Surviving critical illness: what is next? An expert consensus statement on physical rehabilitation after hospital discharge.

BACKGROUND: The study objective was to obtain consensus on physical therapy (PT) in the rehabilitation of critical illness survivors after hospital discharge. Research questions were: what are PT goals, what are recommended measurement tools, and what constitutes an optimal PT intervention for survivors of critical illness? METHODS: A Delphi consensus study was conducted. Panelists were included based on relevant fields of expertise, years of clinical experience, and publication record. A literature review determined five themes, forming the basis for Delphi round one, which was aimed at generating ideas. Statements were drafted and ranked on a 5-point Likert scale in two additional rounds with the objective to reach consensus. Results were expressed as median and semi-interquartile range, with the consensus threshold set at ≤0.5. RESULTS: Ten internationally established researchers and clinicians participated in this Delphi panel, with a response rate of 80 %, 100 %, and 100 % across three rounds. Consensus was reached on 88.5 % of the statements, resulting in a framework for PT after hospital discharge. Essential handover information should include information on 15 parameters. A core set of outcomes should test exercise capacity, skeletal muscle strength, function in activities of daily living, mobility, quality of life, and pain. PT interventions should include functional exercises, circuit and endurance training, strengthening exercises for limb and respiratory muscles, education on recovery, and a nutritional component. Screening tools to identify impairments in other health domains and referral to specialists are proposed. CONCLUSIONS: A consensus-based framework for optimal PT after hospital discharge is proposed. Future research should focus on feasibility testing of this framework, developing risk stratification tools and validating core outcome measures for ICU survivors.

Granivory of invasive, naturalized, and native plants in communities differentially susceptible to invasion.

Seed predation is an important biotic filter that can influence abundance and spatial distributions of native species through differential effects on recruitment. This filter may also influence the relative abundance of nonnative plants within habitats and the communities' susceptibility to invasion via differences in granivore identity, abundance, and food preference. We evaluated the effect of postdispersal seed predators on the establishment of invasive, naturalized, and native species within and between adjacent forest and steppe communities of eastern Washington, USA that differ in severity of plant invasion. Seed removal from trays placed within guild-specific exclosures revealed that small mammals were the dominant seed predators in both forest and steppe. Seeds of invasive species (Bromus tectorum, Cirsium arvense) were removed significantly less than the seeds of native (Pseudoroegneria spicata, Balsamorhiza sagittata) and naturalized (Secale cereale, Centaurea cyanus) species. Seed predation limited seedling emergence and establishment in both communities in the absence of competition in a pattern reflecting natural plant abundance: S. cereale was most suppressed, B. tectorum was least suppressed, and P. spicata was suppressed at an intermediate level. Furthermore, seed predation reduced the residual seed bank for all species. Seed mass correlated with seed removal rates in the forest and their subsequent effects on plant recruitment; larger seeds were removed at higher rates than smaller seeds. Our vegetation surveys indicate higher densities and canopy cover of nonnative species occur in the steppe compared with the forest understory, suggesting the steppe may be more susceptible to invasion. Seed predation alone, however, did not result in significant differences in establishment for any species between these communities, presumably due to similar total small-mammal abundance between communities. Consequently, preferential seed predation by small mammals predicts plant establishment for our test species within these communities but not between them. Accumulating evidence suggests that seed predation can be an important biotic filter affecting plant establishment via differences in consumer preferences and abundance with important ramifications for plant invasions and in situ community assembly.

Movement disorders of the mouth: a review of the common phenomenologies.

Movement disorders of the mouth encompass a spectrum of hyperactive movements involving the muscles of the orofacial complex. They are rare conditions and are described in the literature primarily in case reports originating from neurologists, psychiatrists, and the dental community. The focus of this review is to provide a phenomenological description of different oral motor disorders including oromandibular dystonia, orofacial dyskinesia and orolingual tremor, and to offer management strategies for optimal treatment based on the current literature. A literature search of full text studies using PubMed/Medline and Cochrane library combined with a manual search of the reference lists was conducted until June 2021. Results from this search included meta-analyses, systematic reviews, reviews, clinical studies, case series, and case reports published by neurologists, psychiatrists, dentists and oral and maxillofacial surgeons. Data garnered from these sources were used to provide an overview of most commonly encountered movement disorders of the mouth, aiding physicians in recognizing these rare conditions and in initiating appropriate therapy.

The Use of Radiofrequency in the Treatment of Pelvic Pain.

Radiofrequency ablation (RFA) is a procedure in which radio waves are used to destroy abnormal or dysfunctional tissue. It has been an increasingly utilized treatment option for a variety of medical conditions, such as chronic pain, wherein sensory nerves are targeted and ablated, eliminating their ability to transmit pain signals to the brain. There is a lack of clarity regarding the indications, technique, and efficacy of RFA for chronic pelvic pain. This article reviews recent literature and discusses these topics, including adverse events for different pelvic ablation and pulsed radiofrequency treatment of chronic pelvic pain.

Neuromuscular blockade in patients with ARDS: a rapid practice guideline.

The aim of this Intensive Care Medicine Rapid Practice Guideline (ICM-RPG) is to formulate an evidence-based guidance for the use of neuromuscular blocking agents (NMBA) in adults with acute respiratory distress syndrome (ARDS). The panel comprised 20 international clinical experts from 12 countries, and 2 patient representatives. We adhered to the methodology for trustworthy clinical practice guidelines and followed a strict conflict of interest policy. We convened panelists through teleconferences and web-based discussions. Guideline experts from the guidelines in intensive care, development, and evaluation Group provided methodological support. Two content experts provided input and shared their expertise with the panel but did not participate in drafting the final recommendations. We followed the Grading of Recommendations Assessment, Development, and Evaluation approach to assess the certainty of evidence and grade recommendations and suggestions. We used the evidence to decision framework to generate recommendations. The panel provided input on guideline implementation and monitoring, and suggested future research priorities. The overall certainty in the evidence was low. The ICM-RPG panel issued one recommendation and two suggestions regarding the use of NMBAs in adults with ARDS. Current evidence does not support the early routine use of an NMBA infusion in adults with ARDS of any severity. It favours avoiding a continuous infusion of NMBA for patients who are ventilated using a lighter sedation strategy. However, for patients who require deep sedation to facilitate lung protective ventilation or prone positioning, and require neuromuscular blockade, an infusion of an NMBA for 48 h is a reasonable option.

An exploratory study of the association between reactive attachment disorder and attachment narratives in early school-age children.

OBJECTIVE: To explore attachment narratives in children diagnosed with reactive attachment disorder (RAD). METHOD: We compared attachment narratives, as measured by the Manchester Child Attachment Story Task, in a group of 33 children with a diagnosis of RAD and 37 comparison children. RESULTS: The relative risk (RR) for children with RAD having an insecure attachment pattern was 2.4 (1.4-4.2) but 30% were rated as securely attached. Within the RAD group, children with a clear history of maltreatment were more likely to be Insecure-Disorganised than children without a clear history of maltreatment. CONCLUSIONS: Reactive attachment disorder is not the same as attachment insecurity, and questions remain about how attachment research informs clinical research on attachment disorders.

Case report: systolic murmur associated with pulmonary embolism.

BACKGROUND: This case study's novelty lies in the potential to link a new sign in pulmonary embolism diagnosis which does not increase cost but could lead to more rapid treatment. Early intervention in these cases is vital to decrease morbidity and mortality. CASE PRESENTATION: An otherwise healthy 20-year-old female patient presents to the emergency department for evaluation of a syncopal episode which occurred just prior to arriving to the emergency department. Patient also complains of ongoing shortness of breath while performing activities of daily living for 3 weeks. In this patient with no known valvular disease, physical exam revealed a systolic murmur heard only posteriorly. Subsequent emergency department workup revealed bilateral massive pulmonary emboli. IMPLICATIONS: A new flow murmur heard in atypical locations could be an early sign to aid in the detection and diagnosis of pulmonary embolism. This is especially important in rural community hospitals with limited access to advanced imaging modalities.

Tuning porosity in macroscopic monolithic metal-organic frameworks for exceptional natural gas storage.

Widespread access to greener energy is required in order to mitigate the effects of climate change. A significant barrier to cleaner natural gas usage lies in the safety/efficiency limitations of storage technology. Despite highly porous metal-organic frameworks (MOFs) demonstrating record-breaking gas-storage capacities, their conventionally powdered morphology renders them non-viable. Traditional powder shaping utilising high pressure or chemical binders collapses porosity or creates low-density structures with reduced volumetric adsorption capacity. Here, we report the engineering of one of the most stable MOFs, Zr-UiO-66, without applying pressure or binders. The process yields centimetre-sized monoliths, displaying high microporosity and bulk density. We report the inclusion of variable, narrow mesopore volumes to the monoliths' macrostructure and use this to optimise the pore-size distribution for gas uptake. The optimised mixed meso/microporous monoliths demonstrate Type II adsorption isotherms to achieve benchmark volumetric working capacities for methane and carbon dioxide. This represents a critical advance in the design of air-stable, conformed MOFs for commercial gas storage.

Physical monitoring of mating type switching in Saccharomyces cerevisiae.

The kinetics of mating type switching in Saccharomyces cerevisiae can be followed at the DNA level by using a galactose-inducible HO (GAL-HO) gene to initiate the event in synchronously growing cells. From the time that HO endonuclease cleaves MAT a until the detection of MAT alpha DNA took 60 min. When unbudded G1-phase cells were induced, switched to the opposite mating type in "pairs." In the presence of the DNA synthesis inhibitor hydroxyurea, HO-induced cleavage occurred but cells failed to complete switching. In these blocked cells, the HO-cut ends of MATa remained stable for at least 3 h. Upon removal of hydroxyurea, the cells completed the switch in approximately 1 h. The same kinetics of MAT switching were also seen in asynchronous cultures and when synchronously growing cells were induced at different times of the cell cycle. Thus, the only restriction that confined normal homothallic switching to the G1 phase of the cell cycle was the expression of HO endonuclease. Further evidence that galactose-induced cells can switch in the G2 phase of the cell cycle was the observation that these cells did not always switch in pairs. This suggests that two chromatids, both cleaved with HO endonuclease, can interact independently with the donors HML alpha and HMRa.

Membranous duodenal stenosis: initial experience with balloon dilatation in four children.

INTRODUCTION: We present a novel approach to the treatment of membranous duodenal stenosis (MDS). To our knowledge this is the first paper to describe balloon dilatation for this entity. MATERIAL AND METHODS: Four children, 2 boys and 2 girls, aged between 8 and 28 days, underwent duodenal balloon dilatation. Balloon dilatation was performed under general anaesthesia using standard angiography balloons per os. Balloon diameters ranged from 6 to 14 mm. RESULTS: All balloon dilatations were successful. None of the procedures showed procedural or post-procedural complications. None of the patients subsequently required surgical intervention. To date all children are doing well. DISCUSSION: The initial experience with balloon dilation of MDS showed a 100% success rate, without procedural or post-procedural complications. The results obtained in this small group of patients suggest that the use of balloon dilatation in cases of MDS may be a safe technique that can be readily performed by an experienced interventional radiologist.

Unusual 2-aminopurine fluorescence from a complex of DNA and the EcoKI methyltransferase.

The methyltransferase, M.EcoKI, recognizes the DNA sequence 5'-AACNNNNNNGTGC-3' and methylates adenine at the underlined positions. DNA methylation has been shown by crystallography to occur via a base flipping mechanism and is believed to be a general mechanism for all methyltransferases. If no structure is available, the fluorescence of 2-aminopurine is often used as a signal for base flipping as it shows enhanced fluorescence when its environment is perturbed. We find that 2-aminopurine gives enhanced fluorescence emission not only when it is placed at the M.EcoKI methylation sites but also at a location adjacent to the target adenine. Thus it appears that 2-aminopurine fluorescence intensity is not a clear indicator of base flipping but is a more general measure of DNA distortion. Upon addition of the cofactor S-adenosyl-methionine to the M.EcoKI:DNA complex, the 2-aminopurine fluorescence changes to that of a new species showing excitation at 345 nm and emission at 450 nm. This change requires a fully active enzyme, the correct cofactor and the 2-aminopurine located at the methylation site. However, the new fluorescent species is not a covalently modified form of 2-aminopurine and we suggest that it represents a hitherto undetected physicochemical form of 2-aminopurine.

Improving dideoxynucleotide-triphosphate utilisation by the hyper-thermophilic DNA polymerase from the archaeon Pyrococcus furiosus.

Polymerases from the Pol-I family which are able to efficiently use ddNTPs have demonstrated a much improved performance when used to sequence DNA. A number of mutations have been made to the gene coding for the Pol-II family DNA polymerase from the archaeon Pyrococcus furiosus with the aim of improving ddNTP utilisation. 'Rational' alterations to amino acids likely to be near the dNTP binding site (based on sequence homologies and structural information) did not yield the desired level of selectivity for ddNTPs. However, alteration at four positions (Q472, A486, L490 and Y497) gave rise to variants which incorporated ddNTPs better than the wild type, allowing sequencing reactions to be carried out at lowered ddNTP:dNTP ratios. Wild-type Pfu-Pol required a ddNTP:dNTP ratio of 30:1; values of 5:1 (Q472H), 1:3 (L490W), 1:5 (A486Y) and 5:1 (Y497A) were found with the four mutants; A486Y representing a 150-fold improvement over the wild type. A486, L490 and Y497 are on analpha-helix that lines the dNTP binding groove, but the side chains of the three amino acids point away from this groove; Q472 is in a loop that connects this alpha-helix to a second long helix. None of the four amino acids can contact the dNTP directly. Therefore, the increased selectivity for ddNTPs is likely to arise from two factors: (i) small overall changes in conformation that subtly alter the nucleotide triphosphate binding site such that ddNTPs become favoured; (ii) interference with a conformational change that may be critical both for the polymerisation step and discrimination between different nucleotide triphosphates.

Linked oligodeoxynucleotides show binding cooperativity and can selectively impair replication of deleted mitochondrial DNA templates.

Mutations in mitochondrial DNA (mtDNA) cause a spectrum of human pathologies, which predominantly affect skeletal muscle and the central nervous system. In patients, mutated and wild-type mtDNAs often co-exist in the same cell (mtDNA heteroplasmy). In the absence of pharmacological therapy, a genetic strategy for treatment has been proposed whereby replication of mutated mtDNA is inhibited by selective hybridisation of a nucleic acid derivative to the single-stranded replication intermediate, allowing propagation of the wild-type genome and correction of the associated respiratory chain defect. Previous studies have shown the efficacy of this anti-genomic approach in vitro, targeting pathogenic mtDNA templates with only a single point mutation. Pathogenic molecules harbouring deletions, however, present a more difficult problem. Deletions often occur at the site of two short repeat sequences (4-13 residues), only one of which is retained in the deleted molecule. With the more common larger repeats it is therefore difficult to design an anti-genomic molecule that will bind selectively across the breakpoint of the deleted mtDNA. To address this problem, we have used linker-substituted oligodeoxynucleotides to bridge the repeated residues. We show that molecules can be designed to bind more tightly to the deleted as compared to the wild-type mtDNA template, consistent with the nucleotide sequence on either side of the linker co-operating to increase binding affinity. Furthermore, these bridging molecules are capable of sequence-dependent partial inhibition of replication in vitro.

Comparative study of linear and curvilinear ultrasound probes to assess quadriceps rectus femoris muscle mass in healthy subjects and in patients with chronic respiratory disease.

INTRODUCTION: Ultrasound measurements of rectus femoris cross-sectional area (RFCSA) are clinically useful measurements in chronic obstructive pulmonary disease (COPD) and critically ill patients. Technical considerations as to the type of probe used, which affects image resolution, have limited widespread clinical application. We hypothesised that measurement of RFCSA would be similar with linear and curvilinear probes. METHODS: Four studies were performed to compare the use of the curvilinear probe in measuring RFCSA. Study 1 investigated agreement of RFCSA measurements using linear and curvilinear probes in healthy subjects, and in patients with chronic respiratory disease. Study 2 investigated the intra-rater and inter-rater agreement using the curvilinear probe. Study 3 investigated the agreement of RFCSA measured from whole and spliced images using the linear probe. Study 4 investigated the applicability of ultrasound in measuring RFCSA during the acute and recovery phases of an exacerbation of COPD. RESULTS: Study 1 showed demonstrated no difference in the measurement of RFCSA using the curvilinear and linear probes (308±104 mm(2) vs 320±117 mm(2), p=0.80; intraclass correlation coefficient (ICC)>0.97). Study 2 demonstrated high intra-rater and inter-rater reliability of RFCSA measurement with ICC>0.95 for both. Study 3 showed that the spliced image from the linear probe was similar to the whole image RFCSA (308±103.5 vs 263±147 mm(2), p=0.34; ICC>0.98). Study 4 confirmed the clinical acceptability of using the curvilinear probe during an exacerbation of COPD. There were relationships observed between admission RFCSA and body mass index (r=+0.65, p=0.018), and between RFCSA at admission and physical activity levels at 4 weeks post-hospital discharge (r=+0.75, p=0.006). CONCLUSIONS: These studies have demonstrated that clinicians can employ whole and spliced images from the linear probe or use images from the curvilinear probe, to measure RFCSA. This will extend the clinical applicability of ultrasound in the measurement of muscle mass in all patient groups.

Interaction of the E. coli DNA G:T-mismatch endonuclease (vsr protein) with oligonucleotides containing its target sequence.

The Escherichia coli vsr endonuclease recognises G:T base-pair mismatches in double-stranded DNA and initiates a repair pathway by hydrolysing the phosphate group 5' to the incorrectly paired T. The enzyme shows a preference for G:T mismatches within a particular sequence context, derived from the recognition site of the E. coli dcm DNA-methyltransferase (CC[A/T]GG). Thus, the preferred substrate for the vsr protein is (CT[A/T]GG), where the underlined T is opposed by a dG base. This paper provides quantitative data for the interaction of the vsr protein with a number of oligonucleotides containing G:T mismatches. Evaluation of specificity constant (k(st)/K(D); k(st)=rate constant for single turnover, K(D)=equilibrium dissociation constant) confirms vsr's preference for a G:T mismatch within a hemi-methylated dcm sequence, i.e. the best substrate is a duplex (both strands written in the 5'-3' orientation) composed of CT[A/T]GG and C(5Me)C[T/A]GG. Conversion of the mispaired T (underlined) to dU or the d(5Me)C to dC gave poorer substrates. No interaction was observed with oligonucleotides that lacked a G:T mismatch or did not possess a dcm sequence. An analysis of the fraction of active protein, by "reverse-titration" (i.e. adding increasing amounts of DNA to a fixed amount of protein followed by gel-mobility shift analysis) showed that less than 1% of the vsr endonuclease was able to bind to the substrate. This was confirmed using "competitive titrations" (where competitor oligonucleotides are used to displace a (32)P-labelled nucleic acid from the vsr protein) and burst kinetic analysis. This result is discussed in the light of previous in vitro and in vivo data which indicate that the MutL protein may be needed for full vsr activity.

Effects of co-factor and deoxycytidine substituted oligonucleotides upon sequence-specific interactions between MspI DNA methyltransferase and DNA.

MspI methyltransferase (M.MspI) catalyses the transfer of a methyl group from S-adenosyl-L-methionine to the C-5 position of the outer deoxycytidine base in the DNA sequence 5'-CCGG-3'. Recombinant M.MspI when expressed and purified as a translational fusion with glutathione-S-transferase, shows all of the properties of the wild-type enzyme. We report the kinetic analysis of M.MspI binding to DNA, which suggests a two-stage methylation process, whose initial DNA binding rate is governed by the presence of a positively charged sulphonium centre on the cofactor. Results are also presented that indicate that M.MspI binds preferentially to hemi-methylated DNA and that full methylation of either deoxycytidine on both strands significantly impairs sequence-specific protein-DNA interactions. Furthermore, the importance of the 4-amino group of the inner deoxycytidine for sequence-specific protein-DNA interactions is demonstrated by substituting deoxycytidine with 2-pyrimidinone-1-beta-D-2-deoxyriboside. In addition, we detail the intrinsic structural elements of a cofactor, required to enhance the binding of M.MspI to its recognition sequence, by using S-adenosyl-L-methionine and a range of derivatives.

The roles of arginine 41 and tyrosine 76 in the coupling of DNA recognition to phosphodiester bond cleavage by DNase I: a study using site-directed mutagenesis.

Bovine pancreatic deoxyribonuclease I is an endonuclease of low specificity that interacts with the minor groove of DNA. Two amino acids, R41 and Y76, completely fill this groove, with R41 hydrogen bonding to the O2/N3 positions of pyrimidines and purines, and Y76 contacting a deoxyribose via an unusual hydrophobic "stacking" interaction. The roles of these amino acids in phosphodiester bond cleavage and in DNA hydrolysis selectivity have been studied by site-directed mutagenesis. Alterations have been made that are either conservative (R41K, Y76F) or more drastic (R41A, R41G, Y76A, Y76G). The surface loop (residues 73 to 76) that contains Y76 has also been deleted. Several double mutants in which both R41 and Y76 have been altered have also been prepared. The integrity of the catalytic site of the mutants has been investigated using the small, non-DNA, chromophoric substrate deoxythymidine-3',5'-di-(p-nitrophenyl)-phosphate. Hydrolysis of this compound was hardly changed, even by the most extreme alterations to R41 and Y76. In contrast, all the mutants bound DNA about ten times more weakly than the wild-type and, with the exception of R41K and Y76F, hydrolysed DNA much more slowly. This suggests that changes to R41 and Y76 have little effect on catalytic amino acids at the hydrolysis site, but are required to bind DNA and, more importantly, to correctly position the scissile phosphate for efficient hydrolysis. The selectivity of DNA hydrolysis for all the mutants has been tested using the 160 base-pair Escherichia coli Tyr T promoter DNA fragment. Very small differences were seen in global hydrolysis selectivity when either amino acid was altered. However, changes to R41 resulted in some differences to local cutting specificity that could be explained by the role of this amino acid in hydrogen bonding to particular bases relative to the scissile phosphate.

Site-directed mutagenesis of the catalytic residues of bovine pancreatic deoxyribonuclease I.

Bovine pancreatic deoxyribonuclease I (DNase I) is a well characterised endonuclease which cleaves double-stranded DNA to yield 5' phosphorylated polynucleotides. Co-crystal structures of DNase I with two different oligonucleotides have revealed the presence of several residues (R9, E78, H134, D168, D212 and H252) close to the scissile phosphate. The roles that these amino acids play in the catalytic mechanism have been investigated using site-directed mutagenesis. The following variants were used: R9A, E78T, H134Q, D168S, D212S and H252Q. The kinetics of all six mutants with both DNA and a small chromophoric substrate, thymidine-3',5'-di(p-nitrophenyl)-phosphate, were studied. Only R9A and E78T showed any significant turnover of the two substrates. D168S, H134Q, D212S and H252Q showed vanishingly low activities towards DNA and no detectable activity with thymidine-3',5'-di(p-nitrophenyl)-phosphate. These results demonstrate that H134, D168, D212 and H252 play a critical role in the catalytic mechanism. It is suggested that H134 and H252 (which are hydrogen-bonded to E78 and D212, respectively) provided general acid and general base catalysis. DNase I also requires Mg2+ and E39 has been identified as a ligand for this metal ion. We propose that D168 serves as a ligand for a second Mg2+, and thus DNase I, uses a two metal-ion hydrolytic mechanism. Both magnesium ions are used to supply electrophilic catalysis. Role assignment is based on the mutagenesis results, structural information, homologies between DNase I from different species and a comparison with exonuclease III. However, it is still not feasible to unequivocally assign a particular catalytic role to each amino acid/metal ion.

The DNA binding characteristics of the trimeric EcoKI methyltransferase and its partially assembled dimeric form determined by fluorescence polarisation and DNA footprinting.

The type I DNA restriction and modification systems of enteric bacteria display several enzymatic activities due to their oligomeric structure. Partially assembled forms of the EcoKI enzyme from E. coli K12 can display specific DNA binding properties and modification methyltransferase activity. The heterodimer of one specificity (S) subunit and one modification (M) subunit can only bind DNA whereas the addition of a second modification subunit to form M2S1 also confers methyltransferase activity. We have examined the DNA binding specificity of M1S1 and M2S1 using the change in fluorescence anisotropy which occurs on binding of a DNA probe labelled with a hexachlorofluorescein fluorophore. The dimer has much weaker affinity for the EcoKI target sequence than the trimer and slightly less ability to discriminate against other DNA sequences. Binding of both proteins is strongly dependent on salt concentration. The fluorescence results compare favourably with those obtained with the gel retardation method. DNA footprinting using exonucleaseIII and DNaseI, and methylation interference show no asymmetry, with both DNA strands being protected by the dimer and the trimer. This indicates that the dimer is a mixture of the two possible forms, M1S1 and S1M1. The dimer has a footprint on the DNA substrate of the same length as the trimer implying that the modification subunits are located on either side of the DNA helical axis rather than lying along the helical axis.

Synthesis and characterisation of oligodeoxynucleotides containing thio analogues of (6-4) pyrimidine-pyrimidinone photo-dimers.

A method for the preparation of an oligodeoxynucleotide, 20 bases in length, containing centrally located thio analogues of (6-4) pyrimidine-pyrimidinone thymine photo-dimers is reported. The approach is based on the selective irradiation, at 350 nm, of a Tp4ST (4ST = 4-thiothymidine) step within a 20-mer having the sequence: d(ACTCGGACCT(4sT)CGCTGTGAT). Conversion of the S5-(6-4)/S5-thietane pyrimidine-pyrimidinone, initially formed, to its S5-Dewar isomer is by a subsequent irradiation at 300 nm. Both of the photo-dimer-containing oligonucleotides were purified by HPLC (ion exchange and reverse phase) and characterised by base composition analysis. The S5-(6-4)/S5-thietane pyrimidine-pyrimidinone containing 20-mer has a characteristic UV absorbance at 320 nm and exhibits strong fluorescence when excited at this wavelength. As expected, conversion to the S5-Dewar isomer abolished both the 320 nm absorbance and the fluorescence emission. The lengths of the oligonucleotides produced allowed the formation of stable double-stranded DNA, by hybridisation to a complementary sequence. Examination of these duplexes by circular dichroism spectroscopy showed that they formed B-DNA, with little changes to their gross structure as compared to the parent duplex. However, local structural perturbations in the region of the photo-dimer cannot be excluded. The S5-(6-4)/S5-thietane photoproduct lowered the tm by 10.5 deg. C and the Dewar isomer by 12 deg. C. The degree of curvature induced in the DNA sequence by the introduction of the photo-dimers was assessed by analysing the migration of modified and unmodified multimer ladders on polyacrylamide gels. Both photoproducts induced considerable bending into the DNA. A comparison with a six-base-pair T tract, a bending standard that has a known bend angle of 19 degrees, gave values of around 47 degrees for the S5-(6-4)/S5-thietane product and about 28 degrees for the S5-Dewar isomer.