Isolation and characterization of monoclonal antibodies directed against subunits of human RNA polymerases I, II, and III

Human nuclei contain three different RNA polymerases: polymerases I, II, and III. Each polymerase is a multi-subunit enzyme with 12-17 subunits. The localization of these subunits is limited by the paucity of antibodies suitable for immunofluorescence. We now describe eight different monoclonal antibodies that react specifically with RPB6 (also known as RPA20, RPB14.4, or RPC20), RPB8 (RPA18, RPB17, or RPC18), RPC32, or RPC39 and which are suitable for such studies. Each antibody detects one specific band in immunoblots of nuclear extracts; each also immunoprecipitates large complexes containing many other subunits. When used for immunofluorescence, antibodies against the subunits shared by all three polymerases (i.e., RPB6, RPB8) gave a few bright foci in nucleoli and nucleoplasm, as well as many fainter nucleoplasmic foci; all the bright foci were generally distinct from speckles containing Sm antigen. Antibodies against the two subunits found only in polymerase III (i.e., RPC32, RPC39) gave a few bright and many faint nucleoplasmic foci, but no nucleolar foci. Growth in two transcriptional inhibitors-5, 6-dichloro-1-beta-d-ribofuranosylbenzimidazole and actinomycin D-led to the redistribution of each subunit in a characteristic manner.

Endoscopic partial inferior turbinoplasty

Endoscopic partial inferior turbinoplasty with a microdebrider has been introduced as an alternative to other inferior turbinectomy techniques for the treatment of nasal airway obstruction. Between June 1994 and December 1997, 100 patients underwent endoscopic partial inferior turbinoplasty. Concurrent septoplasty was performed in 81 patients, and functional endoscopic sinus surgery was performed in 43 patients. Synechiae formation in 12 patients was the most common complication and resolved in nearly all cases. Postoperative improvement in nasal patency occurred in 93% of the patients. In the 48 patients for whom preoperative subjective scores were available, a significant difference was noted when comparing preoperative and postoperative subjective and outcome scores of nasal patency (P < 0.0001). Patients with underlying allergy and chronic sinusitis tended to have lower outcome scores. Postoperative rhinomanometry was obtained in 21 patients and revealed a normalized mean total nasal resistance of 0.23 Pa/mL/second. This improved to 0. 17 Pa/mL/second with topical decongestion (P = 0.0029), revealing the retention of the turbinate mucosa's vasoactive capability. We conclude that endoscopic partial inferior turbinoplasty provides a good alternative to other inferior turbinectomy techniques and is associated with excellent outcomes and minimal morbidity.

Quantitation of RNA polymerase II and its transcription factors in an HeLa cell: little soluble holoenzyme but significant amounts of polymerases attached to the nuclear substructure

Various complexes that contain the core subunits of RNA polymerase II associated with different transcription factors have been isolated from eukaryotes; their precise molecular constitution depends on the purification procedure. We estimated the numbers of various components of such complexes in an HeLa cell by quantitative immunoblotting. The cells were lysed with saponin in a physiological buffer; approximately 140,000 unengaged polymerases (mainly of form IIA) were released. Only approximately 4,000 of these soluble molecules sedimented in glycerol gradients as holoenzyme-sized complexes. About 180,000 molecules of polymerases (approximately 110,000 molecules of form IIO) and 10,000 to 30,000 molecules of each of TFIIB, TFIIEalpha, TFIIEbeta, TFIIF-RAP74, TFIIF-RAP30, and TFIIH-MAT1 remained tightly associated with the nuclear substructure. Most proteins and run-on activity were retained when approximately 50% of the chromatin was detached with a nuclease, but approximately 45,000 molecules of bound TATA binding protein (TBP) were detached. Similar results were obtained after cross-linking living cells with formaldehyde. The results provide little support for the existence of a large pool of soluble holoenzyme; they are consistent with TBP-promoter complexes in nuclease-sensitive chromatin being assembled into preinitiation complexes attached to the underlying structure.

The organization of replication and transcription

Models for replication and transcription often display polymerases that track like locomotives along their DNA templates. However, recent evidence supports an alternative model in which DNA and RNA polymerases are immobilized by attachment to larger structures, where they reel in their templates and extrude newly made nucleic acids. These polymerases do not act independently; they are concentrated in discrete "factories," where they work together on many different templates. Evidence for models involving tracking and immobile polymerases is reviewed.

Regional specialization in human nuclei: visualization of discrete sites of transcription by RNA polymerase III

Mammalian nuclei contain three different RNA polymerases defined by their characteristic locations and drug sensitivities; polymerase I is found in nucleoli, and polymerases II and III in the nucleoplasm. As nascent transcripts made by polymerases I and II are concentrated in discrete sites, the locations of those made by polymerase III were investigated. HeLa cells were lysed with saponin in an improved 'physiological' buffer that preserves transcriptional activity and nuclear ultrastructure; then, engaged polymerases were allowed to extend nascent transcripts in Br-UTP, before the resulting Br-RNA was immunolabelled indirectly with fluorochromes or gold particles. Biochemical analysis showed that approximately 10 000 transcripts were being made by polymerase III at the moment of lysis, while confocal and electron microscopy showed that these transcripts were concentrated in only approximately 2000 sites (diameter approximately 40 nm). Therefore, each site contains approximately five active polymerases. These sites contain specific subunits of polymerase III, but not the hyperphosphorylated form of the largest subunit of polymerase II. The results indicate that the active forms of all three nuclear polymerases are concentrated in their own dedicated transcription sites or 'factories', suggesting that different regions of the nucleus specialize in the transcription of different types of gene.

Bridging the resolution gap: Imaging the same transcription factories in cryosections by light and electron microscopy

The resolution of conventional light microscopy is limited to approximately 200 nm in the x- and y-axes and >500 nm in the z-axis. A simple way of improving z-axis resolution is to analyze thin sections of 100-200 nm. The utility of such an approach is illustrated by reference to transcription sites imaged in cryosections of human nuclei. Cells are permeabilized, allowed to extend nascent transcripts in Br-UTP, fixed, cryosectioned, and Br-RNA-immunolabeled with fluorochromes and gold particles. As expected, physical sectioning improves resolution and brings other advantages. First, sections allow improved antibody access and better immunolabeling. Second, more sites (with a more representative range of intensities) can now be resolved against lower backgrounds, facilitating quantitative analysis. Third, problems associated with chromatic aberration when two differently colored images of the same objects are collected can be sidestepped by refocusing between image collection. Fourth, exactly the same sites can be imaged by light and electron microscopy, allowing direct comparison between the two techniques. Immunogold labeling and electron microscopy provided the most accurate counts of site number. The results confirm that nascent transcripts in the nucleoplasm are confined to several thousand sites, or "factories," with diameters of approximately 40 nm. (J Histochem Cytochem 47:471-480, 1999)

Direct imaging of DNA in living cells reveals the dynamics of chromosome formation

Individual chromosomes are not directly visible within the interphase nuclei of most somatic cells; they can only be seen during mitosis. We have developed a method that allows DNA strands to be observed directly in living cells, and we use it to analyze how mitotic chromosomes form. A fluorescent analogue (e.g., Cy5-dUTP) of the natural precursor, thymidine triphosphate, is introduced into cells, which are then grown on the heated stage of a confocal microscope. The analogue is incorporated by the endogenous enzymes into DNA. As the mechanisms for recognizing and removing the unusual residues do not prevent subsequent progress around the cell cycle, the now fluorescent DNA strands can be followed as they assemble into chromosomes, and segregate to daughters and granddaughters. Movies of such strands in living cells suggest that chromosome axes follow simple recognizable paths through their territories during G2 phase, and that late replicating regions maintain their relative positions as prophase chromosomes form. Quantitative analysis confirms that individual regions move little during this stage of chromosome condensation. As a result, the gross structure of an interphase chromosome territory is directly related to that of the prophase chromosome.

In vitro testing in pediatric food allergy

Food allergies are an important cause of morbidity in the pediatric population. We used a questionnaire to assess the value of in vitro testing in evaluating children for food allergy. The patient population was divided into two groups: those who tested positive (Class I or greater) for food allergy (combined food/inhalant allergy or food allergy alone) and those who tested negative for food allergy (inhalant only or negative test). Although we recognize that a significant proportion of food allergies may not be IgE-mediated, for the purposes of this study we considered a patient food allergy--positive if in vitro testing was positive and food allergy--negative if testing was negative. Thirty-eight of 77 patients tested (49%) were positive for food allergies. Those with food allergies did not have pretreatment scores significantly different from those of patients negative for food allergies (55 vs. 65, p = 0.11). Similarly, we detected no statistically significant difference between the symptom-improvement scores of the two groups (37 vs. 40, p = 0.57). We conclude that in vitro testing for food allergies is warranted in children with allergic symptoms, for several reasons: The prevalence of IgE-mediated food allergy in children may be higher than previously thought, and children with food allergies experience the same severity of symptoms as those without. It must be remembered that in vitro testing only detects IgE levels, and therefore a negative test does not mean that the patient does not have food allergies. However, when positive, in vitro testing gives the physician the opportunity to modify the treatment plan, helping avoid time-consuming and demanding oral food challenges. Our questionnaire also showed that food allergy and non-food allergy patients had similar pretreatment and posttreatment symptom scores.

The size of sites containing SR proteins in human nuclei. Problems associated with characterizing small structures by immunogold labeling

Some SR proteins are associated with eukaryotic transcripts as they move from synthetic sites (transcription "factories"), through downstream sites, to nuclear pores. Downstream sites can also be isolated as large nuclear ribonucleoprotein particles of approximately 200 S (diameter approximately 50 nm). In ultrathin sections of HeLa nuclei, indirect immunogold labeling with a specific antibody gives many small clusters of approximately 10 gold particles (diameter 50-80 nm). We gauged errors in estimating the diameter of underlying structures marked by immunogold probes (lengths approximately 20 nm). We examined systematically how probe dimensions affected cluster diameter. Probes contained one to three immunoglobulin molecules, sometimes a protein A molecule, and a gold particle of 5-15 nm. We found that (a) immunolabeling particles were tightly packed, (b) reducing particle size by 5 nm reduced cluster diameter by 10 nm, (c) reducing the number of immunoglobulins in the immunolabeling sandwich from three to two reduced cluster diameter by approximately 4 nm, (d) replacing the last immunoglobulin in a sandwich with protein A increased diameter by approximately 7 nm and led to a peripheral concentration of particles, and (e) increasing the number of layers in the sandwich increased sensitivity. Assuming that underlying structures had diameters of 50 nm, we find that errors ranged from -20% to +50%.

The path of transcripts from extra-nucleolar synthetic sites to nuclear pores: transcripts in transit are concentrated in discrete structures containing SR proteins

The route taken by transcripts from synthetic sites in the nucleus to the cytoplasm has been under scrutiny for years, but details of the pathway remain obscure. A new high-resolution method for mapping the pathway is described; HeLa cells are grown in Br-U so that the analogue is incorporated into RNA and exported to the cytoplasm, before Br-RNA is localized by immuno-electron microscopy. After exposure to low concentrations of Br-U for short periods, cells grow normally. Br-RNA is first found in several thousand extra-nucleolar transcription sites or factories (diameter 50–80 nm), before appearing in several hundred new downstream sites (diameter 50–80 nm) each minute; subsequently, progressively more downstream sites become labelled. These sites can be isolated on sucrose gradients as large nuclear ribonucleoprotein particles of approximately 200 S. Later, Br-RNA is seen docked approximately 200 nm away from approximately 20% nuclear pores, before exiting to the cytoplasm. Individual downstream sites are unlikely to contain individual transcripts; rather, results are consistent with groups of transcripts being shipped together from synthetic sites to pores. A subset of SR proteins are excellent markers of this pathway; this subset is concentrated in tens of thousands of sites, which include transcription, downstream and docking sites. Growth in high concentrations of Br-U for long periods is toxic, and Br-RNA accumulates just inside nuclear pores.

Numbers and organization of RNA polymerases, nascent transcripts, and transcription units in HeLa nuclei

Using HeLa cells, we have developed methods to determine 1) the number of RNA polymerases that are active at any moment, 2) the number of transcription sites, and 3) the number of polymerases associated with one transcription unit. To count engaged polymerases, cells were encapsulated in agarose, permeabilized, treated with ribonuclease, and the now-truncated transcripts extended in [32P]uridine triphosphate; then, the number of growing transcripts was calculated from the total number of nucleotides incorporated and the average increment in length of the transcripts. Approximately 15, 000 transcripts were elongated by polymerase I, and approximately 75,000 were elongated by polymerases II and III. Transcription sites were detected after the cells were grown in bromouridine for <2.5 min, after which the resulting bromo-RNA was labeled with gold particles; electron microscopy showed that most extranucleolar transcripts were concentrated in approximately 2400 sites with diameters of approximately 80 nm. The number of polymerases associated with a transcription unit was counted after templates were spread over a large area; most extranucleolar units were associated with one elongating complex. These results suggest that many templates are attached in a "cloud" of loops around a site; each site, or transcription "factory," would contain approximately 30 active polymerases and associated transcripts.

The safety of allergen immunotherapy: a literature review

Allergen immunotherapy is a safe form of therapy with a very low incidence of systemic allergic reactions and fatalities. Over the past few years, as a result of several investigations, risk factors have been identified, although some disagreement remains. Asthmatics, patients on beta-blockers and highly sensitive patients are groups at increased risk for systemic reactions. Reactions are more common among individuals receiving extracts of pollens, particularly grass and ragweed. Most authors have also reported that reactions are more common in season. Chest tightness or wheezing, urticaria, pruritus and throat congestion were frequent symptoms of severe systemic reactions. The recommendations of Greenburg et al (Table 1) and Davis et al (Table 2) serve as valuable guidelines. Otolaryngologic allergists have found that home maintenance immunotherapy is a safe treatment option (in low-risk patients). In any case, immunotherapy should be supervised by a physician well trained in its use and indications, and should be administered by personnel trained in the treatment of medical emergencies, specifically those related to allergy. This training should include cardiac resuscitation. In addition, consideration should be given to premedicating patients with antihistamines or corticosteroids and to measuring peak flows prior to injection. Because asthmatics are a very high-risk group, it is recommended that these patients not undergo immunotherapy at home. In patients who have had multiple reactions or in those with severe asthma, consideration should be given to discontinuing injections. Finally, optimal or moderate allergen dosing may provide the needed balance between therapeutic efficacy and safety.

Regional and temporal specialization in the nucleus: a transcriptionally-active nuclear domain rich in PTF, Oct1 and PIKA antigens associates with specific chromosomes early in the cell cycle

PTF (PSE-binding transcription factor) activates transcription of snRNA and related genes. We investigated its distribution in HeLa nuclei by immunofluorescence, and found it spread throughout the nucleoplasm in small foci. In some cells, PTF is also concentrated in one, or very few, discrete regions (diameter approximately 1.3 micron) that appear during G1 phase and disappear in S phase. Oct1, a transcription factor that interacts with PTF, is also enriched in these domains; RNA polymerase II, TBP and Sp1 are also present. Each domain typically contains 2 or 3 transcription 'factories' where Br-UTP is incorporated into nascent transcripts. Accordingly, we have christened this region the Oct1/PTF/transcription (OPT) domain. It colocalizes with some, but not all, PIKA domains. It is distinct from other nuclear domains, including coiled bodies, gemini bodies, PML bodies and the perinucleolar compartment. A small region on chromosome 6 (band 6p21) containing only approximately 30 Mbp DNA, and chromosomes 6 and 7, associate with the domain significantly more than other chromosomes. The domains may act like nucleoli to bring particular genes on specific chromosomes together to a region where the appropriate transcription and processing factors are concentrated, thereby facilitating the expression of those genes.

Diagnosing and Treating Pediatric Allergy

Allergy is a significant problem in as much as 60% of patients seeking care at an otolaryngologist's office. This raises the issue of the most effective means of diagnosing allergy, especially in pediatric patients, who often may not tolerate skin testing. The RAST and CAP (Pharmacia) tests have been shown to be quite comparable with skin testing in diagnosing allergy. This study was undertaken to assess the effectiveness of treatment of children with allergies who had undergone in vitro testing. This was done by obtaining subjective symptom scores both before and after treatment. These were obtained from patients with different in vitro results, including some with negative testing. Overall, 77 of 155 mailed questionnaires were returned. Results showed overall improvement of 38.81 points in 12 symptoms ( p = 0.001; n = 62). Each symptom was rated on a visual scale of 1 to 10. A small portion of the patient population received surgical treatment (tympanostomy tube placement with or without adenoidectomy) in addition to medical treatment and avoidance. These patients did not have significantly higher pretreatment scores and did not have a higher improvement rate for all symptoms. We believe this study shows the validity of in vitro testing and treatment of allergy in children.

Allergic rhinitis. Outcomes of immunotherapy on symptom control

Recent scientific studies have demonstrated the efficacy of various forms of immunotherapy for the treatment of allergic diseases. Traditional subcutaneous immunotherapy, sublingual, oral, and intranasal immunotherapy have been shown to significantly reduce symptoms and favorably modulate the immune response. Outcome studies that use patient response data from standardized surveys represent the next challenge to all practicing allergists.

Comparison of mRAST and CAP with skin end point titration for Alternaria tenuis and dermatophagoides pteronyssinus

There has been a recent explosion of new in vitro tests for the diagnosis of allergies. At present there is no general agreement on which type of in vitro test is best. Recently our hospital switched in vitro testing from the modified radioallergosorbent system (mRAST) to the Pharmacia CAP system (CAP). While changing in vitro testing techniques, 47 patients were tested with both the mRAST and CAP tests. Comparisons were made between the mRAST and CAP results of Alternaria tenuis and Dermatophagoides pteronyssinus allergens. These results were then compared with the results of patients who also underwent intradermal skin testing based on end point titration techniques.

Botryomycosis: improved therapy for a difficult infection

Botryomycosis is a chronic bacterial granulomatous disease often involving the skin and subcutaneous tissue. Head and neck involvement is rare. Botryomycosis presents with clinical and histological features similar to actinomycosis or mycetoma, but the causative organism is usually Staphylococcus aureus. Microscopically the organisms appear to be encapsulated in granules, which are thought to protect them from the effects of standard courses of antibiotics. Botryomycosis usually requires surgical intervention for cure. Major debilitating surgery has been required for most patients, because the infection has been unresponsive to seemingly appropriate medical therapy. We present an 8-month-old male with periorbital botryomycosis. Surgical specimens for diagnosis were obtained, but complete resection would have created debilitating functional and cosmetic defects. The lesion failed to respond to nafcillin alone or combination therapy with hyperbaric oxygen, but showed slow, steady improvement with long-term clindamycin. The patient has been disease free for more than 4 years, with minimal scarring and no functional impairment. Prolonged medical therapy for botryomycosis may be a viable alternative to the traditionally recommended surgical resection, thereby reducing cosmetic and functional morbidity.

The transcriptional basis of chromosome pairing

Pairing between homologous chromosomes is essential for successful meiosis; generally only paired homologs recombine and segregate correctly into haploid germ cells. Homologs also pair in some somatic cells (e.g. in diploid and polytene cells of Drosophila). How homologs find their partners is a mystery. First, I review some explanations of how they might do so; most involve base-pairing (i.e. DNA-DNA) interactions. Then I discuss the remarkable fact that chromosomes only pair when they are transcriptionally active. Finally, I present a general model for pairing based upon the DNA-protein interactions involved in transcription. Each chromosome in the haploid set has a unique array of transcription units strung along its length. Therefore, each chromatin fibre will be folded into a unique array of loops associated with clusters of polymerases and transcription factors; only homologs share similar arrays. As these loops and clusters, or transcription factories, move continually, they make and break contact with others. Correct pairing would be nucleated when a promoter in a loop tethered to one factory binds to a homologous polymerizing site in another factory, before transcription stabilizes the association. This increases the chances that adjacent promoters will bind to their homologs, so that chromosomes eventually become zipped together with their partners. Pairing is then the inevitable consequence of transcription of partially-condensed chromosomes.

Long-term outcome analysis of functional endoscopic sinus surgery: correlation of symptoms with endoscopic examination findings and potential prognostic variables

One hundred eighty-two patients were evaluated after functional endoscopic sinus surgery. The goal was to establish whether any anatomical finding correlated with symptoms and to find any historical predictors of symptomatic failure. Of all physical findings reviewed, only scarring of middle meatal antrostomy and scarring of the ethmoids approached significance in predicting poor outcome. Surprisingly, of the historical factors reviewed, only gastroesophageal reflux disease was statistically significant as a predictor of poor symptomatic outcome.

The localization of sites containing nascent RNA and splicing factors

Sites of transcription in the HeLa nucleus are not diffusely spread throughout euchromatin but are concentrated in approximately 2000 discrete sites or "transcription factories." These sites can be immunolabeled after allowing permeabilized cells to elongate nascent RNA chains in the presence of BrUTP. Splicing factors are also concentrated in a few tens of nuclear domains known as "speckles"; they are also more diffusely spread throughout euchromatin. As there has been some controversy whether the speckles are sites of transcription, we investigated the relative distributions of transcription factories and the speckles (detected using Sm autoimmune antibodies). We used conditions that minimize the redistribution of both the nascent RNA and the antigens during permeabilization and fixation and imaged the sites with high resolution using cryosections and a "confocal" microscope. The speckles contained little-if any-nascent RNA and so were usually not transcriptionally active, but they were often surrounded by a few transcription sites. Whether they are active sites of processing of RNA or merely sites where the machinery is stored remains to be established.

The topology of transcription by immobilized polymerases

Current models for RNA synthesis involve an RNA polymerase that tracks along a static template. However, research on chromatin loops suggests that the template slides past a polymerase immobilized in a large transcription factory. The evidence for immobilized polymerases is reviewed, and a model for transcription by such fixed enzymes is presented. According to the model, gene activation would involve reducing gene-factory distance and increasing the affinity of a promoter for a factory. Locus controlling regions and enhancers would attach to a factory and increase the chances that a promoter could bind to a polymerase; after transcriptional termination, the gene would detach from the factory. As some RNA processing occurs cotranscriptionally, processing sites are also likely to be associated with the factory.

Memory for musical tempo: additional evidence that auditory memory is absolute

We report evidence that long-term memory retains absolute (accurate) features of perceptual events. Specifically, we show that memory for music seems to preserve the absolute tempo of the musical performance. In Experiment 1, 46 subjects sang two different popular songs from memory, and their tempos were compared with recorded versions of the songs. Seventy-two percent of the productions on two consecutive trials came within 8% of the actual tempo, demonstrating accuracy near the perceptual threshold (JND) for tempo. In Experiment 2, a control experiment, we found that folk songs lacking a tempo standard generally have a large variability in tempo; this counters arguments that memory for the tempo of remembered songs is driven by articulatory constraints. The relevance of the present findings to theories of perceptual memory and memory for music is discussed.

Active RNA polymerases are localized within discrete transcription “factories' in human nuclei

Nascent transcripts in permeabilized HeLa cells were elongated by approximately 30–2,000 nucleotides in Br-UTP or biotin-14-CTP, before incorporation sites were immunolabelled either pre- or post-embedding, and visualized by light or electron microscopy. Analogues were concentrated in approximately 2,100 (range 2,000-2,700) discrete sites attached to a nucleoskeleton and surrounded by chromatin. A typical site contained a cluster (diameter 71 nm) of at least 4, and probably about 20, engaged polymerases, plus associated transcripts that partially overlapped a zone of RNA polymerase II, ribonucleoproteins, and proteins rich in thiols and acidic groups. As each site probably contains many transcription units, these results suggest that active polymerases are confined to these sites, which we call transcription ‘factories’. Results are consistent with transcription occurring as templates slide past attached polymerases, as nascent RNA is extruded into the factories.

Seasonal allergic rhinitis

Seasonal allergic rhinitis is the most well understood of the types of allergic rhinitides. The disease is characterized by sneezing, itching, rhinorrhea, and nasal congestion upon exposure to pollen allergens in susceptible individuals. These symptoms can cause considerable misery in affected patients. Recent advances in the diagnosis and treatment of this disorder as well as new insights into the pathophysiology of allergic rhinitis enable practitioners to provide more effective therapy.

The structure of 4-way DNA junctions: specific binding of bis-intercalators with rigid linkers

During replication and recombination, two DNA duplexes lie side by side. We have developed reagents that might be used to probe structure during these critical processes; they contain two intercalating groups connected by a rigid linker that forces those groups to point in opposite directions. If their stereochemistry proves appropriate, such structure-specific agents should intercalate specifically into adjacent duplexes in the Y- and X-shaped structures (i.e. 3- and 4-way junctions, now known as 3H and 4H junctions) found at replication and recombination sites. We prepared DNA structures in which four duplexes were arranged in all possible combinations around 2- and 4-way junctions and then probed the accessibility to DNase I of all their phosphodiester bonds. In the absence of any bis-intercalators, 7-9 nucleotides (nt) in each of the strands in 4-way junctions were protected from attack; protected regions were significantly offset to the 3' side of the junction in continuous strands, but only slightly offset, if at all, in exchanging strands. All the intercalators decreased accessibility throughout the structure, but none did so at specific points in the two adjacent arms of 4-way junctions. However, one bis-intercalator--but not its sister with a shorter linker--strikingly increased access to a particular CpT bond that lay 9 nt away from the centre of some 4-way junctions without reducing access to neighbouring bonds. Binding was both sequence and structure specific, and depended on complementary stereochemistry between bis-intercalator and junction.