Structures of Large RNA Molecules and Their Complexes, by Sarah A Woodson, Frédéric H.T. Allain

By Sarah A Woodson, Frédéric H.T. Allain

This new quantity of Methods in Enzymology keeps the legacy of this most excellent serial with caliber chapters authored through leaders within the box. This quantity covers learn equipment in RNA folding and dynamics, RNA-protein interactions and massive RNPs.

  • Continues the legacy of this most popular serial with caliber chapters on buildings of huge RNA molecules and their complexes

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Extra resources for Structures of Large RNA Molecules and Their Complexes,

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4% Figure 2 HIV-1 TAR exists in dynamic equilibrium with two excited states (ES1 and ES2). Shown are the ES secondary structure, population (pES), lifetime (τ), as well as the forward (k1/k2) and reverse ðkÀ1 =kÀ2 Þ rate constants. The GS is labeled to show sites with slow (red, light gray in the print version), fast (green, gray in the print version), and no chemical exchange (black) measured by R1ρ relaxation dispersion. Note that A35 shows a combination of fast (C10 ) and slow (C8) exchange.

1. 8 μl Master mix (Table 11) 4 μl Labeled primer 2 μM 2. Place each PCR tube, corresponding to each sequencing ladder, into a thermocycler and run a sequencing-ladder PCR program (Table 13). 3. 4 μl of stop mixture (Table 14). 4. At this point, mix both sequencing ladders if using two for the analysis. Add 196 μl of 100% ethanol and incubate at 4 °C for 5 min. 8 μl. 5 Add deionized H2O to 1 ml. Table 13 Sequencing-ladder PCR program Number of cycles Temperature (°C) Time 1 96 1 min 25 96 55 72 20 s 20 s 1 min 1 72 5 min 25 LncRNA Native Purification, Probing, and Folding 5.

In particular, experiments are used to measure the chemical exchange contribution to line-broadening (Rex) during a relaxation period (Trelax) during which the sample is subjected to RF irradiation. Various types of RD experiments differ in the initial state of the magnetization and the type of RF irradiation that is used. , aligned along the Y-axis) and the RF irradiation consists of a series of equally spaced high-power 180° refocusing pulses. In the case of the spin relaxation in the rotating frame experiment, or R1ρ (Akke & Palmer, 1996; Deverell, Morgan, & Strange, 1970; Korzhnev, Skrynnikov, Millet, Torchia, & Kay, 2002; Mulder, de Graaf, Kaptein, & Boelens, 1998), the initial magnetization is typically aligned along an effective field direction (which is defined by both the RF irradiation power and offset) and the irradiation consists of a weaker, but continuous RF with a specified power level (ωSL) and frequency offset (Ω) (Fig.

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