Patient-based pre-classified real-time quality control (PCRTQC).

BACKGROUND: Patient-based real-time quality control (PBRTQC) has gained increasing attention in clinical laboratory management. Although its valuable characteristics complement traditional quality control measures, its performance and practical application have faced scrutiny. In this study, patient-based pre-classified real-time quality control (PCRTQC), an extended approach was devised to enhance real-time quality control protocols. METHODS: PCRTQC distinguishes itself by incorporating an additional patient pre-classification step utilising the OPTICS algorithm, thus addressing interference from diverse patient types. The complete set of patient test results obtained from a clinical chemistry analyser at The First Hospital of China Medical University in 2021 was utilised. Constant error (CE) and proportional error (PE) were introduced as analytical errors. Four analytes were selected to evaluate the PCRTQC, measuring probability for false rejection (Pfr) and the average number of patient samples until error detection (ANPed). Relevant error detection charts were generated. RESULTS: The PCRTQC outperformed regression-adjusted real-time quality control (RARTQC) based on the ANPed by approximately 50% for both the CE and PE, compared to the RARTQC, particularly for the total allowable error threshold. CONCLUSION: The pre-classification step effectively reduced inter-individual variation and improved data preprocessing, filtering, and modelling. The PCRTQC is a robust framework for real-time quality control research.

Effects of Using Different Indirect Techniques on the Calculation of Reference Intervals: Observational Study.

BACKGROUND: Reference intervals (RIs) play an important role in clinical decision-making. However, due to the time, labor, and financial costs involved in establishing RIs using direct means, the use of indirect methods, based on big data previously obtained from clinical laboratories, is getting increasing attention. Different indirect techniques combined with different data transformation methods and outlier removal might cause differences in the calculation of RIs. However, there are few systematic evaluations of this. OBJECTIVE: This study used data derived from direct methods as reference standards and evaluated the accuracy of combinations of different data transformation, outlier removal, and indirect techniques in establishing complete blood count (CBC) RIs for large-scale data. METHODS: The CBC data of populations aged ≥18 years undergoing physical examination from January 2010 to December 2011 were retrieved from the First Affiliated Hospital of China Medical University in northern China. After exclusion of repeated individuals, we performed parametric, nonparametric, Hoffmann, Bhattacharya, and truncation points and Kolmogorov-Smirnov distance (kosmic) indirect methods, combined with log or BoxCox transformation, and Reed-Dixon, Tukey, and iterative mean (3SD) outlier removal methods in order to derive the RIs of 8 CBC parameters and compared the results with those directly and previously established. Furthermore, bias ratios (BRs) were calculated to assess which combination of indirect technique, data transformation pattern, and outlier removal method is preferrable. RESULTS: Raw data showed that the degrees of skewness of the white blood cell (WBC) count, platelet (PLT) count, mean corpuscular hemoglobin (MCH), mean corpuscular hemoglobin concentration (MCHC), and mean corpuscular volume (MCV) were much more obvious than those of other CBC parameters. After log or BoxCox transformation combined with Tukey or iterative mean (3SD) processing, the distribution types of these data were close to Gaussian distribution. Tukey-based outlier removal yielded the maximum number of outliers. The lower-limit bias of WBC (male), PLT (male), hemoglobin (HGB; male), MCH (male/female), and MCV (female) was greater than that of the corresponding upper limit for more than half of 30 indirect methods. Computational indirect choices of CBC parameters for males and females were inconsistent. The RIs of MCHC established by the direct method for females were narrow. For this, the kosmic method was markedly superior, which contrasted with the RI calculation of CBC parameters with high |BR| qualification rates for males. Among the top 10 methodologies for the WBC count, PLT count, HGB, MCV, and MCHC with a high-BR qualification rate among males, the Bhattacharya, Hoffmann, and parametric methods were superior to the other 2 indirect methods. CONCLUSIONS: Compared to results derived by the direct method, outlier removal methods and indirect techniques markedly influence the final RIs, whereas data transformation has negligible effects, except for obviously skewed data. Specifically, the outlier removal efficiency of Tukey and iterative mean (3SD) methods is almost equivalent. Furthermore, the choice of indirect techniques depends more on the characteristics of the studied analyte itself. This study provides scientific evidence for clinical laboratories to use their previous data sets to establish RIs.

Reference intervals of 14 biochemical markers for children and adolescence in China: the PRINCE study.

OBJECTIVES: The Pediatric Reference Intervals in China (PRINCE) was initiated to establish the reference intervals (RIs) of Chinese children, as well as to make it possible to compare the variability of biochemical markers among countries internationally. METHODS: Healthy participants, aged up to 20 years, from 11 provinces across China, were enrolled in PRINCE and according to a standard screening procedure, that included a questionnaire survey, physical examinations and laboratory tests. Fasting venous blood specimens were collected. All serum specimens were analyzed with Cobas C702 in the center laboratory, i.e. clinical laboratory of Beijing Children's Hospital, with certified qualification (ISO15189). The nonparametric method recommended by Clinical Laboratory Standards Institute guidelines, was used to calculate the age- and sex-specified RIs. RESULTS: Among the 15,150 participants enrolled, 12,352 children (6,093 males and 6,259 females) were included to calculate RIs. The RIs for total protein, albumin, globulin, calcium, phosphate, potassium, sodium, chlorine, alkaline phosphatase, γ-glutamyl transpeptadase, alanine aminotransferase, aspartate aminotransferase, creatinine and urea were established by age- or sex-partitions. Most biochemical markers displayed larger variability and higher dispersion during the periods between 28 days and 1 year old, and included 4-6 age partitions commonly during 1 to <20 years old. In addition, differences of RIs between sexes usually occurs around the initiation of puberty at 12-13 years old. CONCLUSIONS: The age- and sex-specified RIs of 14 biochemical markers in PRINCE study can provide a solid reference, which will be transferred into relevant RIs for other clinical laboratory's platforms according to the CLSI guidelines.

The development of autoverification system of lymphocyte subset assays on the flow cytometry platform.

OBJECTIVES: Peripheral blood lymphocyte subsets are important parameters for monitoring immune status; however, lymphocyte subset detection is time-consuming and error-prone. This study aimed to explore a highly efficient and clinically useful autoverification system for lymphocyte subset assays performed on the flow cytometry platform. METHODS: A total of 94,402 lymphocyte subset test results were collected. To establish the limited-range rules, 80,427 results were first used (69,135 T lymphocyte subset tests and 11,292 NK, B, T lymphocyte tests), of which 15,000 T lymphocyte subset tests from human immunodeficiency virus (HIV) infected patients were used to set customized limited-range rules for HIV infected patients. Subsequently, 13,975 results were used for historical data validation and online test validation. RESULTS: Three key autoverification rules were established, including limited-range, delta-check, and logical rules. Guidelines for addressing the issues that trigger these rules were summarized. The historical data during the validation phase showed that the total autoverification passing rate of lymphocyte subset assays was 69.65% (6,941/9,966), with a 67.93% (5,268/7,755) passing rate for T lymphocyte subset tests and 75.67% (1,673/2,211) for NK, B, T lymphocyte tests. For online test validation, the total autoverification passing rate was 75.26% (3,017/4,009), with 73.23% (2,191/2,992) for the T lymphocyte subset test and 81.22% (826/1,017) for the NK, B, T lymphocyte test. The turnaround time (TAT) was reduced from 228 to 167 min using the autoverification system. CONCLUSIONS: The autoverification system based on the laboratory information system for lymphocyte subset assays reduced TAT and the number of error reports and helped in the identification of abnormal cell populations that may offer clues for clinical interventions.

Annual biological variation and personalized reference intervals of clinical chemistry and hematology analytes.

OBJECTIVES: A large number of people undergo annual health checkup but accurate laboratory criterion for evaluating their health status is limited. The present study determined annual biological variation (BV) and derived parameters of common laboratory analytes in order to accurately evaluate the test results of the annual healthcare population. METHODS: A total of 43 healthy individuals who had regular healthcare once a year for six consecutive years, were enrolled using physical, electrocardiogram, ultrasonography and laboratory. The annual BV data and derived parameters, such as reference change value (RCV) and index of individuality (II) were calculated and compared with weekly data. We used annual BV and homeostatic set point to calculate personalized reference intervals (RIper) which were compared with population-based reference intervals (RIpop). RESULTS: We have established the annual within-subject BV (CVI), RCV, II, RIper of 24 commonly used clinical chemistry and hematology analytes for healthy individuals. Among the 18 comparable measurands, CVI estimates of annual data for 11 measurands were significantly higher than the weekly data. Approximately 50% measurands of II were <0.6, the utility of their RIpop were limited. The distribution range of RIper for most measurands only copied small part of RIpop with reference range index for 8 measurands <0.5. CONCLUSIONS: Compared with weekly BV, for annual healthcare individuals, annual BV and related parameters can provide more accurate evaluation of laboratory results. RIper based on long-term BV data is very valuable for "personalized" diagnosis on annual health assessments.

A review on the biology and properties of adipose tissue macrophages involved in adipose tissue physiological and pathophysiological processes.

Obesity exhibits a correlation with metabolic inflammation and endoplasmic reticulum stress, promoting the progression of metabolic disease such as diabetes, hyperlipidemia, hyperuricemia and so on. Adipose tissue macrophages (ATMs) are central players in obesity-associated inflammation and metabolic diseases. Macrophages are involved in lipid and energy metabolism and mitochondrial function in adipocytes. Macrophage polarization is accompanied by metabolic shifting between glycolysis and mitochondrial oxidative phosphorylation. Here, this review focuses on macrophage metabolism linked to functional phenotypes with an emphasis on macrophage polarization in adipose tissue physiological and pathophysiological processes. In particular, the interplay between ATMs and adipocytes in energy metabolism, glycolysis, OXPHOS, iron handing and even interactions with the nervous system have been reviewed. Overall, the understanding of protective and pathogenic roles of ATMs in adipose tissue can potentially provide strategies to prevent and treat obesity-related metabolic disorders.

Determination of high-sensitivity cardiac troponin T upper reference limits under the improved selection criteria in a Chinese population.

BACKGROUND: There is no common consensus on how to define the reference population for determination of high-sensitivity cardiac troponin (hs-cTn) upper reference limit (URL). This study aimed to establish 99th percentile URLs of hs-cTnT under both 2018 AACC/IFCC criteria and improved selection criteria for further judging whether two URLs are different. METHODS: Applying the stratified cluster sampling protocol, this study took 1848 apparently healthy subjects in communities of Shenyang China as the screening objects. We first followed 2018 AACC/IFCC criteria using surrogate biomarker for diabetes, myocardial dysfunction, renal dysfunction, and electrocardiogram. Then, we followed improved selection criteria to exclude hypertension, overweight and obesity, and dyslipidemia by physical examination and laboratory screening. Accordingly, 99th percentile URLs of hs-cTnT were established. RESULTS: If the 2018 AACC/IFCC criteria were applied, 99th percentile URLs (90% confidence interval) of hs-cTnT male, female, and total were 19 (17-20) ng/L, 16 (15-17) ng/L, and 18 (16-19) ng/L, respectively. If added a single supplementary selection criteria, 99th percentile URLs of hs-cTnT total reduced to 16 ng/L, 17 ng/L, and 16 ng/L, respectively. If the improved selection criteria were applied, 99th percentile URLs (90% confidence interval) of hs-cTnT male, female, and total were 18 (14-24) ng/L, 13 (11-16) ng/L, and 16 (13-17) ng/L, respectively. The 99th percentile URLs of hs-cTnT male were higher than those of female in every age group. CONCLUSIONS: Improved selection criteria through questionnaire survey, physical examination, and laboratory screening to further exclude hypertension, overweight and obesity, and dyslipidemia can avoid overestimation of the 99th percentile URL of hs-cTnT.

Design and evaluation of a LIS-based autoverification system for coagulation assays in a core clinical laboratory.

BACKGROUND: The autoverification system for coagulation consists of a series of rules that allow normal data to be released without manual verification. With new advances in medical informatics, the laboratory information system (LIS) has growing potential for the autoverification, allowing rapid and accurate verification of clinical laboratory tests. The purpose of the study is to develop and evaluate a LIS-based autoverification system for validation and efficiency. METHODS: Autoverification decision rules, including quality control, analytical error flag, critical value, limited range check, delta check and logical check, as well as patient's historical information, were integrated into the LIS. Autoverification limited range was constructed based on 5 and 95% percentiles. The four most commonly used coagulation assays, prothrombin time (PT), activated partial thromboplastin time (APTT), thrombin time (TT), and fibrinogen (FBG), were followed by the autoverification protocols. The validation was assessed by the autoverification passing rate, the true-positive cases, the true-negative cases, the false-positive cases, the false-negative cases, the sensitivity and the specificity; the efficiency was evaluated in the turnaround time (TAT). RESULTS: A total of 157,079 historical test results of coagulation profiles from January 2016 to December 2016 were collected to determine the distribution intervals. The autoverification passing rate was 77.11% (29,165/37,821) based on historical patient data. In the initial test of the autoverification version in June 2017, the overall autoverification passing rate for the whole sample was 78.75% (11,257/14,295), with 892 true-positive cases, 11,257 true-negative cases, 2146 false-positive cases, no false-negative cases, sensitivity of 100% and specificity of 83.99%. After formal implementation of the autoverification system for 6 months, 83,699 samples were assessed. The average overall autoverification passing rate for the whole sample was 78.86% and the 95% confidence interval (CI) of the passing rate was [78.25, 79.59%]. TAT was reduced from 126 min to 101 min, which was statistically significant (P < 0.001, Mann-Whitney U test). CONCLUSIONS: The autoverification system for coagulation assays based on LIS can halt the samples with abnormal values for manual verification, guarantee medical safety, minimize the requirements for manual work, shorten TAT and raise working efficiency.

A study on reference interval transference via linear regression.

Background Reference intervals (RIs) transference can expand the applicability of established RIs. However, the study on transference methodology is insufficient, and RIs validation based on small samples cannot adequately identify transferred risk under complex situations. This study aimed to find appropriate conditions to ensure the effect of transference. Methods We established the RIs of Roche and Beckman systems for 27 analytes based on 681 healthy individuals. Roche RIs were converted into the Beckman RIs using linear regression (least squares method) which is divided into two methods - Methodref (500 test numbers with relatively narrow data range) and Methodep (80 test numbers with relatively wide data range). Taking the RIs established by Beckman results as standard, we assessed the accuracy, precision and trueness of transferred results under various conditions. Results A total of 29.6% and 48.1% of analytes were consistent between the two systems for the lower and upper reference limits, respectively. The concordance rates between transferred and measured RIs for Methodref were up to 74.1% and 92.6%, which were better than Methodep (44.4% and 59.3%). The CV of transferred reference limits decreased gradually with increasing test number under the same data range. For most analytes, excluding some electrolyte tests, we could obtain accurate results when r > 0.800 and the test number was sufficient regardless of the regression equation types. Conclusions Transferability of RIs is affected by many factors, such as correlation, test number, regression equation type, and quality requirement. To reduce the risk of transference, it is very important to select right method with reasonable conditions.

Pediatric reference intervals in China (PRINCE): design and rationale for a large, multicenter collaborative cross-sectional study.

There is a lack of accurate pediatric reference intervals (RIs) in China, with most commonly used RIs established without consideration of the effect of age and gender. The Pediatric Reference Intervals in China (PRINCE) project aims to establish and verify pediatric RIs for 31 common laboratory measurands. The project will be a large, multicenter cross-sectional study: 14,490 healthy children and adolescents aged up to 19 years will be surveyed by 10 children's hospitals and one pediatric department of a university hospital. To evaluate the feasibility and efficiency of the study methods, 602 children were surveyed in the pilot phase of the PRINCE study in April 2017: it found that some measurands were distinctly age dependent and that there were differences between values for males and females. The results of the pilot study affirmed the necessity of the PRINCE project for Chinese pediatrics. The pilot also indicated potential difficulties in the full survey, e.g., difficulties in recruiting children aged under 3 years and insufficient collection of blood samples from infants. The operation of the PRINCE project has been modified based on the findings in the pilot study toward improving the validity of the PRINCE project and promoting its openness and transparency.

Biological variation of serum neuron-specific enolase and carbohydrate antigen 724 tumor markers.

BACKGROUND: The aim of our study was to assess two tumor markers, carbohydrate antigen 724 (CA724) and neuron-specific enolase (NSE), in 20 healthy individuals. Then, we determined their average intra- and inter-individual biological variations (CVI and CVG ). METHODS: Blood samples were taken at weekly intervals for five weeks from 20 healthy subjects through a detailed questionnaire and physical examination. These samples were stored at -80°C and analyzed in a single run in duplicate. We calculated the biological variations, the reference change value (RCV), and the index of individuality (II) for the two tumor markers. RESULTS: The intra-individual and inter-individual biological variations were 50.3% and 103.4% for CA724, and 10.1% and 12.0% for NSE, respectively. The II values for CA724 and NSE were 0.48 and 0.85, respectively. CONCLUSION: We determined the biological variations and indices of individuality for CA724 and NSE among 20 healthy subjects. These results will improve clinical applications of the markers.

The effect of thalassemia on erythrocyte reference intervals in a representative Han Chinese adult population.

BACKGROUND: The data from apparently healthy individuals with thalassemia has been demonstrated to have an effect on the reference intervals for the erythrocyte indices in areas with a high incidence of thalassemia. METHODS: Six clinical centers screened apparently healthy individuals using a questionnaire and a physical examination. Then, the qualified reference individuals were selected by hematological indices and a genotypic thalassemia diagnosis. Statistical comparisons were conducted for the erythrocyte reference intervals in the Chinese population with and without thalassemia. The constituent ratios and the mean (SD) of erythrocyte indices according to the thalassemia genotype were calculated. The relationship between the MCV values and the thalassemia genotype was also estimated. RESULTS: 4,636 reference individuals were included using hematological indices and genotypic thalassemia screening. The results of the erythrocyte reference intervals for individuals in Guangzhou with thalassemia demonstrated that the RBC, MCV, and MCH values significantly differed by gender compared with other regions (p < 0.01). In contrast, for individuals without thalassemia, the results tended to be similar and clinically acceptable. In addition, the results of the erythrocyte indices revealed significant differences among α-thalassemia patients, ß-thalassemia patients, and the control group. CONCLUSIONS: Apparently healthy individuals with thalassemia in the high prevalence zone of thalassemia could not be excluded by the questionnaire, physical examination or laboratory indices (Fe < 6 µmol/L, Hb < 90 g/L). The screening of genotypic thalassemia based on the MCV or MCH values to exclude unqualified individuals is the most effective way to obtain accurate and reliable reference intervals for the erythrocyte indices.

Complete blood count reference intervals for healthy Han Chinese adults.

BACKGROUND: Complete blood count (CBC) reference intervals are important to diagnose diseases, screen blood donors, and assess overall health. However, current reference intervals established by older instruments and technologies and those from American and European populations are not suitable for Chinese samples due to ethnic, dietary, and lifestyle differences. The aim of this multicenter collaborative study was to establish CBC reference intervals for healthy Han Chinese adults. METHODS: A total of 4,642 healthy individuals (2,136 males and 2,506 females) were recruited from six clinical centers in China (Shenyang, Beijing, Shanghai, Guangzhou, Chengdu, and Xi'an). Blood samples collected in K2EDTA anticoagulant tubes were analyzed. Analysis of variance was performed to determine differences in consensus intervals according to the use of data from the combined sample and selected samples. RESULTS: Median and mean platelet counts from the Chengdu center were significantly lower than those from other centers. Red blood cell count (RBC), hemoglobin (HGB), and hematocrit (HCT) values were higher in males than in females at all ages. Other CBC parameters showed no significant instrument-, region-, age-, or sex-dependent difference. Thalassemia carriers were found to affect the lower or upper limit of different RBC profiles. CONCLUSION: We were able to establish consensus intervals for CBC parameters in healthy Han Chinese adults. RBC, HGB, and HCT intervals were established for each sex. The reference interval for platelets for the Chengdu center should be established independently.

Correlation of IL-1F genetic polymorphisms with the risk of colorectal cancer among Chinese populations.

Inflammatory/immune cells have the power of infiltrating almost all human solid tumors and influencing all stages of carcinogenesis because of their stimulation of various cytokine subsets. This study aims to determine the correlation of single nucleotide polymorphisms in the IL-17F gene and the risk of colorectal cancer (CRC). One thousand patients diagnosed with CRC and a control group of 354 healthy controls were involved. Peripheral blood samples were collected. The PCR-RFLP method was used to detect the 7383A>G (rs2397084) and 7488T>C (rs763780) in the IL-17F gene. Statistical analyses were conducted with version 12.0 STATA statistical software. We found that the allele model suggested that patients carrying C allele were 1.67 times more likely to develop CRC than healthy controls (odds ratio (OR) = 1.67, 95% confidence interval (CI) = 1.22-2.27, P = 0.001). Similarly, the homozygous and dominant models also revealed that the minor IL-17F 7488C allele conferred an increased CRC risk compared to the major T allele among our study participants (CC vs. TT: OR = 4.15, 95% CI = 1.26-13.36, P = 0.011; TC+CC vs. TT: OR = 1.46, 95% CI = 1.04-2.05, P = 0.027). However, all genetic models indicated that the IL-17F 7383A>G (rs2397084) polymorphism was not associated with CRC risk (all P > 0.05). The results of this study indicate that the 7488T>C (rs763780) in the IL-17F gene may be correlated with increased risk of CRC.

Reference Intervals of Serum Sodium, Potassium, and Chlorine in Chinese Han Population and Comparison of Two ISE Methods.

BACKGROUND: Currently there are no reference intervals (RIs) of sodium (Na), potassium (K), and chlorine (Cl) on Chinese population. Two kinds of ion-selective electrode (ISE) methods were commonly used to determine K, Na, and Cl levels in China, the difference between these two methods needs to be evaluated. METHODS: A total of 4,524 healthy participants (1,916 males and 2,608 females) between 20-79 years old from six cities in China were selected by strict criteria. Serum K, Na, and CL were tested on Roche Modular analyzers in six assigned laboratories. According to EP-9A2, using Roche Modular analyzer (indirect ISE) as comparative method, Olympus AU 5400 analyzer (indirect ISE) and Johnson&Johnson Fusion 5.1 analyzer (direct ISE) were evaluated. RESULTS: In Chinese population, the RIs for K, Na, and CL are 3.6-5.2, 136-146, and 99-110 mmol/l, respectively. Compared to the Roche indirect ISE method, Johnson direct ISE method showed a positive bias; and Olympus indirect ISE method just showed a very slight bias. CONCLUSION: The RIs of K, Na, and Cl of Han Chinese healthy adult population were found to be smaller than those provided by the manufacturer. By a criteria of biological variations for CV, the differences of Na and K between Roche analyzer and Johnson analyzer were not acceptable for clinical application, while the differences of Na, K, and Cl between Roche and Olympus analyzers were acceptable for clinical application.

LNA-modified isothermal oligonucleotide microarray for differentiating bacilli of similar origin.

Oligonucleotide microarray has been one of the most powerful tools in the 'Post-Genome Era' for its high sensitivity, high throughput and parallel processing capability. To achieve high detection specificity, we fabricated an isothermal microarray using locked nucleic acid (LNA)-modified oligonucleotide probes, since LNA has demonstrated the advanced ability to enhance the binding affinity toward their complementary nucleotides. After designing the nucleotide sequences of these oligonucleotide probes for gram-positive bacilli of similar origin (Bacillus subtilis, Bacillus licheniformis, Bacillus pumilus, Bacillus megaterium and Bacillus circulans), we unified the melting temperatures of these oligonucleotide probes by modifying some nucleotides using LNA. Furthermore, we optimized the experimental procedures of hydrating microarray slides, blocking side surface as well as labelling the PCR products. Experimental results revealed that KOD Dash DNA polymerase could efficiently incorporate Cy3-dCTP into the PCR products, and the LNA-isothermal oligonucleotide microarray were able to distinguish the bacilli of similar origin with a high degree of accuracy and specificity under the optimized experimental condition.

Effects of 2'-O-methyl nucleotide on ligation capability of T4 DNA ligase.

To further understand the ligation mechanism, effects of 2'-O-methyl nucleotide (2'-OMeN) on the T4 DNA ligation efficiency were investigated. Fluorescence resonance energy transfer assay was used to monitor the nick-joining process by T4 DNA ligase. Results showed that substitutions at 5'- and 3'-ends of the nick decreased the ligation efficiency by 48.7% ± 6.7% and 70.6% ± 4.0%, respectively. Substitutions at both 5'- and 3'-ends decreased the ligation efficiency by 76.6% ± 1.3%. Corresponding kinetic parameters, Vmax, Km, and kcat, have been determined in each case by using the Michaelis-Menten equation. The kinetic data showed that the 2'-OMeN substitutions reduced the maximal initial velocity and increased the Michaelis constant of T4 DNA ligase. Mismatches at 5'- and 3'-ends of the nick have also shown different influences on the ligation. Results here showed that the sugar pucker conformation at 3'-end impairs the ligation efficiency more profoundly than that at 5'-end. Different concentrations of Mg(2+), Ca(2+), K(+), Na(+), and ATP were also demonstrated to affect the T4 DNA ligase activity. These results enriched our knowledge about the effects of 2'-OMeN substitutions on the T4 DNA ligase.

Effects of 2'-O-methyl nucleotide substitution on EcoRI endonuclease cleavage activities.

To investigate the effect of sugar pucker conformation on DNA-protein interactions, we used 2'-O-methyl nucleotide (2'-OMeN) to modify the EcoRI recognition sequence -TGAATTCT-, and monitored the enzymatic cleavage process using FRET method. The 2'-O-methyl nucleotide has a C3'-endo sugar pucker conformation different from the C2'-endo sugar pucker conformation of native DNA nucleotides. The initial reaction velocities were measured and the kinetic parameters, Km and Vmax were derived using Michaelis-Menten equation. Experimental results showed that 2'-OMeN substitutions for the EcoRI recognition sequence decreased the cleavage efficiency for A2, A3 and T4 substitutions significantly, and 2'-OMeN substitution for T5 residue inhibited the enzymatic activity completely. In contrast, substitutions for G1 and C6 could maintain the original activity. 2'-fluoro nucleic acid (2'-FNA) and locked nucleic acid (LNA) having similar C3'-endo sugar pucker conformation also demonstrated similar enzymatic results. This position-dependent enzymatic cleavage property might be attributed to the phosphate backbone distortion caused by the switch from C2'-endo to C3'-endo sugar pucker conformation, and was interpreted on the basis of the DNA-EcoRI structure. These 2'-modified nucleotides could behave as a regulatory element to modulate the enzymatic activity in vitro, and this property will have potential applications in genetic engineering and biomedicine.