Midterm results of modular hinge total knee arthroplasty using cementless osseointegrating stems: low fixation associated complications and good functional outcome in primary and revision knee arthroplasty.

PURPOSE: This study aimed to investigate functional outcome and complications after primary and revision modular H-TKA using hybrid fixation with cementless stems. METHODS: Between 2015 and 2018, 48 patients with 50 implants were included after hybrid implantation of a single design H-TKA system using cementless osseointegrating stems and modular components. Complications and clinical outcome were analysed using Knee Society Score (KSS), the Western Ontario McMasters Universities Osteoarthritis Index (WOMAC) and the Short-Form Health Survey 12 (SF-12) score. RESULTS: Indications for implantation were aseptic revision (n = 29, 58%), primary TKA (n = 19, 38%) and two-stage septic revisions (n = 2, 4%). Complications were reported in 26% (n = 12), whereas complications associated with hybrid fixation occurred in 5 (10%) cases, with 2 (4%) requiring revision surgery for aseptic loosening and 3 (6%) treated with an adapted postoperative protocol for perioperative fractures. Implant survivorship was 84% after a mean follow-up of 54 months. Postoperative KSS significantly improved from 51.50 (12-100) to 78.36 (41-99; p < 0.001). The mean WOMAC score was 19.26 (0-55), SF-12 PCS was 41.56 points (22.67-57.66) and SF-12 MCS was 49.21 points (23.87-63.21). CONCLUSION: Hybrid modular implantation in H-TKA provides satisfactory clinical and functional results in primary and revision TKA. Clinical outcomes significantly improve with reduced pain, increased mobility, and good-to-excellent functional scores after implantation. Whilst implant survival is comparable to previous studies and complications associated with hybrid fixation are low, general complication rates are comparably high.

The optimal diagnostic cut-off of WBC and PMN counts for joint aspiration in periprosthetic joint infection is 2479/µL and 67%, respectively: ICM criteria thresholds are too high.

BACKGROUND: Various organizations have published definitions for periprosthetic joint infection (PJI) with significant differences in the cut-offs of white blood cell (WBC) count and polymorphonuclear (PMN) leukocyte cells. Herein, we aim to analyze optimal cut-offs in patients which are planned to undergo a prosthesis revision and compare them with the actual published thresholds of the International Consensus Meeting (ICM) and European Bone and Joint Infection Society (EBJIS). METHODS: A test kit was compiled in a monocentric prospective study, according to the ICM criteria (2018) and 2021 EBJIS criteria. The kit was implemented using: blood samples (including leukocyte count and C-reactive protein); samples for examining the synovial fluid (WBC count, PMN cell differentiation, microbiological culture for incubation over 14 days, alpha-defensin ELISA laboratory test, and leukocyte-esterase test). The cut-offs for WBC and PMN counts were investigated using ROC analyses and Youden index. The ICM 2018 criteria were applied, using alpha-defensin in all cases. Patients which have to undergo a prosthesis revision were included, a pre-operative joint aspiration had been performed, and the patients had been followed up prospectively. RESULTS: 405 patients were examined with the compiled test kit; 100% had a complete dataset with respect to alpha-defensin; 383 patients, according to WBC count; and 256, according to PMN cell differentiation The cut-off of 2478.89 cells/µl in the WBC count (sensitivity: 87.70%; specificity: 88.10%) and the cut-off of 66.99% in PMN differentiation showed the best accuracy (sensitivity: 86.00%; specificity: 88.80%). Other published cut-offs for WBC were tested in this cohort and showed the following accuracy: 3000/µl (EBJIS/ICM; sensitivity: 82.10%; specificity: 91.00%), 2000/µl (sensitivity: 89.60%; specificity: 83.40%), and 1500/µl (sensitivity: 91.50%; specificity: 75.00%). The published cut-offs for PMN had the following accuracy in this cohort: 80% (ICM; sensitivity: 66.3%; specificity: 96.50%), 70% (sensitivity: 82.6%; specificity: 90%), and 65% (EBJIS, sensitivity: 86%; specificity: 88.8%). CONCLUSIONS: This study aims to improve current cut-offs for PMN- and WB-Count, even though PJI diagnosis is based on the combination of all defined tests. The optimal diagnostic cut-off of WBC and PMN counts was found to be 2479/µL and 67%, respectively, whereas ICM cut-offs in this cohort seem too high, as they provide high specificity but very low sensitivity. On the other hand, a cut-off for WBC count of 1500/µl alone would be very low, leading to low specificity and very high suspicion of PJI. The current consensus guidelines could be actualized considering these results to significantly improve the diagnostic quality. LEVEL OF EVIDENCE: II.

[Implementation of a standardized clinical test kit for diagnostics of periprosthetic infections in the clinical routine. German version]. / Implementierung eines standardisierten Test-Kits zur Diagnostik von periprothetischen Infektionen in der klinischen Routine.

BACKGROUND: The number of primary arthroplasties is increasing and the proportion of revision arthroplasties is becoming increasingly more important. The need for standardized and guideline-based diagnostics for the safe detection of a periprosthetic joint infection (PJI) is becoming apparent. In the past 10 years various organizations have published definitions and diagnostic guidelines. The implementation of an inhouse standard test kit could help to simplify the process and could improve the diagnostic quality. METHOD: In 2016 a test kit was compiled in a monocentric prospective study, taking the International Consensus Meeting (ICM) criteria 2014 and the Infectious Diseases Society of America (IDSA) criteria into account, which also fulfils the definitions of the ICM criteria 2018 and criteria of the European Bone and Joint Infection Society 2021. The test kit was implemented in the clinical setting of a special department for aseptic and septic revision arthroplasty. The usability and accuracy of the test kit were examined. RESULTS: The test kit was implemented using blood samples (leukocyte count; C­reactive protein, CRP), samples for examining the synovial fluid (white blood cell count, PMN cell differentiation, microbiological culture for incubation over 14 days, alpha-defensin enzyme-linked immunosorbent assay, ELISA, leukocyte esterase test strips) together with information and request forms. Between April 2016 and February 2020 a total of 405 patients were investigated. Within 3 calendar years, the use of the test kit increased from 59% initially to 86%, and finally to 96% of cases in the third calendar year. The leukocyte esterase test strip was reliable in only 72%, due to undifferentiated readability or blood contamination. The costs increased by the only commercially available alpha-defensin ELISA test by approx. 52€ per puncture. The best individual test showed a sensitivity/specificity of 92.8%/95.2% with alpha-defensin. It was calculated which combinations showed a similar test quality and different combinations, such as CRP+ cell count+ microbiology showed a sensitivity/specificity both of around 90%. Metallosis is a challenge for preoperative PJI diagnostics. DISCUSSION: In a prospective study it was shown, that the implementation of the standardized test kit lead to a guideline based PJI diagnostic in all cases and thus to a significantly increase of the diagnostic quality. There is currently no single test that reliably excludes or proves an infection. The alpha-defensin laboratory ELISA test showed the best test accuracy, whereby the consideration of test combinations is obligatory and at the same time safe.

Modular knee arthrodesis secures limb, mobility, improves quality of life, and leads to high infection control in periprosthetic knee infection, when revision knee arthroplasty is not an option.

INTRODUCTION: This study compared the outcome of knee arthrodesis versus hinged total knee arthroplasty (TKA) in patients suffering from periprosthetic joint infection (PJI). METHODS: 104 patients with PJI were treated using a two-stage exchange of failed TKA. In case of non reconstructable bone loss or loss of extension mechanism, a modular intramedullary arthrodesis nail was used for reimplantation [Knee Arthrodesis Module (KAM); n = 52]. The control group was retrospectively matched treated using a hinged revision TKA [Rotating Hinge Knee (RHK); n = 52]. PJI remission rates, functional outcome (WOMAC; KSS) and quality of life (SF-12), as well as comorbidities and pain were evaluated. RESULTS: Mean age was 72.5 years. Charlson Comorbidity Index was higher in the KAM group (3.3 vs. 2.8). PJI remission rate was 89.4% (88.5% vs. 90.4%, respectively). In case of reinfection, implant retention was mostly possible in the RHK group (7.7%), whereas amputations were mostly performed in the KAM group (9.6%). Significant pain reduction (VAS 7.9-2.8) was achieved in both groups. Walking distance was significantly reduced in the KAM groups versus the RHK group (504 vs. 1064 m). WOMAC and KSS function scores were significantly reduced in the KAM group (25 vs. 40 and 35 vs. 64). Only moderate reduction in quality of life in the KAM group was observed (SF-12 physical: 34 vs. 40; SF-12 mental: 51 vs. 56) respectively. CONCLUSIONS: Arthrodesis using a modular intramedullary nail is an alternative for limb salvage, pain reduction, and preservation of quality of life and everyday mobility, when revision TKA is not an option. This study presents the largest number of case, comparing the outcome after performing an arthrodesis versus hinged TKA after septic failed TKA.

Implementation of a standardized clinical test kit for diagnostics of periprosthetic infections in the clinical routine.

BACKGROUND: The number of primary arthroplasties is increasing and the proportion of revision arthroplasties is becoming increasingly more important. The need for standardized and guideline-based diagnostics for the safe detection of a periprosthetic joint infection (PJI) is becoming apparent. In the past 10 years various organizations have published definitions and diagnostic guidelines. The implementation of an inhouse standard test kit could help to simplify the process and could improve the diagnostic quality. METHOD: In 2016 a test kit was compiled in a monocentric prospective study, taking the International Consensus Meeting (ICM) criteria 2014 and the Infectious Diseases Society of America (IDSA) criteria into account, which also fulfils the definitions of the ICM criteria 2018 and criteria of the European Bone and Joint Infection Society 2021. The test kit was implemented in the clinical setting of a special department for aseptic and septic revision arthroplasty. The usability and accuracy of the test kit were examined. RESULTS: The test kit was implemented using blood samples (leukocyte count; C­reactive protein, CRP), samples for examining the synovial fluid (white blood cell count, PMN cell differentiation, microbiological culture for incubation over 14 days, alpha-defensin enzyme-linked immunosorbent assay, ELISA, leukocyte esterase test strips) together with information and request forms. Between April 2016 and February 2020 a total of 405 patients were investigated. Within 3 calendar years, the use of the test kit increased from 59% initially to 86%, and finally to 96% of cases in the third calendar year. The leukocyte esterase test strip was reliable in only 72%, due to undifferentiated readability or blood contamination. The costs increased by the only commercially available alpha-defensin ELISA test by approx. 52€ per puncture. The best individual test showed a sensitivity/specificity of 92.8%/95.2% with alpha-defensin. It was calculated which combinations showed a similar test quality and different combinations, such as CRP+ cell count+ microbiology showed a sensitivity/specificity both of around 90%. Metallosis is a challenge for preoperative PJI diagnostics. DISCUSSION: In a prospective study it was shown, that the implementation of the standardized test kit lead to a guideline based PJI diagnostic in all cases and thus to a significantly increase of the diagnostic quality. There is currently no single test that reliably excludes or proves an infection. The alpha-defensin laboratory ELISA test showed the best test accuracy, whereby the consideration of test combinations is obligatory and at the same time safe.

Salvage procedure for chronic periprosthetic knee infection: the application of DAIR results in better remission rates and infection-free survivorship when used with topical degradable calcium-based antibiotics.

PURPOSE: Debridement, systemic antibiotics and implant retention (DAIR) is very successful for early periprosthetic joint infection (PJI), but can fail in late-onset cases. We selected patients with PJI who were unsuitable for two-stage exchange total knee arthroplasty (TKA) and compared the outcomes of DAIR with or without degradable calcium-based antibiotics. METHODS: All patients fulfilled the criteria for late-onset PJI of TKA, as defined by an International Consensus Meeting in 2013, but were unsuitable for multistage procedures and TKA exchange due to operative risk. Fifty-six patients (mean age: 70.6 years, SD ± 10.8), in two historical collectives, were treated using a single-stage algorithm consisting of DAIR without antibiotics (control group, n = 33, 2012-2014), or by DAIR following the implantation of degradable antibiotics as indicated by an antibiogram (intervention group, n = 23, 2014-2017). OSTEOSET® (admixed vancomycin/tobramycin), and HERAFILL-gentamicin® were used as carrier systems. The primary endpoint was re-infection or surgical intervention after DAIR. RESULTS: There were no significant differences between the two groups in terms of mean age, Charlson comorbidity index or the rate of mixed infections. Overall, 65.2% of patients achieved remission in the intervention group compared with only 18.2% in the control group (p < 0.001); 50% of re-infections in the intervention group even occurred after 36 months. Kaplan-Meier analysis showed that, compared with controls, the intervention group experienced significantly longer 3-year infection-free survival. CONCLUSION: DAIR shows poor efficacy in difficult-to-treat cases, as demonstrated in our control group, which had a re-infection rate of 81.8%. In contrast, a DAIR group receiving topical calcium-based antibiotics showed significantly higher 3-year infection-free survival. Therefore, the combination of DAIR and degradable antibiogram-based local antibiotics is a reasonable salvage procedure for this body of patients. This is important as the number of severely sick patients who are too old for appropriate PJI treatment is estimated to increase significantly due to demographic change.

Involvement of histone H1 in the organization of the nucleosome and of the salt-dependent superstructures of chromatin.

We describe the results of a systematic study, using electron microscopy, of the effects of ionic strength on the morphology of chromatin and of H1-depleted chromatin. With increasing ionic strength, chromatin folds up progressively from a filament of nucleosomes at approximately 1 mM monovalent salt through some intermediate higher-order helical structures (Thoma, F., and T. Koller, 1977, Cell 12:101-107) with a fairly constant pitch but increasing numbers of nucleosomes per turn, until finally at 60 mM (or else in approximately 0.3 mM Mg++) a thick fiber of 250 A diameter is formed, corresponding to a structurally well-organized but not perfectly regular superhelix or solenoid of pitch approximately 110 A as described by Finch and Klug (1976, Proc. Natl. Acad. Sci. U.S.A. 73:1897-1901). The numbers of nucleosomes per turn of the helical structures agree well with those which can be calculated from the light-scattering data of Campbell et al. (1978, Nucleic Acids Res. 5:1571-1580). H1-depleted chromatin also condenses with increasing ionic strength but not so densely as chromatin and not into a definite structure with a well-defined fiber direction. At very low ionic strengths, nucleosomes are present in chromatin but not in H1-depleted chromatin which has the form of an unravelled filament. At somewhat higher ionic strengths (greater than 5 mM triethanolamine chloride), nucleosomes are visible in both types of specimen but the fine details are different. In chromatin containing H1, the DNA enters and leaves the nucleosome on the same side but in chromatin depleted of H1 the entrance and exit points are much more random and more or less on opposite sides of the nucleosome. We conclude that H1 stabilizes the nucleosome and is located in the region of the exit and entry points of the DNA. This result is correlated with biochemical and x-ray crystallographic results on the internal structure of the nucleosome core to give a picture of a nucleosome in which H1 is bound to the unique region on a complete two-turn, 166 base pair particle (Fig. 15). In the formation of higher-order structures, these regions on neighboring nucleosomes come closer together so that an H1 polymer may be formed in the center of the superhelical structures.

Capturing the structure of a catalytic RNA intermediate: the hammerhead ribozyme.

The crystal structure of an unmodified hammerhead RNA in the absence of divalent metal ions has been solved, and it was shown that this ribozyme can cleave itself in the crystal when divalent metal ions are added. This biologically active RNA fold is the same as that found previously for two modified hammerhead ribozymes. Addition of divalent cations at low pH makes it possible to capture the uncleaved RNA in metal-bound form. A conformational intermediate, having an additional Mg(II) bound to the cleavage-site phosphate, was captured by freeze-trapping the RNA at an active pH prior to cleavage. The most significant conformational changes were limited to the active site of the ribozyme, and the changed conformation requires only small additional movements to reach a proposed transition-state.

Periodicity of deoxyribonuclease I digestion of chromatin.

Two methods have been used to measure the single-strand lengths of the DNA fragments produced by deoxyribonuclease I digestion of chromatin. The average lengths obtained are muliples of about 10.4 bases, significantly different from the value of 10 previously reported. This periodicity in fragment lengths is closely related to the periodicity of the DNA double helix in chromatin, but the two values need not be exactly the same.

Ribozymes: structure and mechanism in RNA catalysis.

The hammerhead RNA is a small catalytic RNA found in a number of RNA virus genomes and virus-like RNAs. The recently determined crystal structures of hammerhead ribozymes reveal how a small RNA motif can fold up into a conformation suitable for mediating RNA cleavage.

Granzyme K: a novel mediator in acute airway inflammation.

BACKGROUND: Granzymes are a subfamily of serine proteases involved in the pathogenesis of many inflammatory disorders. In contrast with granzyme A and B, the role of granzyme K (GrK) in human lung diseases is unknown. Therefore, the release and expression of GrK in allergic asthma, chronic obstructive pulmonary disease (COPD) and bronchopneumonia were investigated. METHODS: Soluble GrK was quantified using an enzyme linked immunosorbent assay in the bronchoalveolar lavage fluid of patients with allergic asthma (before and after segmental allergen challenge), and in patients with mild COPD, pneumonia and in healthy controls. The molecular form of GrK was analysed by western blot. Flow cytometry was performed to determine the cellular expression of GrK. RESULTS: Compared with healthy controls, there were normal levels of soluble GrK in the bronchoalveolar lavage fluid of patients with COPD, and patients with allergic asthma before allergen challenge. In contrast, soluble GrK was strongly increased in the bronchoalveolar lavage fluid of patients with acute bronchopneumonia. In patients with allergic asthma, there was a significant increase in soluble GrK as well as in GrK expressing CD8(+) T cells in the bronchoalveolar lavage fluid 24 h and 72 h after allergen challenge. After allergen challenge, soluble GrK correlated with the percentage of GrK expressing CD8(+) T cells. Finally, it was shown that the endobronchial release of the CCR5 ligand CCL3 might be a mechanism for the recruitment of GrK(+)CD8(+) T cells after allergen challenge. CONCLUSION: These data provide the first evidence that expression of GrK is upregulated in acute airway inflammation, both in infectious and non-infectious diseases.

Physical basis of a protein-DNA recognition code.

Can a stereochemical recognition code explain sequence-specific protein-nucleic acid interactions? Whereas a code that is generally applicable to DNA-binding proteins of all known structural families is unattainable, the indications are that a code can describe at least some of the interactions of classical zinc fingers with DNA. The crystal structures of related zinc finger-DNA complexes reveal a remarkable mode of interaction that sets the framework for this code, and recent biochemical studies have elucidated the intermolecular contacts (contingent on this framework) that result in specificity.

A rapid, generally applicable method to engineer zinc fingers illustrated by targeting the HIV-1 promoter.

DNA-binding domains with predetermined sequence specificity are engineered by selection of zinc finger modules using phage display, allowing the construction of customized transcription factors. Despite remarkable progress in this field, the available protein-engineering methods are deficient in many respects, thus hampering the applicability of the technique. Here we present a rapid and convenient method that can be used to design zinc finger proteins against a variety of DNA-binding sites. This is based on a pair of pre-made zinc finger phage-display libraries, which are used in parallel to select two DNA-binding domains each of which recognizes given 5 base pair sequences, and whose products are recombined to produce a single protein that recognizes a composite (9 base pair) site of predefined sequence. Engineering using this system can be completed in less than two weeks and yields proteins that bind sequence-specifically to DNA with Kd values in the nanomolar range. To illustrate the technique, we have selected seven different proteins to bind various regions of the human immunodeficiency virus 1 (HIV-1) promoter.

Stabilization of the tertiary structure of yeast phenylalanine tRNA by [Co(NH3)6]3+. X-ray evidence for hydrogen bonding to pairs of guanine bases in the major groove.

The sites of three [Co(NH3)6]3+ ions bound to the phenylalanine tRNA of yeast have been determined by X-ray diffraction analysis. [Co(NH3)6]3+ binds to purine-purine sequences in yeast tRNA Phe. It is different from the binding fo Co2+, which binds to the base and phosphate of residue G15. There are no direct metal-nucleotide bonds, although hydrogen bonding of the coordinated ammines to double-helical guanylguanosine sequences in the major groove and to phosphate oxygen in neighboring polynucleotide strands increases the stability of the structure. Hydrogen-bonding appears to be via cis ammine ligands to N(7) and O(6) positions of adjacent purine bases.

Towards therapeutic applications of engineered zinc finger proteins.

It has long been the goal of molecular biologists to design DNA-binding proteins for the specific control of gene expression. The zinc finger design is ideally suited for such purposes, discriminating between closely related sequences both in vitro and in vivo. Whereas other DNA-binding proteins generally make use of the 2-fold symmetry of the double helix, zinc fingers do not and so can be linked linearly in tandem to recognize DNA sequences of different lengths, with high fidelity. This modular design offers a large number of combinatorial possibilities for the specific recognition of DNA. By fusing zinc finger peptides to repression or activation domains, genes can be selectively targeted and switched off and on. Several recent applications of such engineered zinc finger proteins (ZFPs) are described, including the activation of vascular endothelial growth factor (VEGF) in a human cell line and an animal model. Clinical trials have recently begun on using VEGF-activating ZFPs to treat human peripheral arterial disease, by stimulating vascular growth. Also in progress are pre-clinical studies using ZFPs to target the defective genes in two monogenic disorders, SCID and SCA. The aim is to replace them in each case by a correct copy from an extrachromosomal DNA donor by means of homologous recombination. Promising results are reported.

Zinc finger peptides for the regulation of gene expression.

Zinc fingers are small DNA-binding peptide motifs that were discovered in this laboratory. These motifs can be used as modular building blocks for the construction of larger protein domains that recognise and bind to specific DNA sequences. Phage display has been used to create a large library of different zinc fingers from which selections were made for binding to a given DNA sequence. From this database there have been elucidated elements of recognition rules that relate the amino acid sequence of a finger to its preferred DNA binding site. Control of gene expression using designed zinc finger peptides has been demonstrated by the specific inhibition of an oncogene mouse cell line and also by switching on genes in expression plasmids. These experiments demonstrate that zinc finger DNA-binding domains can be engineered de novo to recognise given DNA sequences. Five to six individual zinc fingers linked together would recognise a DNA sequence 15-18 bp in length, sufficiently long to constitute a rare address in the human genome. By adding functional groups to the engineered DNA-binding domains, e.g. silencing domains, novel transcription factors can be generated to up- or downregulate expression of a target gene. Among potential applications are the repression of oncogene expression and the disruption of the reproductive cycle of virus infection.

Mapping of the sites of protection on a 5 S RNA gene by the Xenopus transcription factor IIIA. A model for the interaction.

The contact points of transcription factor IIIA with the internal control region of the 5 S RNA gene of Xenopus have been investigated by probing the accessibility of the DNA in the protein-DNA complex to dimethylsulphate and to micrococcal nuclease. The results of quantitative measurements, combined with those from earlier DNase I and DNase II protection studies, are consistent with a series of multiple contacts about five base-pairs apart, or half a double-helical turn, along the whole length of the internal control region. The nine patches of contact we have mapped could correspond to nine DNA-binding fingers in the protein. A model for the overall geometry of the interaction is presented in which the protein lies on one face of the DNA double helix.

Location of the primary sites of micrococcal nuclease cleavage on the nucleosome core.

The positions and relative frequencies of the primary cleavages made by micrococcal nuclease on the DNA of nucleosome core particles have been found by fractionating the double-stranded products of digestion and examining their single-stranded compositions. This approach overcomes the problems caused by secondary events such as the exonucleolytic and pseudo-double-stranded actions of the nuclease and, combined with the use of high resolution gel electrophoresis, enables the cutting site positions to be determined with a higher precision than has been achieved hitherto. The micrococcal nuclease primary cleavage sites lie close (on average, within 0.5 nucleotide) to those previously determined by Lutter (1981) for the nucleases DNase I and DNase II. These similarities show that the accessible regions are the same for all three nucleases, the cleavage sites being dictated by the structure of the nucleosome core. The differences in the final products of the digestion are explained in terms of secondary cleavage events of micrococcal nuclease. While the strongly protected regions of the nucleosome core DNA are common to all three nucleases, there are differences in the relative degrees of cutting at the more exposed sites characteristic of the particular enzyme. In particular, micrococcal nuclease shows a marked polarity in the 3'-5' direction in the cutting rates as plotted along a single strand of the nucleosomal DNA. This is explained in terms of the three-dimensional structure of the nucleosome where, in any accessible region of the double helix, the innermost strand is shielded by the outermost strand on the one side and the histone core on the other. The final part of the paper is concerned with the preference of micrococcal nuclease to cleave at (A,T) sequences in chromatin.

The role of the central zinc fingers of transcription factor IIIA in binding to 5 S RNA.

In the nine-zinc finger Xenopus transcription factor TFIIIA the central group of fingers, fingers 4 to 7, have been shown to bind to 5 S RNA. In this study, we have attempted to assess the role of this region of the TFIIIA molecule in more detail than hitherto. High-resolution footprinting by RNases A and CV1 has been used to probe the binding to 5 S RNA of three TFIIIA peptides Tf(1-6), Tf(4-6) and Tf(4-7), consisting of fingers 1 to 6, 4 to 6, and 4 to 7, respectively, and of full-length TFIIIA. The results pinpoint the outer margins of binding of the central fingers within helices IV and II of TFIIIA. A comparison of the footprints reveals that the presence of finger 7 affords protection at positions C19 and U55, the distal portion of helix II and the proximal portion of loop B. In addition, our footprints suggest that the central fingers bind in the same manner, whether in an isolated group or in the intact TFIIIA molecule. In a companion study, we have determined the binding affinities of Tf(4-6) and Tf(4-7) for full-length and three truncated 5 S RNA molecules, the latter selected on the basis of the regions of the 5 S RNA molecule known to be important in the binding of TFIIIA. The analysis uses only fully active protein involved in the binding and the results are consistent with the corresponding footprinting results. This is the first time that a detailed study of the binding site of one particular zinc finger to RNA has been reported; the results should be of use in the design of 5 S RNA molecules and TFIIIA peptides for structural studies of the interaction between zinc fingers and RNA.

Adjacent zinc-finger motifs in multiple zinc-finger peptides from SWI5 form structurally independent, flexibly linked domains.

Peptides containing either one, two or three of the three zinc-finger motifs from the yeast transcription factor SWI5 have been prepared by expression in Escherichia coli. The DNA binding characteristics of these peptides were investigated, and a two-dimensional nuclear magnetic resonance (n.m.r.) study undertaken to establish the three-dimensional structures of the two-finger peptide. The peptide containing fingers 1 and 2 binds sequence specifically to two thirds of the DNA binding site recognized either by intact SWI5 or by the isolated three-finger peptide, and hence has the correct tertiary fold for DNA recognition. These results also establish the polarity of DNA binding, since the N-terminal two fingers of SWI5 bind to the 5' end of the DNA binding site. Mild proteolysis of the three-finger peptide using trypsin results in a small number of discrete products, which is consistent with the presence of three structured mini-domains. Nearly complete n.m.r. signal assignments were obtained for two peptides containing finger 2 alone or fingers 1 + 2. Comparison of two-dimensional spectra of these peptides and others clearly shows that the NOE enhancements and chemical shifts characteristic of each finger are quite insensitive to the presence or absence of neighbouring fingers. This clearly indicates that adjacent zinc-finger domains are structurally independent in these peptides from SWI5. However, there must be some steric limitations on the possible relative orientations of the fingers, and to establish limits for these a set of structures for the peptide containing fingers 1 + 2 was calculated using the YASAP simulated annealing protocol in conjunction with n.m.r.-based constraints. A more detailed description of the three-dimensional structures of finger 1 and finger 2, and their relationship to other previously determined structures of single zinc-fingers, is given in the accompanying paper.