Manipulating a single adsorbed DNA for a critical endpoint

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.Comment: 6 pages, 5 figures, Published versio

Unzipping DNA by force: thermodynamics and finite size behaviour

We discuss the thermodynamic behaviour near the force induced unzipping transition of a double stranded DNA in two different ensembles. The Y-fork is identified as the coexisting phases in the fixed distance ensemble. From finite size scaling of thermodynamic quantities like the extensibility, the length of the unzipped segment of a Y-fork, the phase diagram can be recovered. We suggest that such procedures could be used to obtain the thermodynamic phase diagram from experiments on finite length DNA.Comment: 10 pages, accepted for publication in special issue of Journal of Physics: Condensed Matte

Complete Phase Diagram of DNA Unzipping: Eye, Y-fork and triple point

We study the unzipping of double stranded DNA (dsDNA) by applying a pulling force at a fraction $s$ $(0 \le s \le 1)$ from the anchored end. From exact analytical and numerical results, the complete phase diagram is presented. The phase diagram shows a strong ensemble dependence for various values of $s$. In addition, we show the existence of an ``eye'' phase and a triple point.Comment: 4 pages, 4 figures; revised version: misprints corrected. References corrected/added. To appear in Physical Review Letter

Unzipping an adsorbed polymer in a dirty or random environment

The phase diagram of unzipping of an adsorbed directed polymer in two dimensions in a random medium has been determined. Both the hard-wall and the soft-wall cases are considered. Exact solutions for the pure problem with different affinities on the two sides are given. The results obtained by the numerical procedure adopted here are shown to agree with the exact results for the pure case. The characteristic exponents for unzipping for the random problem are different from the pure case. The distribution functions for the unzipped length, first bubble, and the spacer are determined.Comment: Published version, uses revtex4, 14 page

Effects of Eye-phase in DNA unzipping

The onset of an "eye-phase" and its role during the DNA unzipping is studied when a force is applied to the interior of the chain. The directionality of the hydrogen bond introduced here shows oscillations in force-extension curve similar to a "saw-tooth" kind of oscillations seen in the protein unfolding experiments. The effects of intermediates (hairpins) and stacking energies on the melting profile have also been discussed.Comment: RevTeX v4, 9 pages with 7 eps figure

Thermodynamic relations for DNA phase transitions

The force induced unzipping transition of a double stranded DNA is considered from a purely thermodynamic point of view. This analysis provides us with a set of relations that can be used to test microscopic theories and experiments. The thermodynamic approach is based on the hypothesis of impenetrability of the force in the zipped state. The melting and the unzipping transitions are considered in the same framework and compared with the existing statistical model results. The analysis is then extended to a possible continuous unzipping transition.Comment: 9 Pages, 5 figures. To appear in Indian Journal of Physics, Special Issue on the occasion of 125th Birth Anniversary of Sir C V Rama

Chronic hM4Di-DREADD-Mediated Chemogenetic Inhibition of Forebrain Excitatory Neurons in Postnatal or Juvenile Life Does Not Alter Adult Mood-Related Behavior

AbstractG-protein-coupled receptors (GPCRs) coupled to Gisignaling, in particular downstream of monoaminergic neurotransmission, are posited to play a key role during developmental epochs (postnatal and juvenile) in shaping the emergence of adult anxiodepressive behaviors and sensorimotor gating. To address the role of Gisignaling in these developmental windows, we used a CaMKIIα-tTA::TRE hM4Di bigenic mouse line to express the hM4Di-DREADD (designer receptor exclusively activated by designer drugs) in forebrain excitatory neurons and enhanced Gisignaling via chronic administration of the DREADD agonist, clozapine-N-oxide (CNO) in the postnatal window (postnatal days 2–14) or the juvenile window (postnatal days 28–40). We confirmed that the expression of the HA-tagged hM4Di-DREADD was restricted to CaMKIIα-positive neurons in the forebrain, and that the administration of CNO in postnatal or juvenile windows evoked inhibition in forebrain circuits of the hippocampus and cortex, as indicated by a decline in expression of the neuronal activity marker c-Fos. hM4Di-DREADD-mediated inhibition of CaMKIIα-positive forebrain excitatory neurons in postnatal or juvenile life did not impact the weight profile of mouse pups, and also did not influence the normal ontogeny of sensory reflexes. Further, postnatal or juvenile hM4Di-DREADD-mediated inhibition of CaMKIIα-positive forebrain excitatory neurons did not alter anxiety- or despair-like behaviors in adulthood and did not impact sensorimotor gating. Collectively, these results indicate that chemogenetic induction of Gisignaling in CaMKIIα-positive forebrain excitatory neurons in postnatal and juvenile temporal windows does not appear to impinge on the programming of anxiodepressive behaviors in adulthood.</jats:p

Chronic hM4Di-DREADD mediated chemogenetic inhibition of forebrain excitatory neurons in postnatal or juvenile life does not alter adult mood-related behavior

AbstractG-protein coupled receptors (GPCRs) coupled to Gi-signaling, in particular downstream of monoaminergic neurotransmission, are posited to play a key role during developmental epochs (postnatal and juvenile), in shaping the emergence of adult anxio-depressive behaviors and sensorimotor gating. To address the role of Gi-signaling in these developmental windows, we used a CamKIIα-tTA::TRE hM4Di bigenic mouse line to express the hM4Di-DREADD in forebrain excitatory neurons and enhanced Gi-signaling via chronic administration of the DREADD agonist, CNO in the postnatal (PNCNO: postnatal day 2-14) or juvenile (JCNO: postnatal day 28-40) window. We confirmed that the expression of the HA-tagged hM4Di-DREADD was restricted to CamKII-positive neurons in the forebrain, and administration of CNO in postnatal or juvenile windows evoked inhibition in forebrain circuits of the hippocampus and cortex, as indicated by a decline in expression of the neuronal activity marker, c-fos. hM4Di-DREADD mediated inhibition of CamKIIα-positive forebrain excitatory neurons in postnatal or juvenile life did not impact the weight profile of mouse pups, and also did not influence the normal ontogeny of sensory reflexes. Further, postnatal or juvenile hM4Di-DREADD mediated inhibition of CamKIIα-positive forebrain excitatory neurons did not alter anxiety or despair-like behaviors in adulthood, and did not impact sensorimotor gating. Collectively, these results indicate that chemogenetic induction of Gi-signaling in CamKIIα-positive forebrain excitatory neurons in postnatal and juvenile temporal windows does not appear to impinge on the programming of anxio-depressive behaviors in adulthood.</jats:p