Modeling DNA beacons at the mesoscopic scale

We report model calculations on DNA single strands which describe the equilibrium dynamics and kinetics of hairpin formation and melting. Modeling is at the level of single bases. Strand rigidity is described in terms of simple polymer models; alternative calculations performed using the freely rotating chain and the discrete Kratky-Porod models are reported. Stem formation is modeled according to the Peyrard-Bishop-Dauxois Hamiltonian. The kinetics of opening and closing is described in terms of a diffusion-controlled motion in an effective free energy landscape. Melting profiles, dependence of melting temperature on loop length, and kinetic time scales are in semiquantitative agreement with experimental data obtained from fluorescent DNA beacons forming poly(T) loops. Variation in strand rigidity is not sufficient to account for the large activation enthalpy of closing and the strong loop length dependence observed in hairpins forming poly(A) loops. Implications for modeling single strands of DNA or RNA are discussed.Comment: 15 pages, 17 figures, submitted to Eur. J. Phys.

Observation and Manipulation of a Capillary Jet in a Centrifuge-Based Droplet Shooting Device

We report observation and manipulation of a capillary jet under ultra-high centrifugal gravity in a proposed capillary-based fluidic device for the synthesis of microparticles in a centrifugal tube called Centrifuge-Based Droplet Shooting Device (CDSD). Using a high-speed camera, we directly observed the dripping to jetting transition of a viscous capillary jet of water and Sodium alginate solution generated from a glass capillary-orifice of a diameter of O (100) m under centrifugal gravity ranging from 190 to 450 g. A non-dimensional analysis shows that the mechanism of the dripping-jetting transition in the CDSD may follow that previously reported for a dripping faucet under standard gravity. We also fabricated calcium alginate microparticles by gelating droplets of sodium alginate solution obtained in the break-up of the capillary jet in the jetting regime and demonstrated fabrication of microbeads-on-a-string structures. We confirmed that the jetting regime of the capillary jet could be used to fabricate smaller particles than that of the dripping regime. The results show that the CDSD would be a more useful device to fabricate various polymeric structures and understand the physics of fluid jets under ultra-high gravity

Quantitative design and experimental validation for a single-molecule DNA nanodevice transformable among three structural states

In this work, we report the development and experimental validation of a coupled statistical thermodynamic model allowing prediction of the structural transitions executed by a novel DNA nanodevice, for quantitative operational design. The efficiency of target structure formation by this nanodevice, implemented with a bistable DNA molecule designed to transform between three distinct structures, is modeled by coupling the isolated equilibrium models for the individual structures. A peculiar behavior is predicted for this nanodevice, which forms the target structure within a limited temperature range by sensing thermal variations. The predicted thermal response is then validated via fluorescence measurements to quantitatively assess whether the nanodevice performs as designed. Agreement between predictions and experiment was substantial, with a 0.95 correlation for overall curve shape over a wide temperature range, from 30C to 90C. The obtained accuracy, which is comparable to that of conventional melting behavior prediction for DNA duplexes in isolation, ensures the applicability of the coupled model for illustrating general DNA reaction systems involving competitive duplex formation. Finally, tuning of the nanodevice using the current model towards design of a thermal band pass filter to control chemical circuits, as a novel function of DNA nanodevices is proposed

Hexamer oligonucleotide topology and assembly under solution phase NMR and theoretical modeling scrutiny

The entire family of non-complementary hexamer oligodeoxyribonucleotides d(GCXYGC) (X and Y = A, G, C, or T) were assessed for topological indicators and equilibrium thermodynamics using a priori molecular modeling and solution phase NMR spectroscopy. Feasible modeled hairpin structures formed a basis from which solution structure and equilibria for each oligonucleotide were considered. 1H and 31P variable temperature (VT) and concentration dependent NMR data, NMR signal assignments and diffusion parameters led to d(GCGAGC) and d(GCGGGC) being understood as exceptions within the family in terms of self-association and topological character. A mean diffusion coefficient D298K = (2.0 ± 0.07) × 10-10 m2s-1 was evaluated across all hexamers except for d(GCGAGC) (D298K = 1.7 × 10-10 m2s-1) and d(GCGGGC) (D298K = 1.2 × 10-10 m2s-1). Melting under VT analysis (Tm = 323 K) combined with supporting NMR evidence confirmed d(GCGAGC) as the shortest tandem sheared GA mismatched duplex. Diffusion measurements were used to conclude that d(GCGGGC) preferentially exists as the shortest stable quadruplex structure. Thermodynamic analysis of all data led to the assertion that, with the exception of XY = GA and GG, the remaining non-complementary oligonucleotides adopt equilibria between monomer and duplex, contributed to largely by monomer random-coil forms. Contrastingly d(GCGAGC) showed preference for tandem sheared GA mismatch duplex formation with an association constant K = 3.9 × 105 M-1. No direct evidence was acquired for hairpin formation in any instance although its potential existence is considered possible for d(GCGAGC) on the basis of molecular modeling studies

Rotary motion driven by a direct current electric field

We report the rotary motion of an aqueous microdroplet in an oil phase under a stationary direct current electric field. A droplet exhibits rotary motion under a suitable geometrical arrangement of positive and negative electrodes. Rotary motion appears above a certain critical electric potential and its frequency increases with an increase in the potential. A simple theoretical model is proposed to describe the occurrence of this rotary motion, together with an argument for the future expansion of this micro rotary motor system