Treat to target in Crohn's disease: A practical guide for clinicians

A treat-to-target (T2T) approach applies the principles of early intervention and tight disease control to optimise long-term outcomes in Crohn's disease. The Selecting Therapeutic Targets in Inflammatory Bowel Disease (STRIDE)-II guidelines specify short, intermediate, and long-term treatment goals, documenting specific treatment targets to be achieved at each of these timepoints. Scheduled appraisal of Crohn's disease activity against pre-defined treatment targets at these timepoints remains central to determining whether current therapy should be continued or modified. Consensus treatment targets in Crohn's disease comprise combination clinical and patient-reported outcome remission, in conjunction with biomarker normalisation and endoscopic healing. Although the STRIDE-II guidelines endorse the pursuit of endoscopic healing, clinicians must consider that this may not always be appropriate, acceptable, or achievable in all patients. This underscores the need to engage patients at the outset in an effort to personalise care and individualise treatment targets. The use of non-invasive biomarkers such as faecal calprotectin in conjunction with cross-sectional imaging techniques, particularly intestinal ultrasound, holds great promise; as do emerging treatment targets such as transmural healing. Two randomised clinical trials, namely, CALM and STARDUST, have evaluated the efficacy of a T2T approach in achieving endoscopic endpoints in patients with Crohn's disease. Findings from these studies reflect that patient subgroups and Crohn's disease characteristics likely to benefit most from a T2T approach, remain to be clarified. Moreover, outside of clinical trials, data pertaining to the real-world effectiveness of a T2T approach remains scare, highlighting the need for pragmatic real-world studies. Despite the obvious promise of a T2T approach, a lack of guidance to support its integration into real-world clinical practice has the potential to limit its uptake. This highlights the need to describe strategies, processes, and models of care capable of supporting the integration and execution of a T2T approach in real-world clinical practice. Hence, this review seeks to examine the current and emerging literature to provide clinicians with practical guidance on how to incorporate the principles of T2T into routine clinical practice for the management of Crohn's disease.

Evaluation of Circulating Plasma VEGF-A, ET-1 and Magnesium Levels as the Predictive Markers for Proliferative Diabetic Retinopathy

Diabetic retinopathy (DR) is the most common cause for preventable blindness in India. The onset of micro and macrovascular complications in T2DM is multifactorial and difficult to predict. The status of micronutrients, several inflammatory cytokines, elevated triacylglycerols, oxidative stress etc., are being studied extensively. Hypomagnesemia plays a pivotal role in worsening of insulin resistance. Although, Vascular Endothelial Growth Factor-A (VEGF-A) and Endothelin-1 (ET-1) are known to be elevated in DR, yet few reports cite their role, especially in Indian population. In this study, we included thirty subjects with T2DM in each of the three groups namely, T2DM cases without retinopathy, Non Proliferative DR (NPDR) and Proliferative DR (PDR) retinopathy. The glycemic status, circulating plasma VEGF-A, ET-1 levels, serum magnesium and lipids were estimated and compared among the groups. An ROC was drawn to evaluate VEGF-A, ET-1 and serum magnesium levels as the predictive markers for PDR. On comparison VEGF-A, ET-1 and serum magnesium levels showed a significant difference among the three groups. PDR cases had higher circulating levels of VEGF-A, ET-1 and low serum magnesium levels when compared to others. ROC for VEGF-A and ET-1 showed an optimum cut-off of 1521 ng/ml (AUC 0.975) and 16 pg/ml (AUC 0.96) respectively. A negative ROC was drawn to check the lower cut-off limit for serum magnesium; we documented an optimum cut off of 1.7 mg/dl (AUC 0.837). ET-1, VEGF-A and serum Magnesium levels are significantly altered in PDR and can be used as the predictive markers of PDR.

Urinary 8-hydroxydeoxyguanosine as a marker of oxidative stress induced genetic toxicity in oral cancer patients

CONTEXT

Recently, non-communicable diseases have snatched the lead from infectious diseases in causing mortality. Of these, oral cancer accounts for a significant proportion of deaths. Every year in India significant percentage of newly diagnosed malignancy is oral cancer attributed to various reasons.

AIMS

The aim of this study was to assess the extent of oxidative stress and its effect on modification of DNA by urinary nucleoside 8-hydroxy-2'-deoxyguanosine (8-OHdG) levels in oral cancer subjects. To see the relationship between the nucleoside 8-OHdG and antioxidant capacity ferric reducing ability plasma (FRAP) in oral cancer subjects.

SETTINGS AND DESIGN

Case-control study included three groups with 60 volunteers, who were divided into 30 controls, and equal number of clinically diagnosed oral cancer male patients: (Subdivided into newly diagnosed [n = 15] and 1-year treatment follow-up oral cancer subjects [n = 15]).

MATERIALS AND METHODS

A random urine sample was used for analysis of 8-OHdG concentration. Serum triglycerides, lipid peroxidation, protein thiols, and FRAP assay were performed by spectrophotometric technique.

STATISTICAL ANALYSIS USED

Student's t-test and one-way analysis of variance were performed for group comparison and Pearson's correlation analysis were used. A P < 0.05 was considered the optimum level of significance.

RESULTS

The urinary 8-OHdG and serum malondialdehyde levels were significantly elevated in newly diagnosed oral cancer subjects in their 1-year treatment compared to the control group (P < 0.05). A significant correlation was observed between urinary 8-OHdG and FRAP in both groups of oral cancer subjects.

CONCLUSIONS

Urinary 8-OHdG can be a useful diagnostic marker of oxidative DNA damage in oral cancer subjects.

Association of Glycemic Status with Bone Turnover Markers in Type 2 Diabetes Mellitus

Context

Type 2 diabetes mellitus has profound implications on the skeleton. Even though bone mineral density is increased in type 2 diabetes mellitus patients, they are more prone for fractures. The weakening of bone tissue in type 2 diabetes mellitus can be due to uncontrolled blood sugar levels leading to high levels of bone turnover markers in blood.

Aims

The aim of this study is to find the association between glycemic status and bone turnover markers in type 2 diabetes mellitus.

Settings and Design

This case-control study was carried out in a tertiary health care hospital.

Subjects and Methods

Fifty clinically diagnosed type 2 diabetes mellitus patients in the age group between 30 and 50 years were included as cases. Fifty age- and gender-matched healthy nondiabetics were included as controls. Patients with complications and chronic illness were excluded from the study. Depending on glycated hemoglobin (HbA1c) levels, patients were grouped into uncontrolled (HbA1c >7%, n = 36) and controlled (HbA1c <7%, n = 14) diabetics. Based on duration of diabetes, patients were grouped into newly diagnosed, 1-2 years, 3-5 years, and >5 years. Serum osteocalcin (OC), bone alkaline phosphatase (BAP), acid phosphatase (ACP), and HbA1c levels were estimated. OC/BAP and OC/ACP ratio was calculated.

Statistical Analysis Used

Student's t-test, analysis of variance, and Chi-square tests were used for analysis. Receiver operating characteristic (ROC) curve analysis was done for OC/BAP and OC/ACP ratios.

Results

Serum OC, HbA1c, and OC/BAP ratio were increased in cases when compared to controls and were statistically significant (P < 0.001). OC/ACP ratio was decreased in type 2 diabetes mellitus and was statistically significant (P = 0.01). In patients with >5-year duration of diabetes, HbA1c level was high and was statistically significant (P < 0.042). BAP levels were high in uncontrolled diabetics but statistically not significant. ROC curve showed OC/BAP ratio better marker than OC/ACP ratio.

Conclusions

Uncontrolled type 2 diabetes mellitus affects bone tissue resulting in variations in bone turnover markers. Bone turnover markers are better in predicting recent changes in bone morphology and are cost effective.

Putative Role of Cardio Metabolic Risk Among Poorly Controlled Asthmatics in South Indian Population

Mortality and morbidity attributed to asthma remains to be the biggest nightmare worldwide. Hence, the study was aimed to compare the cardio metabolic risk factors as assessed by Body mass index (BMI), waist hip ratio (WHR), serum triacylglycerol and uric acid in well controlled and poorly controlled asthmatics and to correlate these parameters with the severity of asthma. A case control study was conducted on 90 subjects who were segregated into well controlled asthmatics (n = 30) and poorly controlled asthmatics (n = 30) who were diagnosed based on Global initiative for Asthma management guidelines and healthy volunteers (n = 30). Centrifuged fasting venous blood samples were used for biochemical analysis, pulmonary function test, BMI, and waist hip ratio (WHR) were measured. The statistical analysis was done using SPSS version 17. There was a significant increase in BMI, WHR, lipid profile, serum uric acid and decrease in forced expiratory volume (FEV1), forced vital capacity (FVC), and FEV1/FVC in poorly controlled asthmatics. There was a significant association between FEV1 and serum uric acid, BMI and Triacylgycerol in poorly controlled asthmatics. Poorly controlled asthmatics have greater risk of developing cardiometabolic problems. Serum uric acid can be used as one of the severity markers in asthma to assess cardio metabolic risk.

SERUM magnesium levels as an indicator of status of Diabetes Mellitus type 2

CONTEXT

Magnesium deficiency is commonly associated with endocrine and metabolic disorders, especially with Diabetes Mellitus type 2 though the mechanism of hypomagnesemia in Diabetes Mellitus is not completely known. There is a close association between metabolic control of Diabetes Mellitus and impaired magnesium balance.

AIMS

To estimate the serum levels of magnesium in patients of with Diabetes Mellitus type 2 and to find a correlation if any, with the duration and control (by estimating HbA1c) of Diabetes Mellitus type 2.

MATERIALS AND METHODS

Fifty patients of Diabetes Mellitus type 2 were included in the study. Blood samples were analyzed for fasting and post prandial glucose, HbA1c and magnesium. The patients were grouped into three categories based upon their HbA1c levels into those with good control, need intervention and poor control. The three groups were compared with reference to their mean levels of blood glucose and magnesium. Association of serum magnesium levels with HbA1c, Fasting and postprandial blood glucose and duration of Diabetes Mellitus was also done.

RESULTS

Serum magnesium levels were found to decline with rise in HbA1c levels and with duration of Diabetes Mellitus type 2.

CONCLUSION

Hypomagnesemia is linked to poor control of Diabetes Mellitus type 2 and depletion of serum magnesium occurs exponentially with duration of disease.

Evaluation of Body Mass Index (BMI) Percentile cut-off Levels with Reference to Insulin Resistance: A Comparative Study on South Indian Obese and Non-Obese Adolescents

OBJECTIVES

To investigate the relationship of Body Mass Index (BMI) percentile cut off with Homeostasis Model Assessment-Insulin Resistance (HOMA-IR), a surrogate marker for insulin resistance in obese, overweight and non-obese adolescents.

STUDY DESIGN

A cross-sectional analysis of 120 adolescents (divided into sixty overweight/obese and an equal number of non-obese) was performed on nondiabetic, nonpregnant (11 to 18 year old school going) adolescents in south Indian (Puducherry) population. The main outcome measure of insulin resistance was calculated as HOMA-IR (greater than 3.16). Obesity was defined as per the BMI criteria, BMI greater than or equal to 95(th) percentile,overweight greater than or equal to 85(th) percentile and non-obese less than 84.9(th) percentile. All adolescents were subjected to analysis of anthropometric parameters that included weight, height and BMI (body mass index). Biochemical parameters, namely venous plasma glucose (fasting) and venous plasma insulin (fasting) were included for insulin resistance calculation by HOMA-IR.

RESULTS

Having a BMI of greater than or equal to 85(th) percentilewas associated with high HOMA-IR levels. As the BMI percentile increased, HOMA-IR levels also increased. Prevalence of insulin resistance for a BMI percentile of less than 84.9 was nil. Prevalence of insulin resistance for a BMI percentile of 85-94.9 was 26%.Prevalence of insulin resistance for BMI of greater than or equal to 95(th) percentile was 64%.

CONCLUSION

Insulin resistance is highly prevalent in obese and overweight adolescents as compared to that in non-obese adolescents. The onset of Impaired Fasting Glucose (IFG) is associated with the development of severe hyper-insulinaemia in obese adolescents and early primordial and primary prevention can thus alleviate the burden of future cardiometabolic disorders.

Planning an objective and need based curriculum: the logistics with reference to the undergraduate medical education in biochemistry

PURPOSE

The medical education is recently being transformed into several domains in order to adapt to the need and the value based academics which is required for the quality doctors who serve the community. Presently, the biochemistry curricula for the graduate students of medicine have been questioned by as many experts, because of their multiple lacunae. In this review, we would like to highlight the scenario which is related to the existing biochemistry curricula for graduate medical students, which have been followed in several medical schools and universities and we also hope to share our ideas for implementing objective and pragmatic curricula. Evidence based research, wherein the articles which are related to innovative teaching-learning tools are collected and the pros and cons which are related to the different methods analyzed in biochemistry point of view.

CONCLUSION

Rapid changes in the content of the curriculum may not be required, but a gradual introduction of the novel approach and the methods of teaching biochemistry can be adopted into the curriculum.

Serum lipid peroxides and magnesium levels following three months of treatment with pioglitazone in patients with type-2 diabetes mellitus

BACKGROUND

Higher levels of lipid peroxidation and hypomagnesaemia are frequently associated with Type 2 Diabetes mellitus (T2DM). Addressing these issues would definitely help us in preventing or prolonging the onset of pathogenesis of micro and macrovascular complications. Pioglitazone is used as a trusted insulin sensitizer and an adjuvant to the conventional oral hypoglycemic agents. This study was planned to explore the effects of pioglitazone on oxidative stress, serum magnesium, blood pressure, hepato-biliary and renal systems in addition to its effects on glycemic control.

METHODS

Sixty-three T2DM cases, who were started on pioglitazone were included in this study. All the physiological and biochemical parameters were estimated prior to and following three months of therapy with pioglitazone.

RESULTS

There was significant improvement in the glycemic control, serum magnesium and MDA levels with p values of 0.000, 0.023 and 0.000 respectively. Pioglitazone did not have any significant effects on the serum lipids and blood pressure in T2DM cases following three months of treatment. We did not observe any pronounced changes in hepato-biliary enzymes, serum urea and creatinine levels reaffirming safety of pioglitazone in T2DM.

CONCLUSION

Three-month duration of treatment with Pioglitazone in T2DM cases helps in alleviating the levels of lipid peroxides, besides being associated with improved serum magnesium status and glycemic control.

Status of serum magnesium in type 2 diabetes mellitus with particular reference to serum triacylglycerol levels

Magnesium (Mg) is the fourth most abundant cation in the body and the second most common intracellular cation. The association between hypomagnesemia and insulin resistance (IR) in diabetes mellitus has been documented earlier. However, we wanted to study whether the extracellular status of magnesium (Mg) could be a biochemical mediator between hypertriacylglycerolemia and diabetes mellitus.

AIMS

To find out the probable association among HbA1c, triacylglycerol (TG) and magnesium levels - a predictor of vascular complications in T(2)DM.

MATERIALS AND METHODS

Thirty patients who had attended the diabetic clinics during the period of this study were included. All the samples were analysed for glucose, TG, Mg, and HbA1c. For statistical analysis, SPSS 17 package was used.

RESULTS

Serum TG (236.67*, 195.06) and HbA1C (9.97*, 8.57) levels were independently compared between the two groups and were significantly high in group A subjects (Mg<1.2mg/dl) as compared to group B subjects (Mg>1.2mg/dl) (*p-value<0.05), respectively.

DISCUSSION AND CONCLUSION

Hypertriacylglycerolemia was pronounced in type 2 diabetes mellitus patients with accompanying hypomagnesemia. This compared well with that of the glycemic control. Low Mg levels, high TG levels in association with enhanced HbA1c levels could thus serve as a reliable biochemical indicator of insulin status and action without resorting to the usage of criteria for insulin sensitivity and resistance.

How stiff is DNA?

The natural stiffness of DNA, which contributes to the interactions of the many proteins involved in its biological processing and packaging, also plays an important role in modern nanotechnology. Here we report new Monte-Carlo simulations of deformable DNA molecules of potential utility in understanding the behavior of the long, double-helical polymer in the tight confines of a cell and in the design of novel nanomaterials and molecular devices. We directly determine the fluctuations in end-to-end extension associated with the conventional elastic-rod representation of DNA and with more realistic models that take account of the precise deformability of the constituent base-pair steps. Notably, the variance of end-to-end distance shows a quadratic increase with chain length in short chains of both types. We also consider the contributions to chain extension from the chemical linkages used to attach small molecular probes to DNA. The distribution of computed distances is sensitive to the intrinsic structure and allowed deformations of the tether. Surprisingly, the enhancement in end-to-end variance associated with the presence of the probe depends upon chain length, even when the probe is rigidly connected to DNA. We find that the elastic rod model of DNA in combination with a slightly fluctuating tether accounts satisfactorily for the distributions of end-to-end distances extracted from the small-angle X-ray scattering of gold nanocrystals covalently linked to the ends of short DNAs. There is no need to introduce additional structural fluctuations to reproduce the measured uptake in end-to-end fluctuations with chain length.

Feature extraction using molecular planes for fuzzy relational clustering of a flexible dopamine reuptake inhibitor

Six rigid-body parameters (Shift, Slide, Rise, Tilt, Roll, Twist) are commonly used to describe the relative displacement and orientation of successive base pairs in a nucleic acid structure. The present work adapts this approach to describe the relative displacement and orientation of any two planes in an arbitrary molecule-specifically, planes which contain important pharmacophore elements. Relevant code from the 3DNA software package (Nucleic Acids Res. 2003, 31, 5108-5121) was generalized to treat molecular fragments other than DNA bases as input for the calculation of the corresponding rigid-body (or "planes") parameters. These parameters were used to construct feature vectors for a fuzzy relational clustering study of over 700 conformations of a flexible analogue of the dopamine reuptake inhibitor, GBR 12909. Several cluster validity measures were used to determine the optimal number of clusters. Translational (Shift, Slide, Rise) rather than rotational (Tilt, Roll, Twist) features dominate clustering based on planes that are relatively far apart, whereas both types of features are important to clustering when the pair of planes are close by. This approach was able to classify the data set of molecular conformations into groups and to identify representative conformers for use as template conformers in future Comparative Molecular Field Analysis studies of GBR 12909 analogues. The advantage of using the planes parameters, rather than the combination of atomic coordinates and angles between molecular planes used in our previous fuzzy relational clustering of the same data set (J. Chem. Inf. Model. 2005, 45, 610-623), is that the present clustering results are independent of molecular superposition and the technique is able to identify clusters in the molecule considered as a whole. This approach is easily generalizable to any two planes in any molecule.

Target-site Preferences of Sleeping Beauty Transposons

The Sleeping Beauty (SB) transposon is a Tc1/mariner family transposon that has applications in vertebrate animals for gene transfer, gene-tagging, and human gene therapy. In this study, we analyzed the target-site preferences of the SB transposon. At the genomic level, integration of SB transposons with respect to genes (exons and introns) and intergenic regions appears fairly random but not on a micro-scale. Although there appears to be a consensus sequence around the vicinity of the target sites, the primary sequence is not the determining factor for target selection. When integrations were examined over a limited topography, the sites used most often for integration did not match the consensus sequence. Rather, a unique deformation inherent in the sequence may be a recognition signal for target selection. The deformation is characterized by an angling of the target site such that the axis around the insertion site is off-center, the rotation of the helix (twisting) is non-uniform and there is an increase in the distance between the central base-pairs. Our observations offer several hypothetical insights into the transposition process. Our observations suggest that particular deformations of the double helix predicted by the V(step) algorithm can distinguish TA sites that vary by about 16-fold in their preferences for accommodating insertions of SB transposons.

Accurate representation of B-DNA double helical structure with implicit solvent and counterions

High-resolution nuclear magnetic resonance (NMR) and crystallographic data have been taken to refine the force field used in the torsion angle space nucleic acids molecular mechanics program DUPLEX. The population balance deduced from NMR studies of two carcinogen-modified DNA conformers in equilibrium was used to fine tune a sigmoidal, distance-dependent dielectric function so that reasonable relative energies could be obtained. In addition, the base-pair and backbone geometry from high-resolution crystal structures of the Dickerson-Drew dodecamer was used to re-evaluate the deoxyribose pseudorotation profile and the Lennard-Jones nonbonded energy terms. With a modified dielectric function that assumes a very steep distance-dependent form, a deoxyribose pseudorotation profile with reduced energy barriers between C2'- and C3'-endo minima, and a shift of the Lennard-Jones potential energy minimum to a distance approximately 0.4 A greater than the sum of the van der Waals' radii, the sequence-dependent conformational features of the Dickerson-Drew dodecamer in both the solid state and the aqueous liquid crystalline phase are well reproduced. The robust performance of the revised force field, in conjunction with its efficiency through implicit treatment of solvent and counterions, provides a valuable tool for elucidating conformations and structure-function relationships of DNA, including those of molecules modified by carcinogens and other ligands.

Base sequence effects in bending induced by bulky carcinogen-DNA adducts: experimental and computational analysis

The covalent binding of bulky mutagenic or carcinogenic compounds to DNA can lead to bending, which could significantly alter the interactions of DNA with critical replication and transcription proteins. The impact of adducts derived from the highly reactive bay region enantiomeric (+)- and (-)-anti-7,8-diol-9,10-epoxide derivatives of benzo[a]pyrene (BPDE) are of interest because the (+)-7R,8S,9S,10R-anti-BPDE enantiomer is highly tumorigenic in rodents, while the (-)-7S,8R,9R,10S-anti-BPDE enantiomer is not. Both (+)- and (-)-anti-BPDE bind covalently with DNA predominantly by trans addition at the exocyclic amino group of guanine to yield 10S (+)- and 10R (-)-trans-anti-[BP]-N(2)-dG adducts. We have synthesized a number of different oligonucleotides with single (+)- and (-)-trans-anti-[BP]-N(2)-dG adducts (G) in the base sequence context XG*Y, where X and Y are different DNA bases. The G* residues were positioned at or close to the center of 11 base pair ( approximately 1 helical turn) or 16 base pair ( approximately 1.5 turns) duplexes. All bases, except for X and Y and their partners, were identical. These sequences were self-ligated with T4 ligase to form multimers that yield a ladder of bands upon electrophoresis in native polyacrylamide gels. The extent of bending in each oligonucleotide was assessed by monitoring the decrease in gel mobilities of these linear, self-ligated oligomers, relative to unmodified oligonucleotides of the same base sequence. The extent of global bending was then estimated using a sequence-specific three-dimensional model from which the values of the base-pair step parameter roll adjacent to the lesion site could be extracted. We find that (+)-trans-anti-[BP]-N(2)-dG adducts are considerably more bent than the (-) isomers regardless of sequence and that A-T base pairs flanking the [BP]-N(2)-dG lesion site allow for local flexibility consistent with adduct conformational heterogeneity. Interestingly, the fit of computed versus observed gel mobilities using classical reptation treatments requires enhancement of unmodified DNA flexibility in gels, compared to aqueous salt solution. The differences in bending between the two stereoisomeric adduct duplexes and the observed base sequence context effects may play a significant role in the differential processing of these lesions by cellular replication, transcription, and repair enzymes.

Human topoisomerase I poisoning by protoberberines: potential roles for both drug-DNA and drug-enzyme interactions

Protoberberines represent a structural class of organic cations that induce topoisomerase I-mediated DNA cleavage, a behavior termed topoisomerase I poisoning. We have employed a broad range of biophysical, biochemical, and computer modeling techniques to characterize and cross-correlate the DNA-binding and topoisomerase poisoning properties of four protoberberine analogues that differ with respect to the substituents on their A- and/or D-rings. Our data reveal the following significant features: (i) The binding of the four protoberberines unwinds duplex DNA by approximately 11 degrees, an observation consistent with an intercalative mode of interaction. (ii) Enthalpically favorable interactions, such as stacking interactions between the intercalated ligand and the neighboring base pairs, provide <50% of the thermodynamic driving force for the complexation of the protoberberines to duplex DNA. Computer modeling studies on protoberberine-DNA complexes suggest that only rings C and D intercalate into the host DNA helix, while rings A and B protrude out of the helix interior into the minor groove. (iii) All four protoberberine analogues are topoisomerase I-specific poisons, exhibiting little or no topoisomerase II poisoning activity. (iv) Modifications of the D-ring influence both DNA binding and topoisomerase I poisoning properties. Specifically, transference of a methoxy substituent from the 11- to the 9-position diminishes both DNA binding affinity and topoisomerase I poisoning activity, an observation suggesting that DNA binding is important in the poisoning of topoisomerase I by protoberberines. (v) Modifications of the A-ring have a negligible impact on DNA binding affinity, while exerting a profound influence on topoisomerase I poisoning activity. Specifically, protoberberine analogues containing either 2,3-dimethoxy; 3,4-dimethoxy; or 3, 4-methylenedioxy substituents all bind DNA with a similar affinity. By contrast, these analogues exhibit markedly different topoisomerase I poisoning activities, with these activities following the hierarchy: 3,4-methylenedioxy > 2,3-dimethoxy >> 3, 4-dimethoxy. These differences in topoisomerase I poisoning activity may reflect the differing abilities of the analogues to interact with specific functionalities on the enzyme, thereby stabilizing the enzyme in its cleavable state. In the aggregate, our results are consistent with a mechanistic model in which both ligand-DNA and ligand-enzyme interactions are important for the poisoning of topoisomerase I by protoberberines, with the DNA-directed interactions involving ring D and the enzyme-directed interactions involving ring A. It is reasonable to suggest that the poisoning of topoisomerase I by a broad range of other naturally occurring and synthetic ligands may entail a similar mechanism.

Protein-directed DNA structure II. Raman spectroscopy of a leucine zipper bZIP complex

Mechanisms of transcription may involve protein-directed changes in DNA structure and DNA-directed changes in protein structure. We have employed Raman spectroscopy to characterize vibrational signatures associated with such induced molecular fitting for two classes of transcription factors-the basic leucine-zipper (bZIP) motif and the high-mobility-group (HMG) box-each with a DNA target site. Results for bZIP are described here; findings for the HMG-box are reported in the preceding paper in this issue [Benevides, J. M., Chan, G., Lu, X.-J., Olson, W. K., Weiss, M. A., and Thomas, G. J., Jr. (2000) Biochemistry 39, 537-547]. The yeast activator GCN4 provides a well-studied example of bZIP recognition, wherein B-DNA serves essentially as a template for protein folding. Analysis of Raman spectra of the 57-residue GCN4 bZIP domain, its AP-1 binding site, and their specific complex confirms a DNA-induced increase in alpha-helicity, attributable to folding of GCN4 basic arms with virtually no change in B-DNA structure, consistent with previous X-ray and NMR structure determinations. The absence of DNA perturbations in the bZIP model contrasts sharply with the HMG box, where DNA structure perturbations predominate. The bZIP and HMG-box models represent two opposing extremes in a range of induced fits identifiable by Raman spectroscopy. Previously characterized lambda repressor/operator complexes [Benevides, J. M., Weiss, M. A., and Thomas, G. J. (1994) J. Biol. Chem. 269, 10869-10878] occupy an intermediate position within this range. A comprehensive tabulation of Raman markers proposed as diagnostic of different protein/DNA recognition motifs is presented. The results are analyzed in terms of available DNA crystal structures (Nucleic Acid Database) to identify details of DNA conformation that correlate with specific Raman recognition markers.

The hydration of nucleic acid duplexes as assessed by a combination of volumetric and structural techniques

Using high precision densimetric and ultrasonic measurements, we have determined, at 25 degrees C, the apparent molar volumes PhiV and the apparent molar compressibilities PhiK(S) of four nucleic acid duplexes-namely, the DNA duplex, poly(dIdC)poly(dIdC); the RNA duplex, poly(rA)poly(rU); and the two DNA/RNA hybrid duplexes, poly(rA)poly(dT) and poly(dA)poly(rU). Using available fiber diffraction data on these duplexes, we have calculated the molecular volumes as well as the solvent-accessible surface areas of the constituent charged, polar, and nonpolar atomic groups. We found that the hydration properties of these nucleic acid duplexes do not correlate with the extent and the chemical nature of the solvent-exposed surfaces, thereby suggesting a more specific set of duplex-water interactions beyond general solvation effects. A comparative analysis of our volumetric data on the four duplexes, in conjunction with available structural information, suggests the following features of duplex hydration: (a) The four duplexes exhibit different degrees of hydration, in the order poly(dIdC)poly(dIdC) > poly(dGdC)poly(dGdC) > poly(dAdT)poly(dAdT) approximately poly(dA)poly(dT). (b) Repetitive AT and IC sequences within a duplex are solvated beyond general effects by a spine of hydration in the minor groove, with this sequence-specific water network involving about 8 additional water molecules from the second and, perhaps, even the third hydration layers. (c) Repetitive GC and IC sequences within a duplex are solvated beyond general effects by a "patch of hydration" in the major groove, with this water network involving about 13 additional water molecules from the second and, perhaps, even the third hydration layers. (d) Random sequence, polymeric DNA duplexes, which statistically lack extended regions of repetitive AT, GC, or IC sequences, do not experience such specific enhancements of hydration. Consequently, consistent with our previous observations (T. V. Chalikian, A. P. Sarvazyan, G. E. Plum, and K. J. Breslauer, Biochemistry, 1994, Vol. 33, pp. 2394-2401), duplexes with approximately 50% AT content exhibit the weakest hydration, while an increase or decrease from this AT content causes enhancement of hydration, either due to stronger hydration of the minor groove (an increase in AT content) or due to stronger hydration of the major groove (an increase in GC content). (e) In dilute aqueous solutions, a B-DNA duplex is more hydrated than an A-DNA duplex, a volumetric-based conclusion that is in agreement with previous results obtained on crystals, fibers, and DNA solutions in organic solvent-water mixtures. (f) the A-like, RNA duplex poly(rA)poly(rU) and the structurally similar A-like, hybrid duplex poly(rA)poly(dT), exhibit similar hydration properties, while the structurally distinct A-like, hybrid duplex poly(rA)poly(dT) and non-A-like, hybrid duplex poly(dA)poly(rU) exhibit differential hydration properties, consistent with structural features dictating hydration characteristics. We discuss how volumetric characterizations, in conjunction with structural studies, can be used to describe, define, and resolve the general and sequence/conformation-specific hydration properties of nucleic acid duplexes.

Minor groove-directed and intercalative ligand-DNA interactions in the poisoning of human DNA topoisomerase I by protoberberine analogs

Spectroscopic, calorimetric, DNA cleavage, electrophoretic, and computer modeling techniques have been employed to characterize the DNA binding and topoisomerase poisoning properties of three protoberberine analogs, 8-desmethylcoralyne (DMC), 5,6-dihydro-8-desmethylcoralyne (DHDMC), and palmatine, which differ in the chemical structures of their B- and/or D-rings. DNA topoisomerase-mediated cleavage assays revealed that these compounds were unable to poison mammalian type II topoisomerase. By contrast, the three protoberberine analogs poisoned human topoisomerase I according to the following hierarchy: DHDMC > DMC > palmatine. DNA binding by all three protoberberine analogs induced negative flow linear dichroism signals as well as unwinding of the host duplex. These two observations are consistent with an intercalative mode of protoberberine binding to duplex DNA. However, a comparison of the DNA binding properties for DMC and DHDMC, which differ only by the state of saturation at the 5,6 positions of the B-ring, revealed that the protoberberine analogs do not "behave" like classic DNA intercalators. Specifically, saturation of the 5-6 double bond in the B-ring of DMC, thereby converting it to the DHDMC molecule, was associated with enhanced DNA unwinding as well as a reversal of DNA binding preference from a DNA duplex with an inaccessible or occluded minor groove {poly[d(G-C)]2} to DNA duplexes with accessible or unobstructed minor grooves {poly[d(A-T)]2 and poly[d(I-C)]2}. In addition, a comparison of the DNA binding properties for DHDMC and palmatine revealed that transferring the 11-methoxy moiety on the D-ring of DHDMC to the 9 position, thereby converting it to palmatine, was associated with a reduction in binding affinity for both duplexes with unobstructed minor grooves as well as for duplexes with occluded minor grooves. These DNA binding properties are consistent with a "mixed-mode" DNA binding model for protoberberines in which a portion of the ligand molecule intercalates into the double helix, while the nonintercalated portion of the ligand molecule protrudes into the minor groove of the host duplex, where it is thereby available for interactions with atoms lining the floor and/or walls of the minor groove. Furthermore, saturation at the 5,6 positions of the B-ring, which causes the A-ring to be tilted relative to the plane formed by rings C and D, appears to stabilize the interaction between the host duplex and the minor groove-directed portion of the protoberberine ligand. Computer modeling studies on the DHDMC-poly[d(A-T)]2 complex suggest that this interaction may involve van der Waals contacts between the ligand A-ring and backbone sugar atoms lining the minor groove of the host duplex. The hierarchy of topoisomerase I poisoning noted above suggests that this minor groove-directed interaction may play an important role in topoisomerase I poisoning by protoberberine analogs. In the aggregate, our results presented here, coupled with the recent demonstration of topoisomerase I poisoning by minor groove-binding terbenzimidazoles [Sun, Q., Gatto, B., Yu, C., Liu, A. , Liu, L. F., & LaVoie, E. J. (1995) J. Med. Chem. 38, 3638-3644], suggest that minor groove-directed ligand-DNA interactions may be of general importance in the poisoning of topoisomerase I.

Modulation of nucleic acid structure by ligand binding: induction of a DNA.RNA.DNA hybrid triplex by DAPI intercalation

The aromatic diamidine, DAPI (4',6-diamidino-2-phenylindole), is used as an important biological and cytological tool since it forms highly fluorescent complexes with nucleic acid duplexes via minor groove-directed/intercalative modes of interaction. In this study, we find that DAPI binding can induce the formation of an RNA-DNA hybrid triplex that would not otherwise form. More specifically, through application of a broad range of spectroscopic, viscometric, and molecular modeling techniques, we demonstrate that DAPI intercalation induces the formation of the poly(dT).poly(rA).poly(dT) hybrid triple helix, a structure which does not form in the absence of the ligand. Using UV mixing studies, we demonstrate that, in the presence of DAPI, the poly(rA).poly(dT) duplex and the poly(dT) single strand form a 1:1 complex (a triplex) that does not form in the absence of DAPI. Through temperature-dependent absorbance measurements, we show that the poly(dT).poly(rA).poly(dT) triplex melts via two distinct transitions: initial conversion of the triplex to the duplex state, with the DAPI remaining bound, followed by denaturation of the duplex-DAPI complex to its component single strands and free DAPI. Using optical melting profiles, we show that DAPI binding enhances the thermal stability of the poly(dT).poly(rA).poly(dT) triplex, an observation consistent with the preferential binding of the ligand to the triplex versus the duplex and single-stranded states. Our differential scanning calorimetric measurements reveal melting of the DAPI-saturated poly(dT).poly(rA).poly(dT) triplex to be associated with a lower enthalpy but greater cooperativity than melting of the corresponding DAPI-saturated poly(rA).poly(dT) duplex. Our flow linear dichroism and viscometric data are consistent with an intercalative mode of binding when DAPI interacts with both the poly(dT).poly(rA).poly(dT) triplex and the poly(rA).poly(dT) duplex. Finally, computer modeling studies suggest that a combination of both stacking and electrostatic interactions between the intercalated ligand and the host nucleic acid play important roles in the DAPI-induced stabilization of the poly(dT).poly(rA).poly(dT) triplex. In the aggregate, our results demonstrate that ligand binding can be used to induce the formation of triplex structures that do not form in the absence of the ligand. This triplex-inducing capacity has potentially important implications in the design of novel antisense, antigene, antiviral, and diagnostic strategies.

Flexing and folding double helical DNA

DNA base sequence, once thought to be interesting only as a carrier of the genetic blueprint, is now recognized as playing a structural role in modulating the biological activity of genes. Primary sequences of nucleic acid bases describe real three-dimensional structures with properties reflecting those structures. Moreover, the structures are base sequence dependent with individual residues adopting characteristic spatial forms. As a consequence, the double helix can fold into tertiary arrangements, although the deformation is much more gradual and spread over a larger molecular scale than in proteins. As part of an effort to understand how local structural irregularities are translated at the macromolecular level in DNA and recognized by proteins, a series of calculations probing the structure and properties of the double helix have been performed. By combining several computational techniques, complementary information as well as a series of built-in checks and balances for assessing the significance of the findings are obtained. The known sequence dependent bending, twisting, and translation of simple dimeric fragments have been incorporated into computer models of long open DNAs of varying length and chemical composition as well as in closed double helical circles and loops. The extent to which the double helix can be forced to bend and twist is monitored with newly parameterized base sequence dependent elastic energy potentials based on the observed configurations of adjacent base pairs in the B-DNA crystallographic literature.

Computer models of DNA four-way junctions

A modeling scheme that combines a constrained backbone generating algorithm with simple hard-sphere packing calculations is offered to build the four-stranded structures of DNA found in Holliday junctions. Two standard B-DNA duplexes are oriented side by side with helix axes at different relative inclinations and then systematically rotated and translated to identify closely spaced contact-free states. Attempts are subsequently made to introduce a low-energy sugar-phosphate linkage that serves as the site of strand exchange between the two duplexes. The chemical connection is sought using an algorithm which identifies the possible arrangements of the intervening backbone torsions between arbitrarily positioned bases. The goal is to identify the multiple conformational solutions associated with a particular arrangement of neighboring DNA helices in the four-way junction rather than a single optimum structure. The methodology is general, in terms of accommodating four-way junctions with arms of variable conformation and chain length and of dimensions much greater than treated heretofore. The only deformation in the four-way structures relative to B-DNA occurs at the site of backbone exchange, with base stacking and Watson-Crick pairing completely preserved in all models. The arrangements of neighboring bases at these sites resemble the unusual conformational steps found in a number of small molecule nucleic acid crystal structures. An interesting outcome of the calculations is the formation of sterically acceptable four-arm Holliday junctions over a wide range of angles at the cross. The potential mobility of the Holliday junctions is inferred from visualization and energetic analysis of the various models. Long-range electrostatic energies based on different currently available treatments of the dielectric constant are used to estimate the conformational preferences and flexibility of the four-stranded structures. The various dielectric schemes, however, are not in complete agreement on the likely conformational variability of the four-way junctions. The structures suggest a possible mechanism for branch migration and detail a pathway linking the antiparallel uncrossed Holliday structure inferred from solution measurements and the parallel cross-packed helical arrangements observed in single-crystal X-ray studies.

A systematic method for studying the spatial distribution of water molecules around nucleic acid bases

A new method to analyze the distribution of water molecules around the bases in DNA is presented. This method relies on the notion of a "hydrated building block," which represents the joint observed hydration around all bases of a particular type, in structures of a particular conformation type. The hydrated building blocks were constructed using atomic coordinates from 40 structures contained in the Nucleic Acid Database. Pseudoelectron densities were calculated for water molecules in each hydrated building block using standard crystallographic procedures. The electron densities were fitted to obtain "average building blocks," which represent bases with waters only at average or probable positions. Both types of building blocks were used to construct models of hydrated DNA oligomers. The essential features of the solvent structure around d(CGCGAATTCGCG)2 in the B form and d(CGCGCG)2 in the Z form were reproduced.

Comparative spectroscopic, calorimetric, and computational studies of nucleic acid complexes with 2',5"-versus 3',5"-phosphodiester linkages

We have used a combination of spectroscopic, calorimetric, and computational techniques to characterize the properties of nucleic acid complexes with 2',5''- and 3',5''-phosphodiester linkages. Specifically, we have compared the properties of complexes formed by the association of 3',5'' single-stranded 16-mers of adenylic acid (A16) and thymidylic acid (T16) with the complexes formed by the corresponding single-stranded 16-mers with 2',5''-phosphodiester linkages (A*16 and T*16). Our results reveal the following differential features: (i) the 3',5'' strands form either a duplex or a triplex, depending on the sodium ion concentration, whereas the 2',5'' strands form either a triplex or no complex at all; (ii) the 2',5'' and 3',5'' triplexes exhibit significantly different CD spectra, suggesting that the two triplex states are conformationally nonequivalent; (iii) the 2',5'' triplex has a lower charge density than the 3',5'' triplex; (iv) the thermal stability of the 3',5'' triplex, as expected, is concentration dependent, whereas the thermal stability of the 2',5'' triplex is concentration independent; (v) relative to their component single strands, the 2',5'' triplex is thermodynamically much less stable than the 3',5'' triplex, despite being thermally more stable; (vi) the reduced thermodynamic stability of the 2',5'' triplex relative to the 3',5'' triplex is overwhelmingly enthalpic in origin. In the aggregate, our results reveal and characterize significant differences in the properties of complexes formed by the association of strands with identical base sequences but different phosphodiester linkages. We describe a structural model that is consistent with many of the differential properties observed. We also speculate on how these differential properties may have provided an evolutionary advantage for 3',5'' linkages and how the properties of 2',5'' complexes might be exploited in antisense strategies.

DNA associations: packing calculations in A-, B-, and Z-DNA structures

A detailed theoretical study has been carried out to examine the modes of DNA-DNA interactions on the basis of hard-sphere contact criteria. Two helices of identical structure and length are oriented side-by-side and their relative positions are controlled by translations along and rotations about specific axes. Short atomic contacts between pairs of atoms in the structures are assessed and contact-free configurations are compiled. The computed contact-free arrangements of A, B, and Z double helices are found to be remarkably similar to the packing motifs observed in DNA crystals and stretched fibers. Equally interesting in the study are the broad ranges of sterically acceptable arrangements that preserve the overall packing morphology of neighboring duplexes: Among the most notable morphological features in the helical complexes are extended "super" major and minor grooves which might facilitate the wrapping and packaging of DNA chains in supramolecular assemblies. The hard-sphere computations, however, are insufficient for quantitative interpretation of the packing of DNA helices in the solid state. The results are, nevertheless, a useful starting point for energy based studies as well as relevant to the analysis of long-range interactions in DNA supercoils and cruciforms.

The translation of DNA primary base sequence into three-dimensional structure

A procedure is outlined to obtain a reliable computer-generated representation of the DNA duplex from its primary sequence of base pairs. The calculations are based on the potential energies of interaction of adjacent side groups. The methods are, however, completely general and can be adapted to any set of base sequence dependent conformational rules. Static representations of the DNA are compared with the distributions of conformations obtained from Monte Carlo simulation studies. Direct matrix generator calculations of the average (equilibrium) extension and orientation of various sequences and numerical estimates of the flexibility of the chains as a whole are also reported. The methods are applied to three short fragments of kinetoplast DNA from Crithidia fasciculata which exhibit dramatically different behavior on non-denaturing polyacrylamide gels.

Base sequence effects in double helical DNA. I. Potential energy estimates of local base morphology

A series of potential energy calculations have been carried out to estimate base sequence dependent structural differences in B-DNA. Attention has been focused on the simplest dimeric fragments that can be used to build long chains, computing the energy as a function of the orientation and displacement of the 16 possible base pair combinations within the double helix. Calculations have been performed, for simplicity, on free base pairs rather than complete nucleotide units. Conformational preferences and relative flexibilities are reported for various combinations of the roll, tilt, twist, lateral displacement, and propeller twist of individual residues. The predictions are compared with relevant experimental measures of conformation and flexibility, where available. The energy surfaces are found to fit into two distinct categories, some dimer duplexes preferring to bend in a symmetric fashion and others in a skewed manner. The effects of common chemical substitutions (uracil for thymine, 5-methyl cytosine for cytosine, and hypoxanthine for guanine) on the preferred arrangements of neighboring residues are also examined, and the interactions of the sugar-phosphate backbone are included in selected cases. As a first approximation, long range interactions between more distant neighbors, which may affect the local chain configuration, are ignored. A rotational isomeric state scheme is developed to describe the average configurations of individual dimers and is used to develop a static picture of overall double helical structure. The ability of the energetic scheme to account for documented examples of intrinsic B-DNA curvature is presented, and some new predictions of sequence directed chain bending are offered.

Nucleic acid model building: the multiple backbone solutions associated with a given base morphology

A constrained model building procedure is used to generate nucleic acid structures of the familiar A-, B-, and Z-DNA duplexes. Attention is focused upon the multiple structural solutions associated with the arrangements of nucleic acid base pairs rather than the optimum sugar-phosphate structure. The glycosyl (chi) and sugar torsions (both the ring puckering and the exocyclic C5'-C4' (psi) torsion) are treated as independent variables and the resulting O3'...O5' distances are used as closure determinants. When such distances conform to the known geometry of phosphate chemical bonding, an intervening phosphorus atom with correct C-O-P valence angles can be located. Four sequential torsion angles--phi', omega', omega and phi--about the C3'-O3'-P-O5'-C5' bonds are then obtained as dependent variables. The resulting structures are categorized in terms of conformation, ranked in potential energy, and analyzed for torsional correlations. The numerical results are quite interesting with implications regarding nucleic acid models constructed to fit less than ideal experimental data. The multiple solutions to the problem are useful for comprehending the conformational complexities of the local sugar-phosphate backbone and for understanding the transitions between different helical forms. According to these studies, unique characterization of a nucleic acid duplex involves more than the determination of its base pair morphology, its sugar puckering preferences, or its groove binding features.

Conformational studies of (2'-5') polynucleotides: theoretical computations of energy, base morphology, helical structure, and duplex formation

A detailed theoretical analysis has been carried out to probe the conformational characteristics of (2'-5') polynucleotide chains. Semi-empirical energy calculations are used to estimate the preferred torsional combinations of the monomeric repeating unit. The resulting morphology of adjacent bases and the tendency to form regular single-stranded structures are determined by standard computational procedures. The torsional preferences are in agreement with available nmr measurements on model compounds. The tendencies to adopt base stacked and intercalative geometries are markedly depressed compared to those in (3'-5') chains. Very limited families of regular monomerically repeating single-stranded (2'-5') helices are found. Base stacking, however, can be enhanced (but helix formation is at the same time depressed) in mixed puckered chains. Constrained (2'-5') duplex structures have been constructed from a search of all intervening glycosyl and sugar conformations that form geometrically feasible phosphodiester linkages. Both A- and B-type base stacking are found to generate non-standard backbone torsions and mixed glycosyl/sugar combinations. The 2'- and 5'-residues are locked in totally different arrangements and are thereby prevented from generating long helical structures.

Conformational preferences of cyclopropyl peptides. Crystal structure of (E)-DL-1-benzamido-1-methoxycarbonyl-2-chlorcyclopropane (BCP)

Crystal structure analysis of (E)-DL-1-benzamido-1-methoxycarbonyl-2-chlorocyclopropane (C12H12NO3Cl) is reported. The phi' (about N1-C1 bond) and psi' (about C1-C11 bond) torsional angles for this compound are -62.5 degrees and -33.0 degrees, respectively, and are close to the phi, psi values of the 3(10) helix and the alpha-helix. Semi-empirical potential energy calculations are performed on a cyclopropyl dipeptide which is a special case of alpha,alpha-disubstituted dipeptide where the alpha-carbon and the two substituent carbon atoms form a 3-membered ring. Our calculations show that different types of helics: alpha-, gamma-, pi-, omega-, 3(10-) and delta-helices, are energetically favorable. Another interesting possibility is the formation of a cyclic pentapeptide with five-fold symmetry. The effect of substitutions on C beta atom are also studied with the help of potential energy maps. Selective substitutions on C beta atom may be used effectively to restrict either phi or psi values into a very narrow range.

Influence of the carcinogen 4-aminobiphenyl on DNA conformation

The conformation of the deoxydinucleoside monophosphate dCpdG modified by the carcinogen 4-aminobiphenyl has been elucidated by minimized semi-empirical potential energy calculations. The most important conformers relevant to A or B and Z helices are shown, and the structures of carcinogen-modified polymers, obtained from computer-generated models that incorporate the dimer conformations, are presented. Forms with carcinogen-base stacking and with base-base stacking are found, for both A-B type helices and Z-type helices. In random sequence DNA, the most favored state places the carcinogen at the A or B helix exterior, in the large groove, where it causes no distortion. In this position it might escape repair till a round of replication. At the replication fork, where the DNA is unwound, a low energy carcinogen-base stacked state, easily achieved by rotation primarily about the C5' - O5' bond, could occur. A mutagenic outcome resulting from this conformation might be envisioned.

Protein conformation wheels: cytochromes and lysozymes

Conformation wheels, directly relating to amino acid sequence to the local torsion angles in a protein molecule, are presented for cytochromes c, c2, c550, and c551 and for lysozymes from hen egg-white and T4 bacteriophage. The circular plots for the cytochrome molecules aid in visualizing the common three-dimensional folding ("cytochrome fold") observed in this family of proteins. Conformation wheels for lysozymes from two different species reveal the characteristic differences in their folding patterns. These novel plots are also useful in storing and comparing the several sets of crystallographic data reported for lysozyme.

Yeast tRNAPhe conformation wheels: a novel probe of the monoclinic and orthorhombic models

A series of conformation wheels is constructed from the recently refined X-ray crystallographic data of monoclinic and orthorhombic yeast tRNAPhe. These circular plots relate the primary chemical structure (i.e., base sequence) directly to the secondary and tertiary structure of the molecule. The circular sequence of backbone torsion angles displays a unique pattern that is useful both in distinguishing the ordered and disordered regions of the molecule and in comparing the three sets of experimental data. Composite conformation wheels describe the fluctuations in the "fixed" parameters (phi', phi, chi) and independent conformation wheels reveal the changes in the "variable" parameters (omega', omega, psi, psi') of the three different yeast tRNAPhe models. Additional plots of base-stacking parameters help to visualize the intimate interrelationship between chemical sequence and three-dimensional folding of yeast tRNAPhe. The composite data illustrate several conformational schemes that position the bases of adjacent nucleosides in a parallel stacked array and reveal an even larger number of conformations that introduce bends or turns in the polynucleotide chain.

A novel representation of the conformational structure of transfer RNAs. Correlation of the folding patterns of the polynucleotide chain with the base sequence and the nucleotide backbone torsions

A novel description of the conformational characteristics of all the individual nucleotides and the phosphodiesters in tRNAs is presented in the form of a circular plot. This representation furnishes information of the base sequence with the folding patterns of the polynucleotide chain as one traverses along the circumference and with the individual nucleotide and phosphodiester linkage torsions along the radii. The circular plot obtained for yeast tRNAPhe strikingly distinguishes the helical and the loop regions. The variation of the different nucleotide torsions along the entire chain length and their effect on the secondary helical and tertiary loop regions become readily apparent.

Solvent accessibilities in glycyl, alanyl and seryl dipeptides

Theoretical studies on glycyl-alanyl and seryl dipeptides were performed to determine the probable backbone and side-group conformations that are preferred for solvent interaction. By following the method of Lee & Richards [(1971) J. Mol. Biol. 55, 379-400], a solute molecule is represented by a set of interlocking spheres of appropriate van der Waals radii assigned to each atom, and a solvent (water) molecule is rolled along the envelope of the van der Waals surface, and the surface accessible to the solvent molecule, and hence the solvent accessibility for a particular conformation of the solute molecule, is computed. From the calculated solvent accessibilities for various conformations, solvation maps for dipeptides were constructed. These solvation maps suggest that the backbone polar atoms could interact with solvent molecules selectively, depending on the backbone conformation. A conformation in the right-handed bridge (zetaR) region is favoured for both solvent interaction and intrachain hydrogen-bonding. Also the backbone side-chain hydrogen-bonding within the same dipeptide fragment in proteins is less favoured than hydrogen-bonding between side chain and water and between side chain and atoms of other residues. Solvent accessibilities suggest that very short distorted alphaR-helical and extended-structural parts may be stabilized via solvent interaction, and this could easily be possible at the surface of the protein molecules, in agreement with protein-crystal data.