Directing Uphill Strand Displacement with an Engineered Superhelicase

The ability to finely tune reaction rates and binding energies between components has made DNA strand displacement circuits promising candidates to replicate the complex regulatory functions of biological reaction networks. However, these circuits often lack crucial properties, such as signal turnover and the ability to transiently respond to successive input signals that require the continuous input of chemical energy. Here, we introduce a method for providing such energy to strand displacement networks in a controlled fashion: an engineered DNA helicase, Rep-X, that transiently dehybridizes specific DNA complexes, enabling the strands in the complex to participate in downstream hybridization or strand displacement reactions. We demonstrate how this process can direct the formation of specific metastable structures by design and that this dehybridization process can be controlled by DNA strand displacement reactions that effectively protect and deprotect a double-stranded complex from unwinding by Rep-X. These findings can guide the design of active DNA strand displacement regulatory networks, in which sustained dynamical behavior is fueled by helicase-regulated unwinding.

Achieving single nucleotide sensitivity in direct hybridization genome imaging

Direct visualization of point mutations in situ can be informative for studying genetic diseases and nuclear biology. We describe a direct hybridization genome imaging method with single-nucleotide sensitivity, single guide genome oligopaint via local denaturation fluorescence in situ hybridization (sgGOLDFISH), which leverages the high cleavage specificity of eSpCas9(1.1) variant combined with a rationally designed guide RNA to load a superhelicase and reveal probe binding sites through local denaturation. The guide RNA carries an intentionally introduced mismatch so that while wild-type target DNA sequence can be efficiently cleaved, a mutant sequence with an additional mismatch (e.g., caused by a point mutation) cannot be cleaved. Because sgGOLDFISH relies on genomic DNA being cleaved by Cas9 to reveal probe binding sites, the probes will only label the wild-type sequence but not the mutant sequence. Therefore, sgGOLDFISH has the sensitivity to differentiate the wild-type and mutant sequences differing by only a single base pair. Using sgGOLDFISH, we identify base-editor-modified and unmodified progeroid fibroblasts from a heterogeneous population, validate the identification through progerin immunofluorescence, and demonstrate accurate sub-nuclear localization of point mutations.

Catalytic DNA Polymerization Can Be Expedited by Active Product Release**

The sequence‐specific hybridization of DNA facilitates its use as a building block for designer nanoscale structures and reaction networks that perform computations. However, the strong binding energy of Watson–Crick base pairing that underlies this specificity also causes the DNA dehybridization rate to depend sensitively on sequence length and temperature. This strong dependency imposes stringent constraints on the design of multi‐step DNA reactions. Here we show how an ATP‐dependent helicase, Rep‐X, can drive specific dehybridization reactions at rates independent of sequence length, removing the constraints of equilibrium on DNA hybridization and dehybridization. To illustrate how this new capacity can speed up designed DNA reaction networks, we show that Rep‐X extends the range of conditions where the primer exchange reaction, which catalytically adds a domain provided by a hairpin template to a DNA substrate, proceeds rapidly.

Genome oligopaint via local denaturation fluorescence in situ hybridization

Cas9 in complex with a programmable guide RNA targets specific double-stranded DNA for cleavage. By harnessing Cas9 as a programmable loader of superhelicase to genomic DNA, we report a physiological-temperature DNA fluorescence in situ hybridization (FISH) method termed genome oligopaint via local denaturation (GOLD) FISH. Instead of global denaturation as in conventional DNA FISH, loading a superhelicase at a Cas9-generated nick allows for local DNA denaturation, reducing nonspecific binding of probes and avoiding harsh treatments such as heat denaturation. GOLD FISH relies on Cas9 cleaving target DNA sequences and avoids the high nuclear background associated with other genome labeling methods that rely on Cas9 binding. The excellent signal brightness and specificity enable us to image nonrepetitive genomic DNA loci and analyze the conformational differences between active and inactive X chromosomes. Finally, GOLD FISH could be used for rapid identification of HER2 gene amplification in patient tissue.

Papillary glioneuronal tumor: unexplored entity

Papillary glioneuronal tumors represent a new and rare entity of an uncommon morphologic subtype of low-grade mixed neuronal-glial neoplasms with an unclear etiology. They are described as benign lesions with extraventricular localization. We report the second case of papillary glioneuronal tumor with recurrent nature after gross-total resection, and the third case of this tumor with intraventricular localization. While conventional magnetic resonance imaging of papillary glioneuronal tumors is well described in literature, there are no data based on advanced magnetic resonance techniques. The present article represents a review of clinicopathological and both conventional and advanced magnetic resonance imaging characteristics of papillary glioneuronal tumors, with focus on 2 cases with atypical course and localization.

[The surgical treatment of cervical lymph node metastases in differentiated thyroid carcinoma]

Over the period 1980 through 1994, a total of 297 patients presenting histological evidence of differentiated carcinoma of the thyroid gland are studied. In thirty-two of them (10.8 per cent) palpable metastases in the lymph nodes are found at the time of making the diagnosis. A higher frequency of palpable lymph nodes is established in younger patients with histological diagnosis papillary carcinoma (62.5 per cent). In the 32 patients with palpable metastases in the lymph nodes, discovered during diagnosing of the disease, lymph node dissection is undertaken. The obtained results show that the modified cervical dissection yields favourable results, and at the same time preserves intact the neck structure.

[The correlation between serum thyroglobulin and iodine-131 scanning in detecting metastases in patients with a differentiated thyroid carcinoma]

One-hundred seventy-one patients, operated for differentiated thyroid gland carcinoma, are subjected to serum thyroglobulin assessment and whole-body scanning. In twenty-nine of the total of 171 patients there is evidence of relapses and metastases, discovered by either examination. In 27/29 cases with metastases (positive scan finding) a high serum thyroglobulin level is documented. The correlation between serum thyroglobulin level and whole-body scanning finding among patients without residual normal thyroid parenchyma (status post total thyroidectomy) is much more favourable than the one in patients presenting normal residual parenchyma (status post organ-salvaging operation). The conclusion is drawn that serum thyroglobulin contributes greatly to the diagnosis of recurrences and metastases, especially in patients with normal residual parenchyma missing.

[Histological variants (subtypes) of differentiated thyroid carcinoma]

This is a report on retrospective clinical and pathoanatomical study of seventy-one patients presenting histological diagnosis differentiated carcinoma of the thyroid gland, undertaken with the purpose to identify the histological variants (subtypes) of differentiated thyroid carcinoma. As shown by the obtained results, the follicular variant is the commonest subtype of papillary carcinoma (41.18 per cent) followed by focal papillary carcinoma (25.49 per cent), and encapsulated variant (15.69 per cent). On the other hand, the most frequently met with follicular carcinoma subtype proves to be the least invasive variant (55 per cent).

[The results after an organ-preserving operation and total thyroidectomy in differentiated thyroid carcinoma]

A total of 196 patients with differentiated thyroid gland carcinoma are operated over the period 1980 through 1994, and followed up over periods ranging from 1 to 14 years after the operation. Surgical treatment consists in total thyroidectomy in 39.8 per cent of the cases, and organ salvaging operation--in 60.2 per cent. In 124 instances the histological diagnosis is papillary carcinoma, and in 72--follicular carcinoma. Local relapses and lethality are higher in patients with total thyroidectomy--6.4 per cent local recurrences and 3.8 per cent lethality, whereas in the group of organ-salvaging operations--1.6 and 0.9 per cent, respectively. Analysis of the operative interventions according to risk group, stage of disease and histopathological findings shows that there is no significant difference in lethality, but there is a higher rate of relapses among patients treated with total thyroidectomy.