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Surprising Sequence Effects on GU Closure of Symmetric 2 × 2 Nucleotide RNA Internal Loops.

ABSTRACT: GU base pairs are important RNA structural motifs and often close loops. Accurate prediction of RNA structures relies upon understanding the interactions determining structure. The thermodynamics of some 2 × 2 nucleotide internal loops closed by GU pairs are not well understood. Here, several self-complementary oligonucleotide sequences expected to form duplexes with 2 × 2 nucleotide internal loops closed by GU pairs were investigated. Surprisingly, nuclear magnetic resonance revealed that many of the sequences exist in equilibrium between hairpin and duplex conformations. This equilibrium is not observed with loops closed by Watson-Crick pairs. To measure the thermodynamics of some 2 × 2 nucleotide internal loops closed by GU pairs, non-self-complementary sequences that preclude formation of hairpins were designed. The measured thermodynamics indicate that some internal loops closed by GU pairs are unusually unstable. This instability accounts for the observed equilibria between duplex and hairpin conformations. Moreover, it suggests that future three-dimensional structures of loops closed by GU pairs may reveal interactions that unexpectedly destabilize folding.

SUBMITTER: Berger KD

PROVIDER: S-EPMC5963885 | biostudies-literature | 2018 Apr

REPOSITORIES: biostudies-literature

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Surprising Sequence Effects on GU Closure of Symmetric 2 × 2 Nucleotide RNA Internal Loops.

Berger Kyle D KD Kennedy Scott D SD Schroeder Susan J SJ Znosko Brent M BM Sun Hongying H Mathews David H DH Turner Douglas H DH

Biochemistry 20180323 14

GU base pairs are important RNA structural motifs and often close loops. Accurate prediction of RNA structures relies upon understanding the interactions determining structure. The thermodynamics of some 2 × 2 nucleotide internal loops closed by GU pairs are not well understood. Here, several self-complementary oligonucleotide sequences expected to form duplexes with 2 × 2 nucleotide internal loops closed by GU pairs were investigated. Surprisingly, nuclear magnetic resonance revealed that many ...[more]

PMID: 29570276

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Project description:BackgroundSeroma remains a leading postsurgical complication in plastic surgery. Conventional drains are ineffective in clearing blood and fluid and closing down surgical spaces. The Interi (Internal Closure System, IC Surgical, Grand Rapids, MI) is comprised of a novel branching internal manifold attached to a self-contained portable pump with a higher, consistent, continuous negative pressure, may reduce this long-standing issue. In addition, high-resolution ultrasound (HRUS) has emerged as an ideal tool to visualize structures, fluid collections, and seromas internally.ObjectivesThis study evaluates Interi in full abdominoplasty patients utilizing HRUS to evaluate Interi's ability to evacuate blood and fluid, hold internal tissues together and document, for the first time, what internal tissue healing actually looks like radiographically.MethodsAn IRB approved, Contract Research Organization reviewed retrospective study evaluated consecutive patients undergoing full abdominoplasty utilizing Interi from July 2020 through March 2021 by three plastic surgeons. HRUS visualized and confirmed the presence or absence of fluid collections and healing tissue planes during the postoperative process. Study data and all adverse events were recorded, with HRUS images reviewed by investigators and confirmed by an independent radiologist.ResultsSeventy-one Interi patients were enrolled. Mean age was 43 (range: 21-74) and BMI was 28. Seroma was confirmed clinically and through HRUS in 3/71 patients, and was associated with either clot (2) or failure to activate system (1). Interi's ability to eliminate fluid and approximate/hold surgical tissue planes together was confirmed with HRUS. No other major complications, including abscess, hematomas, or flap necrosis were observed.ConclusionsThis novel Internal Tissue Closure System effectively evacuated blood and fluid, approximated and maintained closure of internal tissue planes in abdominoplasty patients, allowing for primary tissue healing and internal wound closure to occur. Healing tissue planes and any fluid present are easily identified on HRUS visualizing actual internal tissue healing with a simple, widely available radiographic scan.Level of evidence 3

Dataset Information

Surprising Sequence Effects on GU Closure of Symmetric 2 × 2 Nucleotide RNA Internal Loops.

Publications

Surprising Sequence Effects on GU Closure of Symmetric 2 × 2 Nucleotide RNA Internal Loops.

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