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Novel conformation of an RNA structural switch - PubMed

  • ️Sun Jan 01 2012

. 2012 Nov 20;51(46):9257-9.

doi: 10.1021/bi301372t. Epub 2012 Nov 12.

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Free PMC article

Novel conformation of an RNA structural switch

Scott D Kennedy et al. Biochemistry. 2012.

Free PMC article

Abstract

The RNA duplex, (5'GACGAGUGUCA)(2), has two conformations in equilibrium. The nuclear magnetic resonance solution structure reveals that the major conformation of the loop, 5'GAGU/3'UGAG, is novel and contains two unusual Watson-Crick/Hoogsteen GG pairs with G residues in the syn conformation, two A residues stacked on each other in the center of the helix with inverted sugars, and two bulged-out U residues. The structure provides a benchmark for testing approaches for predicting local RNA structure and a sequence that allows the design of a unique arrangement of functional groups and/or a conformational switch into nucleic acids.

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Figures

Figure 1
Figure 1

Imino proton spectra for RNA duplexes with the 5′GAGU/3′UGAG internal loop. Secondary structures of the major conformations are shown at the right. Peaks labeled with X are from the minor duplex conformation. The peak at 14.3 ppm in trace a is from a minor hairpin species. (a and b) Self-complementary sequences. (c and d) Non-self-complementary sequences. Black peaks and nucleotides are from the duplex half that is equivalent to the self-complementary duplex, and green peaks and nucleotides are from the duplex half that has a different sequence. (a and c) Natural nucleotides. (b and d) Duplexes with 8-Br-G6. Sample conditions: 80 mM NaCl, 0.05 mM EDTA, 20 mM sodium phosphate, pH 6, 1 °C.

Figure 2
Figure 2

Watergate–NOESY spectrum of 5′GAC

GA

Br

GU

GAGA/3′ACUG

U

Br

GAG

CUC. Residues labeled with an asterisk are in the second strand. The regions displayed include cross-peaks for A5 and A5* aromatic protons. Two large cross-peaks labeled with blue filled circles are G4 H8–G4 H1′ and G4* H8–G4* H1′ cross-peaks and indicate that G4 and G4* are in the glycosidic syn conformation. Data were acquired at −2 °C with a 200 ms mixing time, except the diagonal panel, which was acquired at 1 °C with a 400 ms mixing time.

Figure 3
Figure 3

Major conformation of the 5′

GAGU

3′/3′

UGAG

5′ RNA internal loop. The secondary structure is shown at the top with residues colored as in the 3D model: (a) front view and (b) 90° rotation. (c) Potential stabilizing hydrogen bonds from A5 amino protons to 2′-oxygens of cross-strand G4* and A5*.

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