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Differential strand separation at critical temperature: a minimally disruptive enrichment method for low-abundance unknown DNA mutations.

ABSTRACT: Detection of low-level DNA variations in the presence of wild-type DNA is important in several fields of medicine, including cancer, prenatal diagnosis and infectious diseases. PCR-based methods to enrich mutations during amplification have limited multiplexing capability, are mostly restricted to known mutations and are prone to polymerase or mis-priming errors. Here, we present Differential Strand Separation at Critical Temperature (DISSECT), a method that enriches unknown mutations of targeted DNA sequences purely based on thermal denaturation of DNA heteroduplexes without the need for enzymatic reactions. Target DNA is pre-amplified in a multiplex reaction and hybridized onto complementary probes immobilized on magnetic beads that correspond to wild-type DNA sequences. Presence of any mutation on the target DNA forms heteroduplexes that are subsequently denatured from the beads at a critical temperature and selectively separated from wild-type DNA. We demonstrate multiplexed enrichment by 100- to 400-fold for KRAS and TP53 mutations at multiple positions of the targeted sequence using two to four successive cycles of DISSECT. Cancer and plasma-circulating DNA samples containing traces of mutations undergo mutation enrichment allowing detection via Sanger sequencing or high-resolution melting. The simplicity, scalability and reliability of DISSECT make it a powerful method for mutation enrichment that integrates well with existing downstream detection methods.

SUBMITTER: Guha M

PROVIDER: S-EPMC3561944 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:ImportanceDespite common goals of frontal sinus fracture treatment (restoring forehead contour and creating a safe sinus), there remains significant variability in evaluation and treatment.ObjectiveTo describe our experience with a minimally disruptive treatment protocol for the treatment of frontal sinus fractures.Design, setting, and participantsAnalysis of prospectively collected data from 2010 through 2015 at a level 1 trauma center. All patients with frontal sinus fractures treated with our protocol from January 2010 to December 2015. Patients with poor follow-up and/or incomplete medical records were excluded from analysis.Main outcomes and measuresPresence of an aerated frontal sinus and aesthetically acceptable forehead contour. Secondary outcome measures were complications related to frontal sinus fractures.ResultsA total of 39 patients were treated under our minimally disruptive protocol, and 25 patients were included in the study; 18 (72%) were male and 7 (28%) were female. Their ages ranged from 6 to 62 years. After review, 22 patients had both clinical and radiographic follow-up. No patients underwent immediate frontal sinus repair. Five of 22 patients underwent surgery for indications other than their frontal sinus fracture: 1 of 5 patients underwent immediate surgical repair due to bilateral LeFort fractures, and 4 of 5 underwent delayed surgery due to nasal polyps (1 patient), scar revision (1 patient), and concomitant LeFort fractures (2 patients). Two of 22 patients (9%) underwent frontal sinus repair after outpatient surveillance due to persistent cerebrospinal fluid leak (1 patient) and orbital roof fracture (1 patient). The remaining 20 patients were treated nonoperatively, and 19 of 20 (95%) had spontaneous improvement in opacification and/or contour deformity. Twelve of 20 patients (60%) had improvement or resolution in both. One patient had ongoing partial opacification and deformity at the 3-month follow-up but was asymptomatic and had bony contour that was aesthetically acceptable to the patient. There were no complications. The median of all follow-up was 3 months.Conclusions and relevanceFrontal sinus fractures treated nonoperatively had a high rate of spontaneous ventilation and bony autoreduction with aesthetically acceptable frontal bone remodeling. There were no complications in the nonoperative group. The initial results of this study support further study of the safety and efficacy of a minimally disruptive protocol for frontal sinus fractures.Level of evidence4.

Project description:The DEAD-box proteins CYT-19 in Neurospora crassa and Mss116p in Saccharomyces cerevisiae are broadly acting RNA chaperones that function in mitochondria to stimulate group I and group II intron splicing and to activate mRNA translation. Previous studies showed that the S. cerevisiae cytosolic/nuclear DEAD-box protein Ded1p could stimulate group II intron splicing in vitro. Here, we show that Ded1p complements mitochondrial translation and group I and group II intron splicing defects in mss116Delta strains, stimulates the in vitro splicing of group I and group II introns, and functions indistinguishably from CYT-19 to resolve different nonnative secondary and/or tertiary structures in the Tetrahymena thermophila large subunit rRNA-DeltaP5abc group I intron. The Escherichia coli DEAD-box protein SrmB also stimulates group I and group II intron splicing in vitro, while the E. coli DEAD-box protein DbpA and the vaccinia virus DExH-box protein NPH-II gave little, if any, group I or group II intron splicing stimulation in vitro or in vivo. The four DEAD-box proteins that stimulate group I and group II intron splicing unwind RNA duplexes by local strand separation and have little or no specificity, as judged by RNA-binding assays and stimulation of their ATPase activity by diverse RNAs. In contrast, DbpA binds group I and group II intron RNAs nonspecifically, but its ATPase activity is activated specifically by a helical segment of E. coli 23S rRNA, and NPH-II unwinds RNAs by directional translocation. The ability of DEAD-box proteins to stimulate group I and group II intron splicing correlates primarily with their RNA-unwinding activity, which, for the protein preparations used here, was greatest for Mss116p, followed by Ded1p, CYT-19, and SrmB. Furthermore, this correlation holds for all group I and group II intron RNAs tested, implying a fundamentally similar mechanism for both types of introns. Our results support the hypothesis that DEAD-box proteins have an inherent ability to function as RNA chaperones by virtue of their distinctive RNA-unwinding mechanism, which enables refolding of localized RNA regions or structures without globally disrupting RNA structure.

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Differential strand separation at critical temperature: a minimally disruptive enrichment method for low-abundance unknown DNA mutations.

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