Smouldering to treat PFAS in sewage sludge

Wastewater treatment plants are accumulation points for per- and polyfluoroalkyl substances (PFAS), and are threfore important facilities for PFAS treatment. This study explored using smouldering combustion to treat PFAS in sewage sludge. Base case experiments at the laboratory scale (LAB) used dried sludge mixed with sand. High moisture content (MC) LAB tests, 75% MC sludge by mass, explored impacts of MC on treatment and supplemented with granular activated carbon (GAC) to achieve sufficient temperatures for thermal destruction of PFAS. Additional LAB tests explored using calcium oxide (CaO) to support fluorine mineralization. Further tests performed at an oil-drum scale (DRUM) assessed scale on PFAS removal. Pre-treatment sludge and post-treatment ash samples from all tests were analyzed for 12 PFAS (2C-8C). Additional emissions samples were collected from all LAB tests and analyzed for 12 PFAS and hydrogen fluoride. Smouldering removed all monitored PFAS from DRUM tests, and 4-8 carbon chain length PFAS from LAB tests. For base case tests, PFOS and PFOA were completely removed from sludge; however, high contents in the emissions (79-94% of total PFAS by mass) showed volatilization without degradation. Smouldering high MC sludge at ∼ 900 °C (30 g GAC/kg sand) improved PFAS degradation compared to treatment below 800 °C (<20 g GAC/kg sand). Addition of CaO before smouldering reduced PFAS content in emissions by 97-99% by mass; with minimal PFAS retained in the ash and minimal hydrofluoric acid (HF) production, as the fluorine from the PFAS was likely mineralized in the ash. Co-smouldering with CaO had dual benefits of removing PFAS while minimizing other hazardous emission by-products.

Exploring PCDD/Fs and potentially toxic elements in sewage sludge during smouldering treatment

Potentially toxic elements (PTEs), persistent organic pollutants, and emerging contaminants make sewage sludge management challenging. There is significant interest in thermal treatment technologies that can destroy these compounds. The most common thermal treatment, incineration, poses risks due to formation and/or release of hazardous substances in process emissions such as polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/Fs) and PTEs. Smouldering has been introduced recently as a potential treatment for managing sewage sludge. Smouldering systems present several advantages over traditional incinerators; however, there are still uncertainties regarding process by-products. This key question was investigated in three laboratory-scale tests (0.08 m radius) and five oil drum-scale tests (0.3 m radius) that were evaluated for PCDD/Fs and PTEs in the mixture before and after treatment as well as in process emissions. Volatile organic compounds (VOCs) were also measured. These experiments represent a broad spectrum of conditions to evaluate process emissions, from robust self-sustaining to extinction of smouldering. Robust smouldering had negligible PCDD/Fs in process emissions. Weak smouldering had low levels of PCDD/Fs (emissions factor: 3.3 ± 0.3 μg TEQ/Mg dried sludge destroyed), levels less than uncontrolled emissions from commercial incinerators. Overall, smouldering acted as a sink for PCDD/Fs, as only 0-3% of the PCDD/Fs originally present in the sludge were released in the emissions, and >99% of the remainder were destroyed with <1% remaining in post-treatment ash. No evidence was found to support de novo synthesis or precursor reactions forming new PCDD/Fs. In addition, 94-100% of all the PTEs analyzed were retained in the post-smouldered material. These results indicate that only minimal emissions treatment for PTEs, PCDD/Fs, and VOCs may be necessary for future sewage sludge smouldering systems. These low emissions risks combined with its unique ability to handle high moisture content waste, indicate that smouldering has significant potential as a valuable waste management technique.

Phosphorus recovery and reuse potential from smouldered sewage sludge ash

Smouldering treatment of sewage sludge - and recapturing phosphorus - provides important steps towards a circular economy. This study reveals that bulking sludge with sand or another organic waste, e.g., woodchips, created a material that was readily converted to ash by self-sustained smouldering. Simultaneous phosphorus and regulated potentially toxic element releases from ash were evaluated using leaching methods from the USEPA Leaching Environmental Assessment Framework (LEAF). Extraction potentials were also determined to evaluate direct recovery as an alternative to land application. Compared to the parent sludge, post-treatment ash from smouldering sludge with sand contained higher quantities of inorganic phosphorus in sorbed and mineral phases, which can provide beneficial slow phosphorus release to plants and avoid early phosphorus washout during land application. Ash also released lower initial and total quantities of potentially toxic elements than virgin sludge. As an alternative to land application, approximately 42% of retained phosphorus can be recovered directly using acidic extraction, and an additional 30% from emissions. In contrast, co-smouldering sludge with woodchips was more suited for direct recovery with 78% of phosphorus potentially recoverable via emissions capture and yield increasing to 99% with acidic extraction of resulting ash. Co-smouldering also produces a single post-treatment ash and can be readily operated continuously, which aligns with current incinerator configurations at wastewater treatment plants and makes adaptation highly feasible. With phosphorus reuse opportunities for land application and direct recovery, smouldering sewage sludge creates an important opportunity for a phosphorus circular economy as part of wastewater treatment sludge management.

USEPA LEAF methods for characterizing phosphorus and potentially toxic elements in raw and thermally treated sewage sludge

Biologically available phosphorus supports plant growth but can also cause environmental contamination. Sequential extraction methods, such as Hedley fractionation, are the most widely used to assess available phosphorus from solids. However, such methods exhibit numerous deficiencies. The USEPA Leaching Environmental Assessment Framework (LEAF) is a tiered system developed to evaluate releases of Potentially Toxic Elements (PTEs) from solids. This study compared the Hedley fractionation method to the LEAF pH-dependent, parallel batch tests (Method 1313) and dynamic leaching column test (Method 1314) to assess the bioavailability of phosphorus. The three methods were applied to wastewater treatment plant sludge before and after thermal treatment. Both methods revealed similar qualitative trends, namely that thermal treatment transformed phosphorus into less immediately available forms. However, the Hedley and LEAF methods were inconsistent in the forms and amounts of available phosphorus recovered from the solids. The Hedley method left 40% of phosphorus unextracted from sludge and 20% from ash, suggesting that it may be less appropriate for organic materials. Moreover, only 2 of the 6 Hedley phosphorus pools were within environmentally relevant pH conditions. Furthermore, the Hedley method overpredicted the readily available phosphorus. In contrast, the LEAF methods allowed for a more detailed analysis of phosphorus availability - while simultaneously assessing PTEs - across a controlled pH range. Moreover, LEAF used simpler procedures and provided more easily interpreted results. Thus, LEAF facilitates more robust and valuable assessment of organic and inorganic solids being considered for land application.

A Type 1 Diabetes Genetic Risk Score Predicts Progression of Islet Autoimmunity and Development of Type 1 Diabetes in Individuals at Risk

OBJECTIVE

We tested the ability of a type 1 diabetes (T1D) genetic risk score (GRS) to predict progression of islet autoimmunity and T1D in at-risk individuals.

RESEARCH DESIGN AND METHODS

We studied the 1,244 TrialNet Pathway to Prevention study participants (T1D patients' relatives without diabetes and with one or more positive autoantibodies) who were genotyped with Illumina ImmunoChip (median [range] age at initial autoantibody determination 11.1 years [1.2-51.8], 48% male, 80.5% non-Hispanic white, median follow-up 5.4 years). Of 291 participants with a single positive autoantibody at screening, 157 converted to multiple autoantibody positivity and 55 developed diabetes. Of 953 participants with multiple positive autoantibodies at screening, 419 developed diabetes. We calculated the T1D GRS from 30 T1D-associated single nucleotide polymorphisms. We used multivariable Cox regression models, time-dependent receiver operating characteristic curves, and area under the curve (AUC) measures to evaluate prognostic utility of T1D GRS, age, sex, Diabetes Prevention Trial-Type 1 (DPT-1) Risk Score, positive autoantibody number or type, HLA DR3/DR4-DQ8 status, and race/ethnicity. We used recursive partitioning analyses to identify cut points in continuous variables.

RESULTS

Higher T1D GRS significantly increased the rate of progression to T1D adjusting for DPT-1 Risk Score, age, number of positive autoantibodies, sex, and ethnicity (hazard ratio [HR] 1.29 for a 0.05 increase, 95% CI 1.06-1.6; P = 0.011). Progression to T1D was best predicted by a combined model with GRS, number of positive autoantibodies, DPT-1 Risk Score, and age (7-year time-integrated AUC = 0.79, 5-year AUC = 0.73). Higher GRS was significantly associated with increased progression rate from single to multiple positive autoantibodies after adjusting for age, autoantibody type, ethnicity, and sex (HR 2.27 for GRS >0.295, 95% CI 1.47-3.51; P = 0.0002).

CONCLUSIONS

The T1D GRS independently predicts progression to T1D and improves prediction along T1D stages in autoantibody-positive relatives.

Self-sustaining smoldering combustion: a novel remediation process for non-aqueous-phase liquids in porous media

Smoldering combustion, the slow burning process associated typically with porous solids (e.g., charcoal), is here proposed as a novel remediation approach for nonaqueous phase liquids (NAPLs) embedded in porous media. Several one-dimensional vertical smoldering experiments are conducted on quartz sand containing fresh coal tar at an initial concentration of 71 000 mg/kg (approximately 25% saturation) and employing an upward darcy air flux of 4.25 cm/s. Following a short-duration energy input to achieve ignition at the lower boundary, a self-sustaining combustion front is observed to propagate upward at 1.3 x 10(-2) cm/s. The process is self-sustaining because the energy released during NAPL smoldering is efficiently trapped and recirculated by the soil matrix, preheating the NAPL ahead of the reaction front. The smoldering process is observed to self-terminate when all of the NAPL is destroyed or when the oxygen source is removed. Pre- and post-soil analysis revealed that NAPL smoldering reduced the concentration of total extractable petroleum hydrocarbons (TPH) from 38 000 mg/kg to below detection limits (< 0.1 mg/kg) throughout the majority of the column. A comparable experiment in which conductive heating is applied in the absence of smoldering demonstrates a 6-fold reduction in the net energy in the system and residual TPH values of 2000-35 000 mg/kg. A further repeat in which the air supply is prematurely terminated demonstrated that the NAPL smoldering process can be extinguished via external control. A suite of 23 demonstration experiments shows that NAPL smoldering is successful across a range of soil types (including simple layered systems) and contaminants (including laboratory mixtures of dodecane, DCA/ grease, TCE/oil, vegetable oil, crude oil, and mineral oil) as well as field-obtained samples of materials containing coal tar, oil drill cutting waste, and oil sands.

Home blood testing for celiac disease: recommendations for management

OBJECTIVE

To provide recommendations for the management of patients who inquire about the Health Canada-approved, self-administered home blood tests for celiac disease or who present with positive test results after using the self-testing kit

SOURCES OF INFORMATION

PubMed and the Cochrane Database of Systematic Reviews were searched from January 1985 to April 2008, using the subject headings diagnosis of celiac disease and management or treatment of celiac disease. Guidelines for serologic testing and confirmation of diagnosis of celiac disease by the American Gastroenterological Association and the North American Society for Pediatric Gastroenterology, Hepatology and Nutrition are used in this review. Level 1 evidence was used.

MAIN MESSAGE

Although blood tests are helpful for screening purposes, the confirmatory test for celiac disease is a small intestinal biopsy.

CONCLUSION

Patients whose blood tests for celiac disease provide positive results should have endoscopic small intestinal biopsies to confirm the diagnosis before starting a gluten-free diet.

The Canadian Celiac Health Survey

The purpose of this study was to characterize the diagnostic process, frequency of associated disorders, family history, and impact of a gluten-free diet in individuals with celiac disease. All members of the Canadian Celiac Association (n=5240) were surveyed with a questionnaire. Respondents included 2681 adults with biopsy-proven celiac disease. The mean age was 56 years. Most common presenting symptoms included abdominal pain (83%), diarrhea (76%), and weight loss (69%). The mean delay in diagnosis was 11.7 years. Diagnoses made prior to celiac disease included anemia (40%), stress (31%), and irritable bowel syndrome (29%). Osteoporosis was common. Prior to diagnosis, 27% of respondents consulted three or more doctors about their symptoms. Delays in diagnosis of celiac disease remain a problem. Associated medical conditions occur frequently. More accurate food labeling is needed. Improved awareness of celiac disease and greater use of serological screening tests may result in earlier diagnosis and reduced risk of associated conditions.

Canadian consensus on medically acceptable wait times for digestive health care

BACKGROUND

Delays in access to health care in Canada have been reported, but standardized systems to manage and monitor wait lists and wait times, and benchmarks for appropriate wait times, are lacking. The objective of the present consensus was to develop evidence- and expertise-based recommendations for medically appropriate maximal wait times for consultation and procedures by a digestive disease specialist.

METHODS

A steering committee drafted statements defining maximal wait times for specialist consultation and procedures based on the most common reasons for referral of adult patients to a digestive disease specialist. Statements were circulated in advance to a multidisciplinary group of 25 participants for comments and voting. At the consensus meeting, relevant data and the results of voting were presented and discussed; these formed the basis of the final wording and voting of statements.

RESULTS

Twenty-four statements were produced regarding maximal medically appropriate wait times for specialist consultation and procedures based on presenting signs and symptoms of referred patients. Statements covered the areas of gastrointestinal bleeding; cancer confirmation and screening and surveillance of colon cancer and colonic polyps; liver, biliary and pancreatic disorders; dysphagia and dyspepsia; abdominal pain and bowel dysfunction; and suspected inflammatory bowel disease. Maximal wait times could be stratified into four possible acuity categories of 24 h, two weeks, two months and six months.

FUTURE DIRECTIONS

Comparison of these benchmarks with actual wait times will identify limitations in access to digestive heath care in Canada. These recommendations should be considered targets for future health care improvements and are not clinical practice guidelines.

The impact of a gluten-free diet on adults with coeliac disease: results of a national survey

OBJECTIVE We sought to evaluate the impact of the gluten-free diet on the 5,240 members of the Canadian Celiac Association (CCA). Data are presented on 2,681 adults (>or=16 years) with biopsy-proven celiac disease (CD).

METHODS

A mail-out survey was used. Quality of life was evaluated using the 'SF12', and celiac-specific questions.

RESULTS

Mean age was 56 years, mean age at diagnosis was 45 years, and 75% were female. The 'SF12' summary scores were similar to normative Canadian data, but were significantly lower for females and newly diagnosed patients. Respondents reported: following a gluten-free (GF) diet (90%), improvement on the diet (83%), and difficulties following the diet (44%), which included: determining if foods were GF (85%), finding GF foods in stores (83%), avoiding restaurants (79%), and avoiding travel (38%). Most common reactions to consumed gluten (among 73%) included pain, diarrhea, bloating, fatigue, nausea, and headache. Excellent information on CD and its treatment was provided by the CCA (64%), gastroenterologists (28%), dietitians (26%) and family doctor (12%).

CONCLUSIONS

Quality of life in those with CD could be increased with early diagnosis, increased availability of gluten-free foods, improved food labelling, and better dietary instruction. Education of physicians and dietitians about CD and its treatment is essential.

Celiac disease: evaluation of the diagnosis and dietary compliance in Canadian children

OBJECTIVES

We sought to characterize the clinical features at presentation as well as the associated disorders, family history, and evaluation of compliance with a gluten-free diet in children with celiac disease from across Canada.

STUDY DESIGN

All members (n = 5240) of the Canadian Celiac Association were surveyed with a questionnaire. Of the 2849 respondents with biopsy-confirmed celiac disease, 168 who were < 16 years old provided the data reported here.

RESULTS

The mean age when surveyed was 9.1 +/- 4.1 years, and 58% were female. Median age at diagnosis was 3.0 years with a range of 1 to 15 years. Presenting symptoms included abdominal pain (90%), weight loss (71%), diarrhea (65%), weakness (64%), nausea/vomiting (53%), anemia (40%), mood swings (37%), and constipation (30%). Almost one third of families consulted > or = 2 pediatricians before confirmation of the diagnosis. Before the recognition of celiac disease, other diagnoses received by these children included anemia (15%), irritable bowel syndrome (11%), gastroesophageal reflux (8%), stress (8%), and peptic ulcer disease (4%). A serological test was performed to screen for celiac disease in 70% of those in this population. Eight percent had either type 1 diabetes mellitus or a first-degree relative with celiac disease. Almost all respondents (95%) reported strict adherence to a gluten-free diet, and 89% noted improved health. Reactions after accidental gluten ingestion developed in 54% of the children between 0.5 and 60 hours after ingestion with a median of 2.0 hours. Reactions included abdominal discomfort (87%), diarrhea (64%), bloating (57%), fatigue (37%), headache (24%), and constipation (8%), and most displayed > 1 symptom. Although most adjusted well to their disease and diet, 10% to 20% reported major disruptions in lifestyle. Twenty-three percent felt angry all or most of the time about following a gluten-free diet. Only 15% avoided traveling all or most of the time, and during travel, 83% brought gluten-free food with them all of the time. More than half of the families avoided restaurants all or most of the time. Twenty-eight percent of the respondents found it extremely difficult to locate stores with gluten-free foods, and 27% reported extreme difficulty in finding gluten-free foods or determining if foods were free of gluten. Sixty-three percent of the respondents felt that the information supplied by the Canadian Celiac Association was excellent. Gastroenterologists provided excellent information to 44%, dietitians to 36%, and the family physician to 11.5%. When asked to select 2 items that would improve their quality of life, better labeling of gluten-containing ingredients was selected by 63%, more gluten-free foods in the supermarket by 49%, gluten-free choices on restaurant menus by 49%, earlier diagnosis of celiac disease by 34%, and better dietary counseling by 7%.

CONCLUSIONS

In Canada, children with celiac disease present at all ages with a variety of symptoms and associated conditions. Delays in diagnosis are common. Most children are compliant with a gluten-free diet. A minority of these children experience difficulties in modifying their lifestyles, and gluten-free foods remain difficult to obtain.

The Canadian celiac health survey--the Ottawa chapter pilot

BACKGROUND

Celiac disease may manifest with a variety of symptoms which can result in delays in diagnosis. Celiac disease is associated with a number of other medical conditions. The last national survey of members of the Canadian Celiac Association (CCA) was in 1989. Our objective was to determine the feasibility of surveying over 5,000 members of the CCA, in addition to obtaining more health related information about celiac disease.

METHODS

The Professional Advisory Board of the CCA in collaboration with the University of Ottawa developed a comprehensive questionnaire on celiac disease. The questionnaire was pre-tested and then a pilot survey was conducted on members of the Ottawa Chapter of the CCA using a Modified Dillmans' Total Design method for mail surveys.

RESULTS

We had a 76% response to the first mailout of the questionnaire. The mean age of participants was 55.5 years and the mean age at diagnosis was 45 years. The majority of respondents presented with abdominal pain, diarrhea, fatigue or weight loss. Prior to diagnosis, 30% of respondents consulted four or more family doctors. Thirty seven percent of individuals were told they had either osteoporosis or osteopenia. Regarding the impact of the gluten-free diet (GFD), 45% of individuals reported that they found following a GFD was very or moderately difficult. The quality of life of individuals with celiac disease was comparable to the mean quality of life of Canadians.

CONCLUSION

On the basis of our results, we concluded that a nationwide survey is feasible and this is in progress. Important concerns included delays in the diagnosis of celiac disease and the awareness of associated medical conditions. Other issues include awareness of celiac disease by health professionals and the impact of the GFD on quality of life. These issues will be addressed further in the national survey.

Clinical experience with infliximab for Crohn's disease: the first 100 patients in Edmonton, Alberta

OBJECTIVE

To determine whether the clinical efficacy and safety of infliximab in diverse clinical referral practices was similar to that seen in the randomized, controlled clinical trials.

METHODS

Data were gathered from a review of charts of 109 consecutive patients with inflammatory and/or fistulizing Crohn's disease who received infliximab infusions. Responses were recorded based on the physician's global clinical assessment and classified as complete, partial or nonresponse.

RESULTS

One hundred nine patients were treated with one to nine infusions of infliximab at a dose of 5 mg/kg and followed up for a median of 24 weeks (range one to 40 weeks). Fifty-four patients were treated for inflammatory disease, 38 for fistulizing disease and 17 for both. Clinical response occurred in 73% (17% complete response, 55% partial response). The clinical response rate did not vary relative to patient demographics, disease distribution, indication for infliximab, or the concomitant use of corticosteroids or immune modifiers. For those taking concomitant immune modifiers, the response rate was 75%. The median time to response was two weeks (range one to six weeks). The median duration of response was 12 weeks (range six to 88 weeks). Reduction or cessation of steroids was possible in 17 of 32 patients. Adverse events related to infliximab occurred in 7% of patients. These events were characterized as mild and did not require stoppage of infliximab therapy, except in one patient who had a treatable anaphylactic-like infusion reaction.

CONCLUSIONS

The patient group in the present study realized significant clinical benefit, with minimal adverse effects, following treatment with infliximab. Clinical response rates paralleled those previously described in placebo controlled trials and retrospective clinical practice reviews. Nevertheless, the complete response rate (ie, remission) in this patient group was lower than that previously described.

DNA bending by asymmetrically tethered cations: influence of tether flexibility

BACKGROUND

We have been studying the proposal that laterally asymmetric charge neutralization along the DNA double helix can induce collapse toward the neutralized surface. Results of previous experiments implied that such a phenomenon can occur, suggesting a role for local interphosphate repulsive forces in DNA shape and rigidity.

RESULTS

We now show that, whereas six ammonium ions tethered to one DNA face on flexible propyl chains can induce detectable DNA curvature, tethering of ammonium ions on rigid propynyl tethers does not induce DNA curvature. Molecular modeling indicates differing propensities for phosphate salt bridge formation between propyl- and propynyl-tethered ammonium ions.

CONCLUSIONS

Ammonium ion localization is suggested as a key factor in induced bending. Rigidification of the double helix by stacking of propyne groups cannot be excluded.

Probing structure and function with alternative nucleic acids bearing 2',5'-linked, zwitterionic, and isocytosine-isoguanine components

The incorporation of alternative functional components into nucleic acids can provide insight into what molecular features are necessary for an informational macromolecule to be successful. It can also provide a means to improve particular physical characteristics of nucleic acids for diagnostic and therapeutic purposes, or probe mechanisms. By testing the fitness of nucleic acid-like molecules derived by structural permutations of RNA, it may also prove possible to trace a path from simple prebiotic precursors to biotic molecules. This article describes the applications of 2',5'-phosphodiester linked, zwitterionic, and base-permuted nucleic acid derivatives.

Nonenzymatic oligomerization on templates containing phosphodiester-linked acyclic glycerol nucleic acid analogues

Nonenzymatic oligomerization reactions represent a model for studying the prebiotic replication of informational macromolecules. To explore the fitness of acyclic oligonucleotides in these reactions, we have synthesized a series of DNA hairpins appended with templates incorporating atactic glyceryl cytosine residues. Atactic glyceryl cytosine units are found to impede, but not to block, template-directed oligomerization of guanosine 5'-phosphoro-2-methylimidazole (2-MeImpG). Evidence suggests that both D and L glyceryl nucleoside configurations at a given template position contribute to product formation. The stability of DNA duplexes bearing isolated glyceryl cytosine residues has also been investigated. Duplex thermal denaturation experiments indicate that an atactic glyC. dG base-pair is intermediate in stability between a dC. dG pair and a dT. dG mismatch.

RecA protein promotes strand exchange with DNA substrates containing isoguanine and 5-methyl isocytosine

The Escherichia coli RecA protein pairs homologous DNA molecules and promotes DNA strand exchange in vitro. We have examined DNA strand exchange between a 70 nucleotide ssDNA fragment and a 40 bp duplex, in which all G and C residues (at 18 positions distributed throughout the 40 bp exchanged region) were replaced with the nonstandard nucleosides 2'-deoxyisoguanosine (iG) and 2'-deoxy-5-methylisocytidine (MiC), respectively. We demonstrate that the nonstandard oligonucleotides are substrates for the RecA protein, permitting DNA strand exchange in vitro at a rate and efficiency comparable to exchange with normal DNA substrates. This observation provides an expanded experimental basis for discussions of potential roles for iG and MiC in a genetic code. Experiments of this type also provide another avenue for exploring RecA-facilitated DNA pairing mechanisms.

A DNA pentaplex incorporating nucleobase quintets

Supramolecular self-assembly is an integral step in the formation of many biological structures. Here we report a DNA pentaplex that derives from a metal-assisted, hydrogen bond-mediated self-assembly process. In particular, cesium ions are found to induce pentameric assembly of DNA bearing the nonstandard nucleobase iso-guanine. The pentaplex was designed by using a simple algorithm to predict nucleobase structural requirements within a quintet motif. The design principles are general and should extend to complexes beyond pentaplex. Structures exhibiting molecularities of five or more were previously accessible to peptides, but not nucleic acids.

2'-Deoxyisoguanosine adopts more than one tautomer to form base pairs with thymidine observed by high-resolution crystal structure analysis

The questions of whether different tautomeric forms of nucleic acid bases exist to any significant extent in DNA, or what their possible roles in mutation may be, are under intense scrutiny. 2'-Deoxyisoguanosine (iG) has been suggested to have a propensity to adopt the enol form. Isoguanine (also called 2-hydroxyadenine) can be found in oxidatively damaged DNA generated from treating DNA with a Fenton-type reactive oxygen-generating system and is known to cause mutation. We have analyzed the three-dimensional structure of the DNA dodecamer d(CGC[iG]AATTTGCG) (denoted iG-DODE) by X-ray crystallography and NMR. The crystal structure of the iG-DODE complexed with the minor groove binder Hoechst 33342, refined to 1.4 A resolution, showed that the two independent iG.T base pairs in the dodecamer duplex adopt different (one in Watson-Crick and the other in wobble) conformations. The high-resolution nature of the structure also affords unprecedented clear information about the conformation and interactions of the Hoechst drug. The Hoechst 33342 binds in the narrow minor groove at the iGAATT site, with the N-methylpiperazine ring near the iG4.T21 base pair. Three hydrogen bonds are found between the NH of the Hoechst ligand and T-O2 DNA atoms. In solution, the two iG.T base pairs in iG-DODE predominantly are in the wobble form at 2 degreesC. At higher temperatures, another duplex form (likely involving the enol form of iG) is in slow exchange with the keto form and becomes significantly populated, reaching approximately 40% at 40 degreesC. Our data support the conclusion that iG pairs with T in a Watson-Crick configuration to a significant extent at physiological temperature (37 degreesC), which may explain the facile incorporation rate of T across from an iG during in vitro DNA replication.

Ribosome-catalyzed peptide-bond formation with an A-site substrate covalently linked to 23S ribosomal RNA

In the ribosome, the aminoacyl-transfer RNA (tRNA) analog 4-thio-dT-p-C-p-puromycin crosslinks photochemically with G2553 of 23S ribosomal RNA (rRNA). This covalently linked substrate reacts with a peptidyl-tRNA analog to form a peptide bond in a peptidyl transferase-catalyzed reaction. This result places the conserved 2555 loop of 23S rRNA at the peptidyl transferase A site and suggests that peptide bond formation can occur uncoupled from movement of the A-site tRNA. Crosslink formation depends on occupancy of the P site by a tRNA carrying an intact CCA acceptor end, indicating that peptidyl-tRNA, directly or indirectly, helps to create the peptidyl transferase A site.

Beyond guanine quartets: cation-induced formation of homogenous and chimeric DNA tetraplexes incorporating iso-guanine and guanine

BACKGROUND

iso-Guanine (iso-G) is the purine component of an isomeric Watson-Crick base pair that may have existed prebiotically. By comparing the abiotic molecular recognition properties of iso-G and its complement, iso-cytosine (iso-C), with those of genomic nucleotide bases, it may be possible to explain the exclusion of the iso-G-iso-C base pair from modern genomes. Whether a nucleobase forms quartets may have a key role in determining its functionality. Biotically, nucleic acid tetraplexes have been implicated in cellular functions; prebiotically, tetraplexes would probably interfere with replication. Recently, in vitro selection has yielded receptors and catalysts that incorporate G quartets. The versatility of these structures could be enhanced by expanding the range of bases that can form the quartet motif.

RESULTS

Native polyacrylamide gel electrophoresis of oligonucleotides bearing runs of iso-G provides strong support for tetraplex formation via cation-promoted DNA strand association. In particular, when strands of different lengths bearing the same iso-G tetrad recognition element were combined, five bands were observed after electrophoresis, corresponding to all possible heterotetraplexes with parallel strand alignment. An analogous experiment with a mixture of strands bearing iso-G or G tetrad recognition domains supports the existence of mixed iso-G/G tetraplexes with antiparallel strand alignment at chimeric junctions. iso-G tetraplex and quartet structure has also been probed by a photo-crosslinking experiment, ultra-violet spectroscopy and theoretical calculations.

CONCLUSIONS

As iso-G and G both have a marked tendency to form tetraplexes, their tandem inclusion in genetic material may be problematic, leading to double-stranded DNA half composed of bases that have a tendency to auto-associate. The resulting density of 'selfish' bases could undermine Watson-Crick pair formation, especially in a prebiotic context devoid of enzymes. Nevertheless, the ability of iso-G to form mixed quartets with G may provide a basis for altering the properties of tetraplexes in the domain of artificial receptors or catalysts from in vitro selections.

Regioselective effect of zwitterionic DNA substitutions on DNA alkylation: evidence for a strong side chain orientational preference

The incorporation of zwitterionic residues (5-substituted omega-aminoalkyl-2'-deoxypyrimidines) into DNA has been reported to bend DNA as measured by aberrant gel mobility [Strauss et al. (1996) Proc. Natl. Acad. Sci. U.S.A. 93, 9515-9520]. Herein we report that DNA methylation by N-methyl-N-nitrosourea at N7-guanine is regioselectively inhibited by point substitutions of the zwitterionic residues 5-(6-aminohexyl)-2'-deoxycytidine, 5-(6-aminohexyl)-2'-deoxyuridine, or 5-(3-aminopropyl)-2'-deoxyuridine. No inhibition is observed for DNA methylation by dimethyl sulfate. On the basis of inhibition patterns for methylation with the different zwitterionic substitutions and the different length tethers, the omega-aminoalkyl side chains prefer to adopt a conformation that points them toward the 3'-base. Molecular modeling grid searches, coupled with energy minimizations, and simulated annealing molecular dynamics studies indicate that unfavorable steric interactions with the 5'-base and backbone, as well as stabilizing electrostatic interactions with electronegative atoms on the 3'-side, are responsible for the observed conformational preference. No evidence for association of the cationic side chain with the phosphate backbone is observed. The observed bending of DNA induced by the tethered ammonium ions may simply arise from their localization in the major groove.

DNA bending by hexamethylene-tethered ammonium ions

DNA is bent when complexed with certain proteins. We are exploring the hypothesis that asymmetric neutralization of phosphate charges will cause the DNA double helix to collapse toward the neutralized face. We have previously shown that DNA spontaneously bends toward one face of the double helix when it is partially substituted with neutral methylphosphonate linkages. We have now synthesized DNA duplexes in which cations are tethered by hexamethylene chains near specific phosphates. Electrophoretic phasing experiments demonstrate that tethering six ammonium ions on one helical face causes DNA to bend by approximately 5 degrees toward that face, in qualitative agreement with predictions. Ion pairing between tethered cations and DNA phosphates provides a new model for simulating the electrostatic consequences of phosphate neutralization by proteins.

DNA bending by a phantom protein

BACKGROUND

Despite its stiffness, duplex DNA is extensively bent and folded during packaging and gene expression in biological systems. Modulation of the electrostatic repulsion between phosphates in the DNA backbone may be important in the bending of DNA by proteins. Here, we analyze the shape of DNA molecules that have been modified chemically to mimic the electrostatic consequences of a bound protein.

RESULTS

We have simulated salt bridges between DNA phosphates and cationic amino acid sidechains of a phantom protein by tethering ammonium cations to one face of the DNA helix. Tethered ammonium cations, but not neutral acetylated controls, induce DNA to bend toward its neutralized surface.

CONCLUSIONS

The shape of DNA molecules bearing a laterally-asymmetric distribution of tethered cations agrees qualitatively with theoretical predictions and with results previously obtained using neutral phosphate analogs. These data suggest principles that might be applied to the design of artificial DNA-bending proteins.

Ribosome-mediated incorporation of a non-standard amino acid into a peptide through expansion of the genetic code

One serious limitation facing protein engineers is the availability of only 20 'proteinogenic' amino acids encoded by natural messenger RNA. The lack of structural diversity among these amino acids restricts the mechanistic and structural issues that can be addressed by site-directed mutagenesis. Here we describe a new technology for incorporating non-standard amino acids into polypeptides by ribosome-based translation. In this technology, the genetic code is expanded through the creation of a 65th codon-anticodon pair from unnatural nucleoside bases having non-standard hydrogen-bonding patterns. This new codon-anticodon pair efficiently supports translation in vitro to yield peptides containing a non-standard amino acid. The versatility of the ribosome as a synthetic tool offers new possibilities for protein engineering, and compares favourably with another recently described approach in which the genetic code is simply rearranged to recruit stop codons to play a coding role.