum particle and the possible conformations of a polymer chain, the existence of a triple-stranded DNA bound state when a double-stranded DNA is not stable was recently predicted by modelling three directed polymer chains in low-dimensional lattices, both fractal (d<1) and euclidean (d=1). A finite melting temperature for double-stranded DNA requires in d≤2 the introduction of a weighting factor penalizing the formation of denaturation bubbles, that is non-base paired portions of DNA. The details of how bubble weighting is defined for a three-chain system were shown to crucially affect the presence of Efimov-like behaviour on a fractal lattice. Here we assess the same dependence on the euclidean 1+1 lattice, by setting up the transfer matrix method for three infinitely long chains confined in a finite size geometry. This allows us to discriminate unambiguously between the absence of Efimov-like behaviour and its presence in a very narrow temperature range, in close correspondence with what was already found on the fractal lattice. When present, however, no evidence is found for triple-stranded bound states other than the ground state at the two-chain melting temperature

show abstract

Complete Phase Diagram of DNA Unzipping: Eye,YFork, and Triple Point

Cited by 55 publications

References 22 publications

Manipulating a single adsorbed DNA for a critical endpoint

Manipulating a single adsorbed DNA for a critical endpoint

Can re-entrance be observed in force-induced transitions?

Efimov-Like Behaviour in Low-Dimensional Polymer Models

Contact Info

Product

Resources

About