Fielding standardized patients in primary care settings: lessons from a study using unannounced standardized patients to assess preventive care practices

OBJECTIVES

To document detection and suspicion rates of unannounced standardized patients visiting community-based practices.

DESIGN

Primary care physicians were recruited to participate in a study using standardized patients. Four standardized patient scenarios were used.

SETTING

Community-based primary care physicians' practices in southern Ontario between September 1994 and August 1995.

STUDY PARTICIPANTS

Sixty-two primary care physicians.

MAIN OUTCOME MEASURES

A 'believability' questionnaire completed after all four standardized patients had visited the practices.

RESULTS

Of the primary care physicians approached, 50% (62) agreed to participate. Twenty-one per cent of all visits were suspected as standardized patient encounters. Forty-six per cent suspected one or more standardized patients. Only five physicians (8%) suspected all four standardized patients. Reasons for suspecting standardized patients were associated with the characteristics of the physician's practices, the physician's practice profile and the standardized patient cover story.

CONCLUSION

The portrayal of asymptomatic patients seeking a new primary care physician presents unique challenges. Carefully constructed cover stories, and detailed knowledge of the local area and of the practices of the participating physicians is required to allow standardized patients cases to be tailored to fit into primary care settings without arousing suspicion.

Crystal structure and evolution of a transfer RNA splicing enzyme

The splicing of transfer RNA precursors is similar in Eucarya and Archaea. In both kingdoms an endonuclease recognizes the splice sites and releases the intron, but the mechanism of splice site recognition is different in each kingdom. The crystal structure of the endonuclease from the archaeon Methanococcus jannaschii was determined to a resolution of 2.3 angstroms. The structure indicates that the cleavage reaction is similar to that of ribonuclease A and the arrangement of the active sites is conserved between the archaeal and eucaryal enzymes. These results suggest an evolutionary pathway for splice site recognition.

Evolution of a transfer RNA gene through a point mutation in the anticodon

The transfer RNA (tRNA) multigene family comprises 20 amino acid-accepting groups, many of which contain isoacceptors. The addition of isoacceptors to the tRNA repertoire was critical to establishing the genetic code, yet the origin of isoacceptors remains largely unexplored. A model of tRNA evolution, termed "tRNA gene recruitment," was formulated. It proposes that a tRNA gene can be recruited from one isoaccepting group to another by a point mutation that concurrently changes tRNA amino acid identity and messenger RNA coupling capacity. A test of the model showed that an Escherichia coli strain, in which the essential tRNAUGUThr gene was inactivated, was rendered viable when a tRNAArg with a point mutation that changed its anticodon from UCU to UGU (threonine) was expressed. Insertion of threonine at threonine codons by the "recruited" tRNAArg was corroborated by in vitro aminoacylation assays showing that its specificity had been changed from arginine to threonine. Therefore, the recruitment model may account for the evolution of some tRNA genes.

What factors influence primary care physicians' charges for their services? An exploratory study using standardized patients

OBJECTIVE

To determine the extent of variation in physicians' charges for health care encounters with unannounced standardized patients and factors associated with the variation.

DESIGN

Cross-sectional study.

SETTING

Family practices open to new patients within 1 hour's drive of Hamilton, Ont.

PARTICIPANTS

A stratified random sample of 125 physicians who had responded to an earlier survey regarding preventive care were invited to participate. Of the 125, 44 (35.2%) declined to participate, and an additional 19 (15.2%) initially consented but later withdrew because they closed their practices to new patients. Sixty-two physicians thus participated in the study.

INTERVENTION

Unannounced standardized patients posing as new patients to the practice visited study physicians' practices between September 1994 and August 1995, portraying 4 scenarios: 28-year-old woman, 52-year-old woman, 48-year-old man and 70-year-old man.

OUTCOME MEASURES

Physician characteristics, encounter characteristics and charges made for services.

RESULTS

The 62 physicians had 246 encounters with the standardized patients. Charges were made to the health insurance plan for services by 59 physicians for up to 4 encounters (215 encounters in all). Charges varied considerably both within and across patient scenarios. Time spent with the patient was an important factor predicting charges made (p < 0.01), although the effect of time spent on charges varied across scenarios (p < 0.01). Fee-for-service physicians charged more for their services than physicians who usually had alternative billing arrangements (p < 0.01). Female physicians charged more for their services than their male colleagues (p = 0.03). No relation was found between quality of preventive care and charges made (p = 0.15).

CONCLUSIONS

Physician-related factors are better able to account for the variability in charges for their services than patient-related factors. Physicians seeing comparable patients may earn much more or less than their colleagues because of differences in the services they provide and the way they apply the fee schedule. Quality-assurance techniques are likely needed to reduce the variability in charges seen and increase value for money spent in health care.

Provision of preventive care to unannounced standardized patients

OBJECTIVE

To examine the relation between physician, training and practice characteristics and the provision of preventive care as described in the guidelines of the Canadian Task Force on the Periodic Health Examination.

DESIGN

Cross-sectional study.

SETTING

Family practices open to new patients within 1 hour's drive of Hamilton, Ont.

PARTICIPANTS

A total of 125 family physicians were randomly selected from respondents to an earlier preventive care survey. Of the 125, 44 (35.2%) declined to participate, and an additional 19 (15.2%) initially consented but later withdrew when they closed their practices to new patients. Sixty-two physicians thus participated in the study.

INTERVENTION

Unannounced standardized patients posing as new patients to the practice visited study physicians' practices between September 1994 and August 1995, portraying 4 scenarios: 48-year-old man, 70-year-old man, 28-year-old woman and 52-year-old woman.

OUTCOME MEASURES

Proportion of preventive care manoeuvres carrying grade A, B, C, D and E recommendations from the Canadian Task Force on the Periodic Health Examination that were performed, offered or advised. A standard score was computed based on the performance of grade A and B manoeuvres (good or fair evidence for inclusion in the periodic health examination) and the non-performance of grade D and E manoeuvres (fair or good evidence for exclusion from the periodic health examination).

RESULTS

Study physicians performed or offered 65.6% of applicable grade A manoeuvres, 31.0% of grade B manoeuvres, 22.4% of grade C manoeuvres, 21.8% of grade D manoeuvres and 4.9% of grade E manoeuvres. The provision of evidence-based preventive care was associated with solo (v. group) practice and capitation or salary (v. fee-for-service) payment method. Preventive care performance was unrelated to physician's sex, certification in family medicine or problem-based (v. traditional) medical school curriculum.

CONCLUSIONS

Preventive care guidelines of the Canadian Task Force on the Periodic Health Examination have been incompletely integrated into clinical practice. Research is needed to identify and reduce barriers to the provision of preventive care and to develop and apply effective processes for the creation, dissemination and implementation of clinical practice guidelines.

Site-specific deoxynucleotide substitutions in yeast U6 snRNA block splicing of pre-mRNA in vitro

We have identified 2'-hydroxyl groups of the U6 phosphate-ribose backbone which are required for reconstitution of splicing activity in U6-depleted yeast extract. To screen the 2'-hydroxyls of yeast U6 at nucleotides 39-88, spanning the conserved central domain, synthetic U6 RNAs were constructed with deoxyribonucleotides incorporated site specifically. Only four individual deoxynucleotide substitutions blocked splicing activity: dA51 (in the ACAGAG sequence), dA62 (next to the AGC triad), and dU70 and dC72 (both in the loop of the 3' intramolecular stem-loop). Native gel analysis revealed that these deoxy-substituted U6 RNAs were competent for assembly of spliceosomes. Interestingly, a 2'-O-methyl substituent at A51, A62, U70 or C72 did not inhibit splicing activity, indicating that the essential 2'-OH groups at these positions in U6 act as hydrogen bond acceptors or neutral coordinated ligands. The requisite 2'-hydroxyls at A62, U70 and C72 show both similarities and differences relative to the positions of essential 2'-hydroxyls of catalytic domain V of group II ribozymes. The identification of the essential 2'-hydroxyls at positions 62, 70 and 72 corroborates that the 3' intramolecular stem-loop in U6 plays an important role in pre-mRNA splicing.

The Saccharomyces cerevisiae Prp5 protein has RNA-dependent ATPase activity with specificity for U2 small nuclear RNA

The Saccharomyces cerevisiae protein Prp5 is a member of the "DEAD box" family of putative RNA-dependent ATPases and helicases. The protein was purified from Escherichia coli and determined to be an RNA-dependent ATPase. The ATPase activity is 7-fold more specific for full-length U2 than for any of the other small nuclear RNAs or nonspecific RNAs tested. An RNaseH assay in extracts was used to demonstrate that Prp5 mediates an ATP-dependent conformational change in the intact U2 small nuclear ribonucleoprotein. We propose that this conformational change makes the branch point pairing sequence of U2 RNA accessible for pairing with the intron allowing formation of the pre-spliceosome.

In vitro studies of the Prp9.Prp11.Prp21 complex indicate a pathway for U2 small nuclear ribonucleoprotein activation

Pre-mRNA splicing takes place on a large ribonucleoprotein particle, the spliceosome which contains the five small nuclear ribonucleoproteins (snRNPs), U1, U2, U4, U5, and U6. In Saccharomyces cerevisiae the mRNA splicing factors, Prp9, Prp11, and Prp21, are necessary for addition of the U2 snRNP to the pre-mRNA in an early step of spliceosome assembly. This paper describes a study of interactions between these proteins and their role in spliceosome assembly. The proteins were expressed in Escherichia coli. Prp9 and Prp11 were purified by metal affinity chromatography. Prp21 was purified using a solubilization/renaturation protocol. We have combined these separately purified proteins and present direct evidence of a Prp9.Prp11.Prp21 protein complex that is functional in in vitro splicing assays. Characteristics of this Prp9.Prp11.Prp21 complex were further investigated using proteins synthesized in vitro. In addition, we found that Prp9, Prp11, and Prp21 influence the structure of the U2 snRNP in a manner that alters the accessibility of the branch point pairing region of the U2 snRNA to oligonucleotide- directed RNaseH cleavage. We present a model, based on the data presented here and in the accompanying paper, for a combined role of Prp9, Prp11, Prp21, and Prp5 in activating the U2 snRNP for assembly into the pre-spliceosome.

In search of informed input: a systematic approach to involving the public in community decision making

Given the task of distributing scarce resources, decision makers are faced with the question of how to involve an increasingly threatened and disenfranchised public in decisions affecting their communities. This article introduces a systematic approach to public involvement in community decision-making and identifies key elements in the design of institutional driven public participation exercises. Examples are drawn from the health care system restructuring experiences of three Ontario communities.

Do female primary care physicians practise preventive care differently from their male colleagues?

OBJECTIVE

To assess whether female primary care physicians' reported coverage of patients eligible for certain preventive care strategies differs from male physicians' reported coverage.

DESIGN

A mailed survey.

SETTING

Primary care practices in southern Ontario.

PARTICIPANTS

All primary care physicians who graduated between 1972 and 1988 and practised in a defined geographic area of Ontario were selected from the Canadian Medical Association's physician resource database. Response rate was 50%.

MAIN OUTCOME MEASURES

Answers to questions on sociodemographic and practice characteristics, attitudes toward preventive care, and perceptions about preventive care behaviour and practices.

RESULTS

In general, reported coverage for Canadian Task Force on the Periodic Health Examination's (CTFPHE) A and B class recommendations was low. However, more female than male physicians reported high coverage of women patients for female-specific preventive care measures (i.e., Pap smears, breast examinations, and mammography) and for blood pressure measurement. Female physicians appeared to question more patients about a greater number of health risks. Often, sex of physician was the most salient factor affecting whether preventive care services thought effective by the CTFPHE were offered. However, when evidence for effectiveness of preventive services was equivocal or lacking, male and female physicians reported similar levels of coverage.

CONCLUSION

Female primary care physicians are more likely than their male colleagues to report that their patients eligible for preventive health measures as recommended by the CTFPHE take advantage of these measures.

Site-specific crosslinks of yeast U6 snRNA to the pre-mRNA near the 5' splice site

We have introduced a single photochemical crosslinking reagent into specific sites in the central domain of U6 to identify the sites that are in close proximity to the pre-mRNA substrate. Four distinct U6 snRNAs were synthesized with a single 4-thiouridine (4-thioU) at positions 46, 51, 54, and 57, respectively. Synthetic U6 RNA containing the 4-thioU modifications can functionally reconstitute splicing activity in cell-free yeast splicing extracts depleted of endogenous U6 snRNA. Upon photoactivation with UV (>300 nm), 4-thioU at position 46 forms crosslinks to pre-mRNA near the 5' splice site at nt +4, +5, +6, and +7 in the intron, whereas 4-thioU at position 51 crosslinks to the pre-mRNA at positions -2, -1, +1, +2, +3, and at the invariant G in the lariat intermediate. All crosslinks are dependent on the presence of ATP and the splicing substrate. The two crosslinks to the pre-mRNA from position 46 and 51 of U6 can also occur in prp2 heat-inactivated yeast splicing extracts blocked immediately prior to the first chemical step. Significantly, the crosslink from position 51 can undergo subsequent splicing when the mutant extract is complemented with functional Prp2 protein in a chase experiment, indicating that the crosslink reflects a functional interaction that is maintained during the first step. The crosslink to lariat intermediate appears when the mutant spliceosomes are complemented with functional Prp2 protein added exogenously. This experiment is a paradigm for future studies in which different mutant extracts are used to establish the stage in assembly at which particular RNA-RNA interactions defined by unique crosslinks occur.

Preventive care and barriers to effective prevention. How do family physicians see it?

OBJECTIVES

To assess how adequately family physicians think they are delivering preventive care and to examine barriers to providing preventive care.

DESIGN

Cross-sectional survey.

SETTING

Primary care medical practices in south-central Ontario.

PARTICIPANTS

Four hundred eighty family physicians and general practitioners who graduated from medical school between 1972 and 1988.

MAIN OUTCOME MEASURES

Satisfactory preventive care delivery versus self-assessed coverage of patients for 15 preventive maneuvers. Perceived reasons for lack of success in providing recommended preventive care.

RESULTS

For 10 of the 15 maneuvers, the proportion of physicians who regarded 90% or higher as satisfactory coverage was twice as great as the proportion who thought they provided that level of coverage. For 11 of the 15 maneuvers, most respondents reported coverage lower than the level they regarded as satisfactory. For six maneuvers, more than two thirds thought they provided less than satisfactory coverage. More than two thirds of respondents suggested these barriers to providing recommended preventive care: patient is healthy and does not visit; patient refuses, is not interested, or does not comply; no effective systems to remind patients to come in for preventive care; and priority given to presenting problem.

CONCLUSION

Many family physicians and general practitioners in south-central Ontario provide preventive care to their patients at lower levels than they consider satisfactory. They identified barriers to providing preventive services successfully; these barriers suggest approaches for improving care.

18S rRNA processing requires the RNA helicase-like protein Rrp3

We report the identification of a new gene, RRP3 (rRNA processing), which is required for pre-rRNA processing. Rrp3 is a 60.9 kDa protein that is required for maturation of the 35S primary transcript of pre-rRNA and is required for cleavages leading to mature 18S RNA. RRP3 was identified in a PCR screen for DEAD box genes. DEAD box genes are part of a large family of proteins homologous to the eukaryotic transcription factor elF-4a. Most of these proteins are RNA-dependent ATPases and some of them have RNA helicase activity. This is the third yeast DEAD box protein that has been shown to be involved in rRNA assembly, but the only one required for the processing of 18S RNA. Mutants of the two other putative helicases, Spb4 and Drsl, both show processing defects in 25S rRNA maturation. In strains where Rrp3 is depleted, 35S precursor RNA is improperly processed. Cleavage normally occurs at sites A0O, Al and A2, but in the Rrp3 depletion stain cleavage occurs between A2 and B1. Rrp3 has been purified to homogeneity and has a weak RNA-dependent ATPase activity which is not specific for rRNA.

HIV testing practices of primary care physicians: an Ontario survey

To determine whether physicians are knowledgeable about the risk factors associated with HIV and whether perceived testing practices coincide with testing guidelines, 1,236 physicians were surveyed about which patients they would recommend for HIV testing. A total of 480 usable responses were obtained (response rate of 50% of the eligible sample). Most would suggest testing to partners of intravenous drug users, patients who received blood transfusions between 1978 and 1985, homosexuals and bisexuals, and patients with more than two sexually transmitted diseases. Only 46.4% would suggest testing to patients with more than two sexual partners, and 65.8% would test anyone who asks. Other patients to whom physicians would recommend testing were listed by 16.2%. Logistic regression (F-step) was used to examine the relationship between physician characteristics and likelihood of recommending testing. As a rule, physicians are knowledgeable about the major risk factors and would recommend testing according to guidelines. However, there may be a difference between questionnaire responses and actual practice.

Does the community want devolved authority? Results of deliberative polling in Ontario

OBJECTIVE

To obtain and contrast the informed opinions of people in five decision-making groups that could have a role in devolved governance of health care and social services.

DESIGN

Deliberative polling.

SETTING

Three rural and three urban communities selected from the 32 areas covered by a district health council in Ontario.

PARTICIPANTS

A total of 280 citizens from five potential decision-making groups: randomly selected citizens, attendees at town-hall meetings, appointees to district health councils, elected officials and experts in health care and social services.

INTERVENTION

Participants' opinions were polled during 29 structured 2-hour meetings.

MAIN OUTCOME MEASURES

Participants' opinions on their personal willingness and their group's suitability to be involved in devolved decision making, desired type of decision-making involvement, information preferences, preferred areas of decision-making involvement and preferred composition of decision-making bodies.

RESULTS

Mean attendance at each meeting was 9.6 citizens. Although there were some significant differences in opinion among the five potential decision-making groups, there were few differences among citizens from different geographic areas. A total of 189 (72%) of people polled were personally willing to take on a role involving responsibility for overall decision-making, but far fewer thought that their group was suited to taking on responsibility (30%) or a consulting role (55%). Elected officials were the most willing (85% personally willing, 50% thought their group was suitable) and randomly selected citizens the least willing (60% personally willing, 17% thought their group was suitable) to take responsibility for overall decision making. Most citizens polled indicated less interest in involvement in specific types of decisions, except for planning and setting priorities, than in overall decision making. Only 24 participants (9%) rated their own group as suitable to take responsibility for raising revenue, 91 (33%) deemed their group suited to distribution of funds and 108 (39%) felt their group was suitable for management of services. People in all five groups ranked health care needs (mean rank 1.5 out of four options) as the most important and preferences (mean rank 3.6) as the least important information. They rated a combination body involving several community groups as the most suitable overall decision-making body (8.8 on 10-point scale). Participants favoured the representation of elected officials, the provincial government and experts on combination bodies responsible for the specific types of decisions. Overall, as the complexity of devolved decision making became clear, participants tended to assign authority to traditional decision makers such as elected officials, experts and the provincial government, but also favoured a consulting role for attendees at town-hall meetings (i.e., interested citizens).

CONCLUSION

There are significant differences among groups in the community in their willingness to be involved, desired roles and representation in devolved decision making on health care and social services in Ontario.

Specificity of Prp24 binding to RNA: a role for Prp24 in the dynamic interaction of U4 and U6 snRNAs

Prp24 was previously isolated as a suppressor of a cold-sensitive U4 mutation and is required for at least the first step of splicing in vitro. Our investigation of the in vitro RNA binding properties of the purified Prp24 protein shows that it binds preferentially to the U4/U6 hybrid snRNAs compared to other snRNAs. The interaction between Prp24 and the U4/U6 hybrid appears to involve two regions in the RNA: the 39-57 region of U6 and stem II of the U4/U6 hybrid. Interestingly, some U4 mutations, which destabilize stem II, increase the affinity of Prp24 for the U4/U6 RNAs compared to the wild type. This suggests that the binding of Prp24 to the U4/U6 RNAs may involve some destabilization of the RNA duplex. We also found that Prp24 can stimulate the annealing of U4 and U6, suggesting that Prp24 participates in both the formation and disassembly of the U4/U6 hybrid during splicing.

Reliability and clinical validity of UM-CIDI DSM-III-R generalized anxiety disorder

This is the first in a series of reports on the long-term test-retest reliability and procedural validity of the UM-CIDI, a modified version of the Composite International Diagnostic Interview used in the US National Comorbidity Survey (NCS). This report focuses on DSM-III-R Generalized Anxiety Disorder (GAD). The NCS administered the UM-CIDI to a nationally representative sample of 8098 respondents in the age range 15-54. A subsample of 36 respondents was subsequently selected for clinical reappraisal of GAD, consisting of reinterviewing by a clinical reappraisal interviewer who blindly readministered the GAD section of the UM-CIDI followed by an expanded version of the GAD section of the Structured Clinical Interview for DSM-III-R (SCID). The test-retest reliability of UM-CIDI/DSM-III-R lifetime GAD is Kappa = .53. When the requirement that the worries be excessive or unrealistic (A2) is removed, as in ICD-10 and partially in DSM-IV, reliability increases to Kappa = .78. The concordance between the baseline UM-CIDI diagnosis and the SCID diagnosis is Kappa = .35, while the cross-sectional concordance is Kappa = .47 (.66 when the Criterion A2 requirement is removed). Item-level analysis shows that lack of concordance between the UM-CIDI and the SCID is due largely to Criteria A2 and D. The A2 problem could be addressed either by deemphasizing the cognitive-evaluative component of GAD as in ICD-10, or by removing consideration of the term "unrealistic" from the criterion as in DSM-IV and more clearly specifying the meaning of the term "excessive". These options require further research on similarities and differences in risk factors, course, family history, and treatment response of more narrowly and broadly defined GAD. The Criterion D problem is due to lack of clarity in what constitutes a symptom occurring "often". This is clarified in DSM-IV. It is likely that this clarification will make it possible to develop more precisely structured questions to evaluate Criterion D in subsequent revisions of the UM-CIDI, resulting in improved reliability and validity.

Novel substrate specificity engineered in the arabinose binding protein

The L-arabinose binding protein (ABP) of Escherichia coli naturally binds L-arabinose and D-galactose with very high affinity and, with reduced affinity, a variety of other sugars that differ only at the C5 position of the pyranose ring. However, there are stringent specificity requirements at the 1, 2, 3 and 4 positions. Based on the high resolution crystallographic structure of the ligand-protein complex, remodelling of the binding pocket was attempted to shift the specificity towards C1-substituted galactosides. To create space in the vicinity of the reducing end of bound galactose, four residues, Lys10, Asp90, Thr147 and Leu145, have been mutated for residues with smaller side chains. Forty-seven mutants containing different combinations of these mutations were tested by fluorometry for their ability to bind methyl-beta-D-galactoside (met-beta-Gal) or iso-propyl-beta-D-thio-galactoside (IPTG). Two double-residue mutants carrying Ser at position 147 and Ala or Gly at position 90 appeared of particular interest for being able to bind met-beta-Gal or IPTG, respectively, and no longer galactose. Fluorescence experiments and molecular modelling indicate that the mode of binding of the new substrates to the mutant proteins might be similar to that of the natural ligands to wild-type ABP.

Is reasonable access what we want? Implications of, and challenges to, current Canadian policy on equity in health care

Considerations of equity in the context of health care systems are often related closely to the presence or level of prices incurred by users of health care services. Some politicians and commentators have suggested that the removal of user charges under the Canadian health care system has led to equal access to care. But it is not clear that the equity principle inferred from these claims corresponds to the equity goals of current Canadian health policy. In this article the authors identify the precise equity principle that lies behind current health policy in Canada and consider the extent to which that principle is reflected in the performance of the system. They then consider other approaches to equity in health care in the context of the stated objectives of Canadian health policy and identify the implications of pursuing reasonable access in future health policy. The authors suggest that the implications of the current equity goals have not been recognized by policy makers, and if they were to be recognized it is not clear that they would be acceptable to Canadian populations and/or policy makers. Moreover, some of the implications would appear to be incompatible with other stated objectives of public policy.

Four yeast spliceosomal proteins (PRP5, PRP9, PRP11, and PRP21) interact to promote U2 snRNP binding to pre-mRNA

We have analyzed the functions of several pre-mRNA processing (PRP) proteins in yeast spliceosome formation. Here, we show that PRP5 (a DEAD box helicase-like protein), PRP9, and PRP11 are each required for the U2 snRNP to bind to the pre-spliceosome during spliceosome assembly in vitro. Genetic analyses of their functions suggest that they and another protein, PRP21, act concertedly and/or interact physically with each other and with the stem-loop IIa of U2 snRNA to bind U2 snRNP to the pre-mRNA. Biochemical complementation experiments also indicate that the PRP9 and PRP11 proteins interact. The PRP9 and PRP11 proteins may be functioning similarly in yeast and mammalian cells. The requirement for ATP and the helicase-like PRP5 protein suggests that these factors might promote a conformational change (involving either the U1 or U2 snRNP) that is required for the association of U2 snRNP with the pre-mRNA.

Recognition of tRNA(Cys) by Escherichia coli cysteinyl-tRNA synthetase

A study of the recognition of tRNA(Cys) by Escherichia coli cysteinyl-tRNA synthetase using in vivo and in vitro methods was performed. All three anticodon nucleotides, the discriminator nucleotide (73), and some elements within the tertiary domain (the D stem/loop, the T psi C stem/loop, and the variable loop) are important for recognition; the anticodon stem and acceptor stem appear to contain no essential elements. A T7 RNA polymerase transcript corresponding to tRNA(Cys) is only a 5.5-fold worse substrate than native tRNA(Cys) (in terms of the specificity constant, kcat/Km), mainly due to an increase in the value of Km for the transcript. The greatest loss of specificity caused by mutation of a single nucleotide occurs when the discriminator U73 is changed; kcat/Km declines 3-4 orders of magnitude depending on the substitution. Mutations in the wobble nucleotide of the anticodon also cause reductions in the specificity constant of 3 orders of magnitude, while mutations in the other anticodon nucleotides caused lesser effects. Interestingly, a C35A mutation (with the phenylalanine anticodon GAA) had no effect on aminoacylation by the cysteinyl-tRNA synthetase. Several amber suppressor tRNAs were constructed whose in vivo identity did not correlate with their in vitro specificity, indicating the need for both types of experiments to understand the factors which maintain tRNA specificity.