Journal: Journal of Biological Physics

Article Title: Re-entrant cholesteric phase in DNA liquid-crystalline dispersion particles

doi: 10.1007/s10867-016-9433-4

Figure Lengend Snippet: Schematic diagram of the formation of liquid-crystalline dispersion as a result of phase exclusion of linear ds DNA molecules [molecular mass (6–8) × 105 Da)] from PEG-containing water-salt solutions. 1. Initial ds DNA molecules in a PEG-containing solution (PEG molecules are shown by filled red circles) at CPEG below the critical value. 2. Particle of the DNA liquid-crystalline dispersion (encircled by an oval) formed at CPEG above the critical value. (P is the pitch of the helical twist of the spatial structure of a dispersion particle.) 3. A quasinematic layer formed by ds DNA molecules (the cross at the center denotes the rotation axis of the helical structure). [Note that DNA molecules in a quasinematic layer are located at a distance, which changes from 2.5 to 5.0 nm depending on the osmotic pressure of the solution (thick red frame and dark arrows are symbols of osmotic pressure of a PEG-containing solution)]

Article Snippet: Calf thymus depolymerized ds DNA (Sigma, USA) with a molecular mass of ∼(0.6–0.8) × 10 6 Da after additional purification was used.

Techniques:

Journal: Journal of Biological Physics

Article Title: Re-entrant cholesteric phase in DNA liquid-crystalline dispersion particles

doi: 10.1007/s10867-016-9433-4

Figure Lengend Snippet: Experimental small-angle X-ray scattering curves from the phase formed via low-speed sedimentation of DNA LCD particles measured at four different temperatures. 1–20 °C, 2–40 °C, 3–60 °C, 4–80 °C. Conditions of DNA LCD particle formation: CDNA = 30 μg ml−1, CPEG = 300 mg ml−1, 0.3 M NaCl + 0.002 M Na+ phosphate buffer; T = 20 °C

Article Snippet: Calf thymus depolymerized ds DNA (Sigma, USA) with a molecular mass of ∼(0.6–0.8) × 10 6 Da after additional purification was used.

Techniques: Sedimentation

Journal: Journal of Biological Physics

Article Title: Re-entrant cholesteric phase in DNA liquid-crystalline dispersion particles

doi: 10.1007/s10867-016-9433-4

Figure Lengend Snippet: Experimental small-angle X-ray scattering curves from phases formed via low-speed sedimentation of DNA LCD particles. Conditions of DNA LCD particle formation: 1 - CPEG = 170 mg ml−1, 2 - CPEG = 300 mg ml−1. CDNA = 30 μg ml−1; 0.3 M NaCl + 0.002 M Na+ phosphate buffer. Inset: the dependence of the mean distance between DNA molecules (d) in liquid crystalline phases upon PEG concentration. a Experimental curves of small-angle X-ray scattering by liquid-crystalline phases formed via low-speed sedimentation of DNA LCD particles. b Fingerprint texture typical of the DNA classical cholesteric liquid-crystalline phase. CPEG = 170 mg ml−1; 0.3 M NaCl + 0.002 M Na+ phosphate buffer. Bar corresponds to 5 μm

Article Snippet: Calf thymus depolymerized ds DNA (Sigma, USA) with a molecular mass of ∼(0.6–0.8) × 10 6 Da after additional purification was used.

Techniques: Sedimentation, Concentration Assay

Journal: Journal of Biological Physics

Article Title: Re-entrant cholesteric phase in DNA liquid-crystalline dispersion particles

doi: 10.1007/s10867-016-9433-4

Figure Lengend Snippet: a Dependence of the amplitude of the abnormal band in the CD spectra of DNA LCDs (λ = 270 nm) formed in water-salt solutions (0.3 M NaCl + 0.002 M Na+ phosphate buffer) with different PEG concentrations on the temperature. 1 - CPEG = 220 mg ml−1, 2 - CPEG = 240 mg ml−1, 3 - CPEG = 260 mg ml−1, 4 - CPEG = 280 mg ml−1, 5 - CPEG = 300 mg ml−1. CDNA = 30 μg/ml. ΔA270 × 10−6 optical units; L = 1 cm. Arrows show the mean values of transition temperature (τtrans.) of DNA LCDs from the optically inactive to optically active state for two different condition sets. b Dependence of the value τtrans. versus PEG concentration. Different points relate to two series of independent experiments

Article Snippet: Calf thymus depolymerized ds DNA (Sigma, USA) with a molecular mass of ∼(0.6–0.8) × 10 6 Da after additional purification was used.

Techniques: Concentration Assay

Journal: Journal of Biological Physics

Article Title: Re-entrant cholesteric phase in DNA liquid-crystalline dispersion particles

doi: 10.1007/s10867-016-9433-4

Figure Lengend Snippet: Dependence of the amplitude of the abnormal band (λ = 270 nm) in the CD spectra of DNA LCDs formed at room temperature (curve 1), heated to 80 °C (curve 2) and cooled to room temperature (curve 3) on PEG concentration. CDNA = 30 μg ml−1, 0.3 M NaCl + 0.002 M Na+ phosphate buffer. ΔA270 × 10−6 optical units; L = 1 cm. Symbols I and II correspond to various PEG domains; arrows show the direction of the CD band amplitude change at temperature increase

Article Snippet: Calf thymus depolymerized ds DNA (Sigma, USA) with a molecular mass of ∼(0.6–0.8) × 10 6 Da after additional purification was used.

Techniques: Concentration Assay

Journal: Journal of Biological Physics

Article Title: Re-entrant cholesteric phase in DNA liquid-crystalline dispersion particles

doi: 10.1007/s10867-016-9433-4

Figure Lengend Snippet: CD spectra of DNA LCD treated with SYBR Green (curves 2–5), measured at different temperatures. 2–22 °C, 3–40 °C, 4–80 °C, 5–80 °C → 22 °C. CDNA = 30 μg ml−1, CPEG = 250 mg ml−1, 0.3 M NaCl + 0.002 M Na+ phosphate buffer. CSG = 0.781 × 10−5 M. 1 – the CD spectrum of the initial DNA LCD (22 °C, control). ΔA = (AL – AR) × 10−6 optical units, L = 1 cm

Article Snippet: Calf thymus depolymerized ds DNA (Sigma, USA) with a molecular mass of ∼(0.6–0.8) × 10 6 Da after additional purification was used.

Techniques: SYBR Green Assay

Journal: Journal of Biological Physics

Article Title: Re-entrant cholesteric phase in DNA liquid-crystalline dispersion particles

doi: 10.1007/s10867-016-9433-4

Figure Lengend Snippet: Hypothetical scheme of hexagonal ds DNA molecule packing in dispersion particles formed in PEG-containing solution. (Dark spots are PEG-molecules outside closely packed DNA molecules) (See text above this Fig.)

Article Snippet: Calf thymus depolymerized ds DNA (Sigma, USA) with a molecular mass of ∼(0.6–0.8) × 10 6 Da after additional purification was used.

Techniques:

Journal: Journal of Biological Physics

Article Title: Re-entrant cholesteric phase in DNA liquid-crystalline dispersion particles

doi: 10.1007/s10867-016-9433-4

Figure Lengend Snippet: Theoretically computed CD spectra of ds DNA cholesteric LCD particles: curve 1 – CD spectrum for classical ds DNA cholesteric LCD (d = 3.5 nm, P = 2,500 nm, φ = 0.5°); curve 2 – CD spectrum for model artificial ds DNA cholesteric LCD (d = 2.5 nm, φ = 0.5°); curve 3 - CD spectrum for model artificial ds DNA cholesteric LCD (d = 2.5 nm, φ = 1.0°); curve 4 - CD spectrum for model artificial ds DNA cholesteric LCD (d = 2.5 nm, φ = 1.5°). D = 550 nm, CDNA = 30 μg ml−1, ΔA = (AL – AR) × 10−6 optical units, L = 1 cm. φ - the twist angle between neighboring quasinematic layers

Article Snippet: Calf thymus depolymerized ds DNA (Sigma, USA) with a molecular mass of ∼(0.6–0.8) × 10 6 Da after additional purification was used.

Techniques:

Journal: Journal of Biological Physics

Article Title: Re-entrant cholesteric phase in DNA liquid-crystalline dispersion particles

doi: 10.1007/s10867-016-9433-4

Figure Lengend Snippet: Theoretically calculated dependence of the abnormal negative band amplitude (∆A 270) upon the pitches (P) of hypothetical ds DNA cholesterics. Point 1 (green) corresponds to the real parameters of ds DNA classical cholesteric. Point 2 (red) corresponds to the P value that is equal to about 500 nm. CDNA = 30 μg ml−1, ΔA270 × 10−6 optical units, L = 1 cm

Article Snippet: Calf thymus depolymerized ds DNA (Sigma, USA) with a molecular mass of ∼(0.6–0.8) × 10 6 Da after additional purification was used.

Techniques:

Journal: Developmental cell

Article Title: A sex chromosome piRNA promotes robust dosage compensation and sex determination in C. elegans

doi: 10.1016/j.devcel.2018.01.025

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: Samples from wild-type and mutants were pretreated with a homemade 5’ Polyphosphatase or RNA 5-Polyphosphatase (Lucigen) and were ligated to the miRNA cloning linker 1 (5' rAppCTGTAGGCACCATCAAT/3ddC/ 3', IDT).

Techniques: Virus, Bacteria, Recombinant, Isolation, SYBR Green Assay, RNA Sequencing, Cloning, Knockdown, Software