Search

Autophagy is a highly conserved catabolic process to maintain cellular homeostasis. However, dysfunctional autophagy contributes to a context-dependent role in cancer. Here, we clarified the exact role of autophagy modulated by the scavenger receptor lectin-like oxidized low-density lipoprotein receptor-1 (LOX-1) in esophageal cancer (EC). A comprehensive analysis in various cancers displayed that LOX-1 was upregulated the most in EC tissues and associated with poor prognosis of patients. Deletion of LOX-1 ex vivo and in vivo suppresses EC development by inducing autophagic cell death. Receptor for activated C kinase 1 (RACK1) was identified as a signal adapter of LOX-1, which incented RAS/MEK/ERK pathway and TFEB nuclear export signal and safeguarded tumorigenesis. A sulfated polysaccharide fucoidan extracted from brown seaweed was found to bind with LOX-1 and mediate its proteasomal degradation but not the lysosome pathway, leading to autophagy-related cell death in EC. These results reveal a central contribution of LOX-1 to EC development and provide genetic ablation or bioactive polysaccharide as an effective intervention for EC therapy.

Background To compare the diagnostic value of prostate cancer (PCa) between holmium laser enucleation of the prostate (HoLEP) and transurethral resection of the prostate (TURP). Methods We retrospectively analyzed the clinical data of 2909 patients who underwent surgery for benign prostatic hyperplasia (BPH) from January 2008 to June 2018. A total of 1362 patients received HoLEP, and 1547 patients received TURP. The baseline patient characteristics were collected. We then compared the perioperative outcomes of these patients who diagnosed with incidentally diagnosed prostatic carcinoma (IDPC) or PCa after BPH surgeries. Results The total detection rate of PCa in HoLEP group was higher than that in TURP group (85/6.24% vs. 61/3.94%, p = 0.005). Specifically, 55(4.6%) patients were diagnosed with IDPC in HoLEP group with prostate-specific antigen (PSA) less than 4 ng/ml, and 37(2.7%) patients in TURP group (p = 0.014). For the patients with PSA between 4 and 10 ng/ml, 15(13.9%) patients were diagnosed with PCa after HoLEP, and 6(5.0%) patients after TURP (p = 0.023). But the detection rate of PCa was not significantly different between the two groups when PSA was over 10 ng/ml. On the other hand, 57 in 1215 patients with no prostate biopsy preoperatively were diagnosed with PCa after HoLEP, while 42 in 1370 patients after TURP (4.7% vs. 3.1%, p = 0.040), respectively. Twenty-six patients received once biopsy and diagnosed with PCa in HoLEP group, while 15 patients in TURP group (18.4% vs. 8.9%, p = 0.018), respectively. However, no significant difference was observed for patients who received twice prostate biopsy in the two groups. Conclusions The present study showed that HoLEP can provide a higher total detection rate of PCa when compared with TURP. Besides, this superiority was especially embodied in patients with PSA less than 10 ng/ml.

As the first-generation targeted therapy, sorafenib remains an effective single-drug treatment for advanced hepatocellular carcinoma (HCC). Unfortunately, the existence of resistance restricts the long-term benefit of patients. UDP-glucose 6-dehydrogenase (UGDH) is the key enzyme of glucuronic acid metabolism which was largely reported in mediating drug systemic elimination. In this study, we explore its critical role in regulating sorafenib sensitivity. Here we find sorafenib exposure could activate glucuronic acid metabolism, accompanied with the elevated expression of UGDH. Interference with the route by silencing UGDH could boost HCC cells sensitivity to sorafenib. Meanwhile, the analysis of HCC patients with sorafenib treatment displayed that low UGDH expression predicted superior prognosis. Further screening assay suggested that unfolded protein response (UPR) involves in UGDH silencing-mediated apoptosis. Xenograft model confirmed that combined UGDH intervention could significantly improve sorafenib efficacy. Our results reveal the impact of sorafenib exposure on glucuronic acid metabolism reprogramming and provide UGDH as a promising target to improve sorafenib efficacy.

The transoral endoscopic thyroidectomy vestibular approach (TOETVA) is receiving increased attention, frequently due to growing requirements for cosmetic incisions. Here, we report our initial experience and discuss the safety and efficacy of the innovative surgical working space suspension system for gasless TOETVA.We retrospectively analyzed 75 consecutive patients for whom gasless TOETVA with our novel working space suspension system was used. This suspension system included self-developed retractors, a sterile bandage, and an anesthesia stand. We also improved some main surgical instruments in gasless TOETVA.The study included 75 patients who successfully underwent thyroidectomy and central neck dissection via gasless TOETVA. The mean operating time was 143.27 ± 34.60 min. The mean number of retrieved lymph nodes was 8.00 ± 5.39. Conversion to open surgery did not occur, nor did patients exhibit serious postoperative complications. Postoperative complications included 4 cases of transient recurrent laryngeal nerve (RLN) palsy, 9 of transient hypoparathyroidism, and 3 of transient mental nerve injury. One patient with subcutaneous fluid after surgery recovered after aspiration. Another patient with submental minor perforation recovered well after suturing. There was no evidence of specific complications related to self-designed retractors.The innovative working space suspension system for gasless TOETVA provided enough and stable working space and optimized the clarity of the surgical field without CO

Objective: To compare the clinical efficacy and safety between diode laser (980 nm) enucleation of the prostate (DiLEP) and holmium laser enucleation of the prostate (HoLEP) for treating b...

Nephrolithiasis is a very common disease in which cell-crystal adhesion is an essential mechanism for kidney stone formation. This study has explored the anti-adhesion function of the microRNA, miR-34a, by targeting CD44, a cell surface receptor, in human renal epithelial (HK-2) cells. The expression of CD44 was monitored by qPCR and western blot. A luciferase assay validated the target of miR-34a in CD44 3' UTR. Immunofluorescence staining under confocal microscopy was used to detect the cell-crystal adhesion effects in vitro. Pizzolato staining was performed to examine the adhesion role of miR-34a in vivo. In HK-2 cells, miR-34a was down-regulated and CD44 was up-regulated when exposed to calcium oxalate monohydrate crystals. Moreover, miR-34a negatively regulated the expression of CD44. According to the luciferase report assay, miR-34a direct targeted a binding site in the CD44 3'UTR. In vitro experiments, miR-34a overexpression inhibited CD44 expression and cell-crystals adhesion; whereas CD44 overexpression showed reversed results. Furthermore, miR-34a suppressed cell-crystals adhesion and stone formation in vivo. These findings indicate that miR-34a targets CD44 in HK-2 cells and inhibits cell-crystal adhesion both in vitro and in vivo. Based on these results, miR-34a may be a potential therapeutic target for renal stone disease.

Some surgeons believe that dissection posterior to the right recurrent laryngeal nerve lymph node (PRRLN-LN) is unnecessary for the low metastasis rate and high complication risk. However, persistent metastatic lymph nodes may have a higher recurrence rate, surgical risk, and complications. Thus, it is important to distinguish patients who require PRRLN-LN dissection. To identify the risk factors for lymph nodes posterior to the right recurrent laryngeal nerve metastasis (LN-prRLN) and establish a scoring system to help determine whether PRRLN-LN dissection is required in patients with papillary thyroid carcinoma.821 participants were randomly allocated to the development and validation cohorts in a 2:1 ratio. A nomogram-based predictive model for LN-prRLN was established based on the risk factors identified in the development cohort.LN-prRLN was diagnosed pathologically in 124 of 821 patients (15.1%) from the entire cohort. Multivariate analysis identified age (odds ratio [OR], 0.964; 95% CI, 0.945-0.983; P.001), tumor size (OR, 1.536; 95% CI, 1.135-2.079; P = .005), extrathyroidal extension (OR 2.271, 95% CI, 1.368-3.770; P = .002), clinically involved right central compartment lymph node metastasis (OR 1.643, 95% CI, 1.055-2.559; P = .028), and right lateral lymph node metastasis (OR 4.271, 95% CI, 2.325-7.844; P.001) as the predictors of LN-prRLN. A risk model was established and well validated. Calibration curves to evaluate the nomogram in both the development and validation cohorts revealed a concordance index of 0.756 ± 0.058 and 0.745 ± 0.042, respectively.Our scoring system may be useful for helping the surgeons decide which patients should undergo the dissection of PRRLN-LN.

Papillary thyroid cancer (PTC) has a continuously increasing incidence and imposes a heavy medical burden to individuals and society due to its high proportion of lymph node metastasis and recurrence in recent years. Circular RNAs, a class of noncoding RNAs, participate in the progression of many cancers, but the role of circRNAs in PTC is still rarely reported. In this study, circRNA deep sequencing was performed to identify differentially expressed circRNAs in PTC. CircRUNX1 was selected for its high expression in PTC, and circRUNX1 silencing was directly associated with the week potential for migration, invasion and proliferation of PTC in vivo and in vitro. Fluorescence in situ hybridization (FISH) was further used to confirm the cytoplasmic localization of circRUNX1, indicating the possible function of circRUNX1 as a ceRNAs in PTC progression through miRNA binding. MiR-296-3p was then confirmed to be regulated by circRUNX1 and to target DDHD domain containing 2 (DDHD2) by luciferase reporter assays. The strong antitumor effect of miR-296-3p and the tumor-promoting effect of DDHD2 were further investigated in PTC, indicating that circRUNX1 modulates PTC progression through the miR-296-3p/DDHD2 pathway. Overall, circRUNX1 plays an oncogenic role in PTC and provides a potentially effective therapeutic strategy for PTC progression.

N6-methyladenosine (m6A) is the most prevalent modification of RNA in mammals. m6A RNA methylation levels are dynamically regulated by m6A RNA methylation regulators. While increasing evidence has suggested that m6A RNA methylation is vital in the initiation and progression of human carcinoma, little is known about the expression and effect of m6A RNA methylation regulators in differentiated thyroid carcinoma (DTC). Herein, we demonstrate that most of the thirteen main m6A RNA methylation regulators are differentially expressed in DTC tissues and normal thyroid tissues. Based on consensus clustering of m6A RNA methylation regulators, DTC cases were divided into two subgroups (TC1 and TC2). Compared with the TC1 subgroup, the TC2 subgroup was associated with a poorer prognosis, older age, higher T grade, higher N grade and higher TNM stage. The results indicated that alteration of m6A RNA methylation regulators was closely related to DTC. We further established a risk signature of four m6A RNA methylation regulators that could evaluate prognosis and clinicopathological features in DTC. Finally, the results of the TCGA analysis were verified by other cohorts from Gene Expression Omnibus (GEO) database. In conclusion, m6A RNA methylation regulators play a crucial part in the progression of DTC and are potentially useful for evaluating the prognosis and providing potential novel insights into treatment strategies.

Genetic alterations are vital in the progression of thyroid carcinoma. Ryanodine receptor 2 (RyR2) is reported to serve an important role in several types of human carcinoma. However, the expression and effect of RyR2 in thyroid carcinoma remain unknown. Therefore, the present study analyzed the status of RyR2 in thyroid carcinoma using bioinformatics tools. The mRNA profiles of thyroid carcinoma were downloaded from The Cancer Genome Atlas. RyR2 was distinguished as a differentially expressed gene that has not been reported in thyroid carcinoma. Further analysis indicated that there was selective downregulation of RyR2 expression in thyroid carcinoma tissues compared with that in normal thyroid tissues. Survival analysis showed that RyR2 expression was associated with poorer disease-free survival (DFS) for all patients with thyroid carcinoma. Univariate analysis revealed that a low expression of RyR2 was significantly associated with lymphatic metastasis, extracapsular extension, and the Tumor-Node-Metastasis stage. Cox analysis demonstrated that RyR2 was an independent prognostic factor in thyroid carcinoma for DFS. The biological processes and signaling pathways of RyR2 were reviewed with Gene Set Enrichment Analysis. In conclusion, the present study has revealed that RyR2 is downregulated in thyroid carcinoma, and that low expression of RyR2 is associated with poor prognosis in patients with thyroid carcinoma. RyR2 may therefore serve as a promising tumor suppressor gene in thyroid carcinoma.

To explore the efficacy and safety of flexible ureteroscopic incision and drainage and flexible ureteroscopic lithotripsy for treatment of parapelvic renal cyst combined with secondary renal stone.28 patients with parapelvic renal cyst combined with renal stone were treated with flexible ureteroscopic incision and drainage and flexible ureteroscopic lithotripsy simultaneously from May 2010 to December 2016. The follow-up was made 1, 3, 6?12 months and 2 years after surgical treatment in our outpatient department. Ultrasonic examination and CT were used to detect the residual stone and recurrence of renal cyst.The mean age of the patients was 45.3 ± 18.6 years. The average size of the parapelvic renal cysts was 4.3 ± 1.6 cm, including 27 with Bosniak category I and 1 patient with Bosniak II renal cysts. The mean size of the renal stones was 14.3 ± 3.9 mm. The mean operative time was 53.4 ± 20.7 minutes and the mean blood loss was 10.8 ± 5.6 ml. The mean hospitalization time was 3.2 ± 0.7 days. No severe complications were encountered. The complications included transient fever (38°C) in 3 patients and significant hemorrhage in 1 patient. The stone-free rates one month and three months after operation were 89.3% and 96.4%, respectively. During the 2 years follow-up, the cyst recurrence rate was 14.3% and the stone recurrence rate was 7.1%.In this study, we firstly demonstrated that it is safe and effective to treat both renal stone and parapelvic renal cyst simultaneously by flexible ureteroscopic lithotripsy and flexible ureteroscopic incision and drainage, with satisfactory stone free rate and low cyst recurrence rate.

BACKGROUND: Transurethral resection of the prostate (TURP) was considered the golden standard to treat benign prostatic hyperplasia (BPH) for decades. However, TURP was associated with low efficiency to alleviate the lower urinary tract symptoms (LUTS) and a significantly higher risk of bladder neck contracture (BNC) for patients with small-volume BPH. Our study aims to compare the therapeutic effect of a transurethral split of the prostate (TUSP) with TURP for patients with small-volume BPH (

The ETS family of transcription factors exemplifies current uncertainty in how eukaryotic genetic regulators with overlapping DNA sequence preferences achieve target site specificity. PU.1 and Ets-1 represent archetypes for studying site discrimination by ETS proteins because their DNA-binding domains are the most divergent in sequence, yet they share remarkably superimposable DNA-bound structures. To gain insight into the contrasting thermodynamics and kinetics of DNA recognition by these two proteins, we investigated the structure and dynamics of site discrimination by their DNA-binding domains. Electrophoretic mobilities of complexes formed by the two homologs with circularly permuted binding sites showed significant dynamic differences only for DNA complexes of PU.1. Free solution measurements by dynamic light scattering showed PU.1 to be more dynamic than Ets-1; moreover, dynamic changes are strongly coupled to site discrimination by PU.1, but not Ets-1. Interrogation of the protein/DNA interface by DNA footprinting showed similar accessibility to dimethyl sulfate for PU.1/DNA and Ets-1/DNA complexes, indicating that the dynamics of PU.1/DNA complexes reside primarily outside that interface. An information-based analysis of the two homologs' binding motifs suggests a role for dynamic coupling in PU.1's ability to enforce a more stringent sequence preference than Ets-1 and its proximal sequence homologs.

Background The purpose of this study was to identify predictors associated with graft function after parathyroid autotransplantation during thyroid surgery. Methods One hundred fifty patients who underwent thyroid surgery with parathyroid autotransplantation were enrolled prospectively. During surgery, the misresected or devascularized parathyroid gland was autografted in the brachioradialis muscle of the forearm. Parathyroid hormone (PTH) levels in both arms were measured regularly after surgery. Patient age, sex, extent of surgery, and postoperative serum calcium levels were recorded. Results Graft function was documented in 115 patients (76.7%). Univariate analysis revealed that graft function had a significant association with lower serum calcium level 1 day after surgery. The cutoff point was 2.11 mmol/L, which was confirmed by a receiver-operating characteristic (ROC) curve. Conclusion Low serum calcium levels in the early postoperative period may stimulate a functional recovery in an autografted parathyroid gland. Therefore, a moderate calcium supplement strategy was recommended for patients who underwent parathyroid autotransplantation during the early stage after total thyroidectomy.

The safety and oncologic completeness of video-assisted lateral neck dissection (VALND) for papillary thyroid carcinoma (PTC) with lateral neck lymph node metastasis (LNM) have been reported. However, their generalization has remained limited because the advantages and drawbacks are not well demonstrated.A total of 64 patients with PTC and unilateral lateral neck LNM who underwent total thyroidectomy with central compartment neck dissection and lateral neck dissection (LND) were prospectively enrolled. They were randomly assigned to the video-assisted (VA) group (n = 32) or open group (n = 32) and were treated either by VALND or conventional open LND, respectively. We compared operating time, complications, oncologic completeness, postoperative pain, and cosmetic results between the two groups.The complication rate and oncologic completeness, including the results of radioactive iodine scans, mean number of lymph nodes retrieved, and mean postoperative serum thyroglobulin levels, were similar between the groups. Postoperative pain was observed less frequently after surgery in the VA group (P .0001). Cosmetic results evaluated by a verbal response scale and a numeric rating scale were in favor of the VA group (P .0001 and P = .0004, respectively). Total operating time was 176 ± 16 minutes in the VA group and 161 ± 16 minutes in the open group (P = .0003).VALND yielded complication and oncologic completeness rates that were similar to those of open LND. However, VALND resulted in less postoperative pain and better cosmetic results.

PA1 is a large hairpin polyamide (dImPyPy-β-PyPyPy-γ-PyPy-β-PyPyPyPy-β-Ta; Py = pyrrole, Im = imidazole, β = beta alanine) that targets the sequence 5′-WWGWWWWWWW-3′ (W = A or T) and is effective in eliminating HPV16 in cell culture (Edwards, T. G., Koeller, K. J., Slomczynska, U., Fok, K., Helmus, M., Bashkin, J. K., Fisher, C., Antiviral Res . 91 (2011) 177–186). Described here are its DNA binding properties toward a natural DNA, a 523 bp portion of HPV16 (2150–2672) containing three predicted perfect match sites. Strategies for obtaining binding data on large fragments using capillary electrophoresis are also described. Using an Fe EDTA conjugate of PA1, 19 affinity cleavage (AC) patterns were detected for this fragment. In many cases, there are multiple possible binding sequences (perfect, single and double mismatch sites) consistent with the AC data. Quantitative DNase I footprinting analysis indicates that perfect and most single mismatch sites bind PA1 with K d s between 0.7 and 4 nM, indicating excellent tolerance for the latter. Double mismatch sites exhibit K d s between 12 and 62 nM. A large fraction of the accessible sequence is susceptible to PA1 binding, much larger than predicted based on the literature of polyamide-DNA recognition rules.

Rules for polyamide–DNA recognition have proved invaluable for the design of sequence-selective DNA binding agents in cell-free systems. However, these rules are not fully transferrable to predicting activity in cells, tissues or animals, and additional refinements to our understanding of DNA recognition would help biomedical studies. Similar complexities are encountered when using internal β-alanines as polyamide building blocks in place of N-methylpyrrole; β-alanines were introduced in polyamide designs to maintain good hydrogen bonding registry with the target DNA, especially for long polyamides or those with several GC bp (P.B. Dervan, A.R. Urbach, Essays Contemp. Chem. (2001) 327–339). Thus, to clarify important subtleties of molecular recognition, we studied the effects of replacing a single pyrrole with β-alanine in 8-ring polyamides designed against the Ets-1 transcription factor. Replacement of a single internal N-methylpyrrole with β-alanine to generate a β/Im pairing in two 8-ring polyamides causes a decrease in DNA binding affinity by two orders of magnitude and decreases DNA binding selectivity, contrary to expectations based on the literature. Measurements were made by fluorescence spectroscopy, quantitative DNA footprinting and surface plasmon resonance, with these vastly different techniques showing excellent agreement. Furthermore, results were validated for a range of DNA substrates from small hairpins to long dsDNA sequences. Docking studies helped show that β-alanine does not make efficient hydrophobic contacts with the rest of the polyamide or nearby DNA, in contrast to pyrrole. These results help refine design principles and expectations for polyamide–DNA recognition.

Purpose Video-assisted lateral neck dissection (VALND) for papillary thyroid carcinoma (PTC) with lateral neck lymph node metastases (LNM) has been described previously, however, the advantages and drawbacks of VALND have not been demonstrated in previous studies. The aim of this study was to compare the surgical outcomes of video-assisted and open lateral neck dissection for PTC with lateral neck LNM. Materials and methods Between May 2013 and November 2014, 92 consecutive patients with PTC and lateral neck lymph node metastases underwent total thyroidectomy with central compartment neck dissection and unilateral lateral neck dissection. These included 54 individuals who underwent video-assisted surgery, and 38 in whom an open approach was used. The two groups were retrospectively compared with respect to their clinicopathological characteristics, surgical outcomes and oncological completeness. Results The mean follow-up period was 18.6 months. The mean tumor size, tumor stage, mean numbers of retrieved lymph nodes, mean postoperative serum thyroglobulin levels, complication rates, and mean postoperative hospital stay were similar between the two groups. The mean operation time was longer (p = 0.0001) and mean age was lower (p = 0.0354) in the video-assisted group. The cosmetic results, evaluated by numerical scale and verbal response scale, were in favor of the video-assisted group (p = 0.0003 and p Conclusions The safety and oncological completeness of VALND was similar to that of open procedures, but the VALND resulted in improved cosmetic results. VALND is an effective treatment for the selected cases of PTC with lateral neck LNM.

Peptide nucleic acid (PNA) is a synthetic mimic of DNA and RNA that can recognize double-stranded B-DNA through direct Watson-Crick base-pairing. Although promising, PNA recognition is presently limited to mostly purine- and pyrimidine-rich targets, because mixed-sequence PNA, in general, does not have sufficient binding free energy to invade B-DNA. In this Article, we show that conformationally preorganized gamma-peptide nucleic acid (gamma-PNA) containing an acridine moiety covalently linked at the C-terminus can invade mixed-sequence B-DNA in a sequence-specific manner. Recognition occurs through direct Watson-Crick base-pairing. This finding is significant because it demonstrates that the same principles that guide the recognition of single-stranded DNA and RNA can also be applied to double-stranded B-DNA.

Establishing a general and effective method for regulating gene expression in mammalian systems is important for many aspects of biological and biomedical research. Herein we report the antisense activities of a cell-permeable, guanidine-based peptide nucleic acid (PNA) called GPNA. We show that a GPNA oligomer designed to bind to the transcriptional start-site of human E-cadherin gene induces potent and sequence-specific antisense effects and is less toxic to the cells than the corresponding PNA-polyarginine conjugate. GPNA confers its silencing effect by blocking protein translation. The findings reported in this study provide a molecular framework for designing the next generation cell-permeable nucleic acid mimics for regulating gene expression in live cells and intact organisms.

The mapping of DNA footprints and affinity cleavage sites for small DNA ligands is affected by the choice of sequencing chemistry and end label, and the potential for indexing errors can be significant when mapping small ligand–DNA interactions. Described here is a mechanism for avoiding such errors based on a summary of standard labeling, cleavage, and indexing chemistries and a comparison among them for analysis of these interactions by capillary electrophoresis. The length dependence of the difference between Sanger and Maxam–Gilbert indexing is examined for a number of duplexes of mixed sequence.

The synthesis and crystal structure of [Zn(10 − x)Cox(PO4)8(HPO4)2](C3N2H12)4(H2O)3 (x ≈ 3.45) (ZCP-THO), which is the first mixed cobalt and zinc phosphate with zeolite THO topology, are described. ZCP-THO is characterized by means of single-crystal and powder X-ray diffraction. The structure has a 3-D 8-ring channel system with protonated 1,3-propanediamine cations and water molecules occupying the channel junctions. The structure collapsed after the removal of the organic template by heating.

There is a long history for the bioorganic and biomedical use of N-methyl-pyrrole-derived polyamides (PAs) that are higher homologs of natural products such as distamycin A and netropsin. This work has been pursued by many groups, with the Dervan and Sugiyama groups responsible for many breakthroughs. We have studied PAs since about 1999, partly in industry and partly in academia. Early in this program, we reported methods to control cellular uptake of polyamides in cancer cell lines and other cells likely to have multidrug resistance efflux pumps induced. We went on to discover antiviral polyamides active against HPV31, where SAR showed that a minimum binding size of about 10 bp of DNA was necessary for activity. Subsequently we discovered polyamides active against two additional high-risk HPVs, HPV16 and 18, a subset of which showed broad spectrum activity against HPV16, 18 and 31. Aspects of our results presented here are incompatible with reported DNA recognition rules. For example, molecules with the same cognate DNA recognition properties varied from active to inactive against HPVs. We have since pursued the mechanism of action of antiviral polyamides, and polyamides in general, with collaborators at NanoVir, the University of Missouri-St. Louis, and Georgia State University. We describe dramatic consequences of β-alanine positioning even in relatively small, 8-ring polyamides; these results contrast sharply with prior reports. This paper was originally presented by JKB as a Keynote Lecture in the 2nd International Conference on Medicinal Chemistry and Computer Aided Drug Design Conference in Las Vegas, NV, October 2013.

Polyamides (PA) are distamycin-type ligands of DNA that bind the minor groove and are capable of sequence selective recognition. This capability provides a viable route to their development as therapeutics. Presented here is a simple and convenient fluorescence assay for polyamide-DNA binding. PAs are titrated into a sample of a hairpin DNA featuring a TAMRA dye attached to an internal dU near the PA binding site. In a study of 6 polyamides, PA binding leads to a steady, reproducible decrease in fluorescence intensity that can be used to generate binding isotherms. The assay works equally well with both short (6–8 ring) and long (14 ring) polyamides, and Kd values ranging from about 1 nM to at least 140 nM were readily obtained using a simple monochromator or filter configuration. Competition assays provide a means to assessing possible dye interference, which can be negligible. The assay can also be used to determine polyamide extinction coefficients, and to measure binding kinetics, and thus is an accessible and versatile tool for the study of polyamide properties and polyamide-DNA interactions.

A three-dimensional well-ordered network of macroporous CdS has been fabricated by a novel solvothermal synthesis route using SiO2 beads as a template; the CdS particles, which were introduced in the voids of the template and used as crystal seeds for the further growth of CdS from the liquid phase, were found to play a very important role in the formation of the final pore structure.

The synthesis and crystal structure of [Zn(10 − x)Cox(PO4)8(HPO4)2](C3N2H12)4(H2O)3 (x ≈ 3.45) (ZCP-THO), which is the first mixed cobalt and zinc phosphate with zeolite THO topology, are described. ZCP-THO is characterized by means of single-crystal and powder X-ray diffraction. The structure has a 3-D 8-ring channel system with protonated 1,3-propanediamine cations and water molecules occupying the channel junctions. The structure collapsed after the removal of the organic template by heating.

The synthesis and crystal structure of Zn (2-x) Co x (PO 4 ) 2 (NH 3 H 2 CH 2 NH 3 ) (x = 0.61) (ZCP-DFT) is described. ZCP-DFT is characterized by means of single-crystal and powder X-ray diffraction. Crystal data for ZCP-DFT: tetragonal, space group P4 2 bc (No. 106), a = 14.7236(6) A, b = 14.7236(6) A, c = 8.9544(5) A, V = 1941.17(16) A 3 , Z = 8. The structure has 3-D 8-ring channel system with protonated ethylenediamine cations in the channel junctions. The framework structure type is the same as the zeolite DFT topology. The synthesis of ZCP-DFT indicates that cobalt can partially substitute the metal sties of zinc phosphate, which can lead to the modification of physical and chemical properties of the parent compounds.

In this communication, we show that peptide nucleic acids (PNAs) with lengths of 15-20 nucleotides, when preorganized into a right-handed helix, can invade mixed-sequence double-helical B-form DNA (B-DNA). Strand invasion occurs in a highly sequence-specific manner through direct Watson-Crick base pairing. Unlike the previously developed double-duplex invasion strategy, which requires simultaneous binding of two strands of pseudocomplementary PNAs to DNA, only a single strand of gammaPNA is required for invasion in this case, and no nucleobase substitution is needed.

Guanidine-based peptide nucleic acid (GPNA) with a D-backbone configuration and alternate spacing binds sequence-specifically to RNA and is readily taken up by both human somatic and embryonic stem (ES) cells.

Polyamides are minor groove DNA-binding agents derived from the natural product distamycin A. PA1 is a large 12 ring polyamide discovered by NanoVir LLC; it is bioactive against the HPV16 virus in cell and tissue culture (Edwards et al., 2011). To better understand the basis of this phenomenon, the interactions of PA1 with the regulatory sequence of the HPV16 genome (7662–122 bp) are being examined. Using affinity cleavage as detected by capillary electrophoresis, with PA1 attached to methyl propyl ethidium iron EDTA, 10 binding sites of PA1 were identified in this part of the HPV genome. Polyamide perfect binding sites were as predicted by recognition rules (Dervan & Edelson, 2003). Quantitative DNaseI footprinting indicates that both perfect and single mismatch sites are bound with Kds in the low nm range. Interestingly, a wide range of Kds are observed for double mismatch sites (1–60 nm) and are under examination. This work will permit us to build a map of PA binding to HPV sequences, thus informing me...

The synthesis and crystal structure of Zn (2-x) Co x (PO 4 ) 2 (NH 3 H 2 CH 2 NH 3 ) (x = 0.61) (ZCP-DFT) is described. ZCP-DFT is characterized by means of single-crystal and powder X-ray diffraction. Crystal data for ZCP-DFT: tetragonal, space group P4 2 bc (No. 106), a = 14.7236(6) A, b = 14.7236(6) A, c = 8.9544(5) A, V = 1941.17(16) A 3 , Z = 8. The structure has 3-D 8-ring channel system with protonated ethylenediamine cations in the channel junctions. The framework structure type is the same as the zeolite DFT topology. The synthesis of ZCP-DFT indicates that cobalt can partially substitute the metal sties of zinc phosphate, which can lead to the modification of physical and chemical properties of the parent compounds.

Despite increasing awareness of their biological importance, mechanisms of DNA site discrimination by structurally homologous and functionally non-redundant transcription factors remain poorly defined concepts. Members of the ETS family of transcription factors, which regulate the differentiation of hematopoietic stem cells to the gamut of blood cell lineages, exemplify this conundrum. While the ETS-family members PU.1 and Ets-1 share structurally superimposable DNA-binding domains, the two homologs direct distinct cohorts of genes and induce mutually exclusive outcomes in hematopoietic cell-fate decisions. Using an array of biochemical, spectroscopic, and calorimetric techniques, we have compared DNA site recognition by PU.1 and Ets-1. The data indicate a startling level of structural, dynamic, thermodynamic, and kinetic heterogeneity associated with DNA site recognition by these proteins, which may be traced to their differential coupling of molecular hydration and counter-ion release with site-specific binding. Whereas site recognition by Ets-1 appears homogeneous with respect to DNA sequence identity, high- and low-affinity sites unmask major heterogeneity in PU.1 binding by all experimental observations. These differences are intrinsic to the two homologous DNA-binding domains; additional intramolecular interactions in adjacent domains exert no effect on the apparent homogeneity in Ets-1/DNA binding. The emerging evidence suggests a strong coupling between molecular hydration, DNA curvature, conformational dynamics, electrostatics as a mechanism for PU.1 to enforce different sequence preferences and kinetic behavior relative to Ets-1, and offer new insight into the functional differences between the two homologs. [This investigation is supported by NIH R15GM112002-01 to GMKP, NIH R01AI083803 to JKB, and NSF MCB1411502 to GMKP and WDW.]