Manipulating a single adsorbed DNA for a critical endpoint

Abstract

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...

Can a double stranded DNA be unzipped by pulling a single strand?: Phases of adsorbed DNA

“…[37]) is shown by the dotted lines. This curve deviates markedly with the data obtained by the exact transfer matrix calculations at intermediate temperatures, but still matches in both the high and the low temperatures.…”

Unzipping DNA by a periodic force: Hysteresis loop area and its scaling

“…It is an initial step in processes such as DNA replication and RNA transcription, where the external force is exerted by enzymes [7]. The unzipping transition has been studied, both theoretically and experimentally, over 15 years and many important results have been established (see [2,3,5,6,[8][9][10][11][12][13][14][15] and references therein). In recent years, the focus has been shifted to study the hysteresis in unbinding and rebinding of biomolecules [16][17][18] because it can provide useful information on the kinetics of conformational transformations, the potential energy landscape, and it can be used in controlling the folding pathway of a single molecule [19].…”

Tricritical points in a compactU(1)lattice gauge theory at strong coupling

“…The location changes slightly with lattice volumes bigger than 10 4 . The PM-FMD transition is found to be strongly first order, and ends at a critical endpoint [18] where the continuous FM-PM transition terminates at first order transitions. The first order FM-FMD transition weakens gradually as κ is increased till the tricritical point where it becomes continuous.…”