Salvage DC ablation of ventricular tachycardia following failed RF attempts

Background

Ablation of ventricular tachycardia (VT) is a frequent clinical necessity. Modification of ventricular substrate can usually be achieved by radiofrequency ablation (RF). We present 4 cases of failed RF for recurrent VT. Two patients had multiple RF failures, one patient had in-procedure failure, and one patient had multiple RF attempts and a failed alcohol ablation (pt4).

Objective

To evaluate success of DC ablation after failed RF

Methods

A 6 Fr 4mm tip steerable ablation catheter, was placed at the site felt to be critical for the circuit following mapping (earliest activation, mid-diastolic, fractionated, site of concealed entrainment, or ventricular breakout). Two connection cables were utilized, one to the recording/mapping system, and one connected to an external biphasic defibrillator (DC). The DF was connected with one pad anterior chest and the other connected by the cable to electrode pins 1 and 2 folded within the second pad. The electrodes were secured by placing a hemostat on the pad. DC energy (360j) was delivered synchronized by electrodes 1–2

Results

During follow-up 3 months to 1 year, no recurrent VT was observed. 3 patients received a total of 4 DC pulses, while the pt4 received 16 (RV and LV septum), complicated by prolonged hypotension. No other complications were observed. Figure shows broad RV breakout from the septum in pt4.

Conclusion

In patients with RF refractory VT, DC ablation may be safely used and in this limited series, provides long-term success. Interestingly, biphasic energy did not induce transient hypotension in 3 of 4 pts. DC ablation should be considered following failed RF, especially when mid-myocardial origin suspected.

Funding Acknowledgement

Type of funding source: None

The nature of fast and slow pathway interaction during premature pacing: evaluation with high density mapping

Background

Dual AV Nodal (AVN) inputs are associated with the fast pathway (FPW) superiorly, while the SPW activates inferiorly. In the present study, we evaluate the impact of PES on dual antegrade conduction.

Objective

To Define Antegrade Conduction Properties of the AV Node during PES

Methods

High density mapping (Orion, Rhythmia) was performed and analyzed in SR and S2 PES in 12 pts. The FPW activates the AVN and travels inferiorly, there is a point where the activation pivots toward the SPW and travels superiorly along the TV. The distance from the pivot point was measured to the HIS location in sinus rhythm and for each coupling interval. Both the distance and prematurity of the S2 coupling was normalized to the BCL during sinus rhythm. The coupling interval was then plotted vs the HIS-Collision distance. A regression analysis was used to compare data sets with significance defined a <0.05.

Results

Data was obtained in all 12 patients. In all patients, as pre-maturity of S2 increased, the pivot point moved superiorly until there was block in the FPW and activation to the AV node was entirely from the SPW. There is a functional line of block (LOB) between the FPW and SPW. Comparing normalized data decrement vs change in pivot point: R=0.8 p<0.0001

Conclusion

During PES, the F/SPW interaction changes: increasing prematurity causes pivot point to move superiorly until the FPW blocks and AVN activates via the SPW. Decremental antegrade conduction occurs within FPW and is associated with the superior pivot shift toward the AVN suggesting a functional LOB. This relationship is linear.

Funding Acknowledgement

Type of funding source: None

Assessment of Celiac Axis and Hepatic Artery Variations in Hepatobiliary and Pancreatic Malignancy with Multidetector Computed Tomography Angiography

Introduction Delineation of variant anatomy in celiac trunk and superior mesenteric artery including its origin and branching pattern and variations in branching pattern of hepatic artery in patients of hepatopancreaticobiliary malignancy with the use of mutidetector CT (computed tomography) angiograpgy was performed.

Materials and Methods All CT examinations were performed on a 64-multidetector computed tomography (MDCT) scanner. Technical features of multislice computed tomography (MSCT) are as follows: 64 mm × 1 mm collimation, minimum slice thickness of 0.625, gantry rotation time of 320 ms, 120 kV, and 320 mAs. CT angiography was performed with intravenous (IV) administration of nonionic contrast material, that is, iodixanol (Visipaque). The contrast medium and saline solution were injected with a Medrad power injector at 3 mL/sec through an 18-gauge plastic intravenous catheter placed in an antecubital vein in most of the cases. Contrast medium volumes varied between 100 and 150 mL at 1.5 mL/kg. Images were obtained in triphasic pattern at arterial (20–30 seconds), portal (60–70 seconds), and equilibrium (at 3 minutes) phases.

Results Five types of celiac axis anatomic variations and nine type of variants in celiac axis branching was found in the study sample of 124 patients. Classical celiac axis anatomy was seen in 92.7% of the cases, while the five types of variation in branching were found in nine patients. Majority of cases showed pattern I (59.6%) followed by patterns V (12.1%), II (9.7%), and III (8.9%). There were three (2.4%) cases each showing pattern VIII and AA, and two (1.6%) cases each showing patterns IV and VI, respectively. There was one (0.8%) case each showing pattern VII and IX. A total of three (2.4%) cases showed right hepatic artery arising from celiac axis.

Conclusion We conclude that most common pattern of celiac axis and superior mesenteric artery (SMA) branching is classical pattern (92.7%) which is in concordance with literature. Type-I pattern of hepatic artery branching was most common (59.6%), similar to that documented in literature. Although the most common variation in our study is type V (12.1%), followed by types II (9.7%) and III (8.9%), the most common variation in most of the literature was found to be type III. CT angiography hence is an excellent diagnostic modality for depiction of arterial anatomic variations and provides a roadmap for surgical treatment.

Feasibility and Results of Cancer Registry and Noncommunicable Disease Cohort Data Linkages in India

Background: Cancer registries worldwide are vital to determine cancer burden, plan cancer control measures, and facilitate research. Population-based cancer registries are a priority for LMICs by the UICC; the National Cancer Registry Program (NCRP) of India oversees 28 such registries. A primary function of registries is to combine data for the same individual from multiple sources. For other disease cohorts where cancer is an outcome of interest, registries can potentially connect information by linking datasets together. Barriers to successful registration and linkages include systems in which cancer is not a notifiable disease, no universal unique individual identifier exists, and lack of trained personnel. This study utilizes technology and infrastructure to develop better linkages, surveillance, and outcomes. Aim: To assess the feasibility of linking large cohorts designed for cardio-metabolic disease research with cancer registries in New Delhi and Chennai; determine additional steps required for linkage accuracy and completeness; and develop detailed protocols for future applications. Methods: A pilot protocol for linkage between a large diabetes cohort and cancer registries in Delhi and Chennai was developed using MatchPro, a probabilistic record linkage program developed for cancer registries. Probabilistic software links datasets together in the presence of uncertainty (eg misspelled or abbreviated names) to identify record pairs with high probability of representing the same individual. For this study, algorithms were developed to address unique aspects of names and demographics in India. The software and algorithms focused on: detecting duplicates in cancer registries; and linking registries with external files from diabetes cohorts. In Delhi, 3 1-year datasets covering 3 years (2010, 2011, 2012) were linked with the diabetes cohort; in Chennai, the linkage included 3 5-year datasets covering 15 years (2000-04, '05-'09, '10-'14). The unique ID (Aadhaar) is not collected or linked systematically between different systems at this point in time. Results: Linkage attempts yielded potential matches ranked according to probabilistic scores; highest scores were reviewed to determine true matches. In Chennai, this process yielded: (2010-2014) 21% self-reported (SR) cases matching perfectly, 36% requiring follow-up, 13 nonreported (NR) cases found; 2005-2009: 33% SR cases matched perfectly, 1 NR case found; 2000-2004: 1 NR case. Also, 2 training workshops on data linkages and software were held. Conclusion: Linkages between cancer registries and other data sources are feasible in LMICs using probabilistic record linkage software augmented by manual matching. Future efforts to use existing epidemiologic resources (cohorts) and cancer research infrastructure (registries and clinical centers) can enhance research including understanding shared risk factors and pathophysiologic mechanisms e.g., between cancer and other NCD.

Exciton Emission Intensity Modulation of Monolayer MoS2 via Au Plasmon Coupling

Modulation of photoluminescence of atomically thin transition metal dichalcogenide two-dimensional materials is critical for their integration in optoelectronic and photonic device applications. By coupling with different plasmonic array geometries, we have shown that the photoluminescence intensity can be enhanced and quenched in comparison with pristine monolayer MoS2. The enhanced exciton emission intensity can be further tuned by varying the angle of polarized incident excitation. Through controlled variation of the structural parameters of the plasmonic array in our experiment, we demonstrate modulation of the photoluminescence intensity from nearly fourfold quenching to approximately threefold enhancement. Our data indicates that the plasmonic resonance couples to optical fields at both, excitation and emission bands, and increases the spontaneous emission rate in a double spacing plasmonic array structure as compared with an equal spacing array structure. Furthermore our experimental results are supported by numerical as well as full electromagnetic wave simulations. This study can facilitate the incorporation of plasmon-enhanced transition metal dichalcogenide structures in photodetector, sensor and light emitter applications.

Endoscopic ultrasound-guided fine-needle aspiration cytology in the evaluation of suspected tuberculosis in patients with isolated mediastinal lymphadenopathy

BACKGROUND AND STUDY AIMS

Patients with suspected tuberculosis without pulmonary lesions and with mediastinal lymphadenopathy often pose a diagnostic challenge. Endoscopic ultrasound (EUS)-guided fine-needle aspiration (FNA) cytology is an established modality to evaluate mediastinal and abdominal lesions. The aim of the present study was to evaluate the role of EUS-FNA in isolated mediastinal lymphadenopathy in patients suspected of having tuberculosis.

METHODS

Consecutive patients suspected of having tuberculosis with isolated mediastinal lymphadenopathy were included in a prospective study. Mediastinal lymphadenopathy was diagnosed on a contrast-enhanced computed tomography scan of the chest. Patients with concomitant lung parenchymal lesions were excluded. Previous attempts to diagnose the etiology of lymphadenopathy had failed in 69 % of patients. EUS-FNA was performed on an outpatient basis under conscious sedation. The sensitivity, specificity, and diagnostic accuracy of EUS-FNA were calculated.

RESULTS

A total of 60 consecutive patients (mean age 39.8 years, 58 % males) with mediastinal lymphadenopathy were included. EUS confirmed the presence of mediastinal lymph nodes ranging in size from 8 mm to 40 mm (mean 26 mm) in all patients. EUS-FNA provided an adequate tissue sample in 54 patients during the first examination and repeat EUS-FNA was necessary in six patients. A final diagnosis was obtained by EUS-FNA in 42 patients (tuberculosis in 32, sarcoidosis in six, and Hodgkin's disease in four patients). An additional 14 patients were treated for tuberculosis based on EUS-FNA and clinical features. Mediastinoscopy was required for diagnosis in the remaining four patients. EUS-FNA had an overall diagnostic yield of 93 %, sensitivity of 71 %, specificity of 100 %, and positive predictive value of 100 %.

CONCLUSION

EUS-FNA is an accurate, safe, and minimally invasive modality for evaluating isolated mediastinal lymphadenopathy in patients suspected of having tuberculosis in an endemic area with a high prevalence of tuberculosis.

Gene expression in peripheral blood mononuclear cells from patients with chronic fatigue syndrome

BACKGROUND

Chronic fatigue syndrome (CFS) is a multisystem disease, the pathogenesis of which remains undetermined.

AIMS

To test the hypothesis that there are reproducible abnormalities of gene expression in patients with CFS compared with normal healthy persons.

METHODS

To gain further insight into the pathogenesis of this disease, gene expression was analysed in peripheral blood mononuclear cells from 25 patients with CFS diagnosed according to the Centers for Disease Control criteria and 25 normal blood donors matched for age, sex, and geographical location, using a single colour microarray representing 9522 human genes. After normalisation, average difference values for each gene were compared between test and control groups using a cutoff fold difference of expression > or = 1.5 and a p value of 0.001. Genes showing differential expression were further analysed using Taqman real time polymerase chain reaction (PCR) in fresh samples.

RESULTS

Analysis of microarray data revealed differential expression of 35 genes. Real time PCR confirmed differential expression in the same direction as array results for 16 of these genes, 15 of which were upregulated (ABCD4, PRKCL1, MRPL23, CD2BP2, GSN, NTE, POLR2G, PEX16, EIF2B4, EIF4G1, ANAPC11, PDCD2, KHSRP, BRMS1, and GABARAPL1) and one of which was downregulated (IL-10RA). This profile suggests T cell activation and perturbation of neuronal and mitochondrial function. Upregulation of neuropathy target esterase and eukaryotic translation initiation factor 4G1 may suggest links with organophosphate exposure and virus infection, respectively.

CONCLUSION

These results suggest that patients with CFS have reproducible alterations in gene regulation.

An isolated left common carotid artery from the main pulmonary artery: possible malseptation of the truncoaortic sac

An isolated left common carotid artery (LCA) is an extremely rare condition with only four reported cases. In each case, the isolated carotid artery connects to the right or left pulmonary artery via the ductus arteriosus and the embryologic basis for the abnormalities is believed to reflect an error in the development of the branchial arches. We present a case of an isolated LCA connecting to the main pulmonary artery in association with a right aortic arch and an anomalous origin of the left subclavian artery from the descending aorta. The left ligamentus arteriosus was identified separately. This may represent a disturbance in the septation of the truncoaortic sac secondary to abnormal migration of neural crest cells rather than a pure developmental anomaly of the branchial arches.

Destabilization of tRNA3(Lys) from the primer-binding site of HIV-1 genome by anti-A loop polyamide nucleotide analog

Initiation of human immunodeficiency virus type 1 (HIV-1) reverse transcription occurs by extension of the cellular tRNA3(Lys) which anneals to the primer-binding site (PBS) on the 5' non-translated region of the viral RNA genome. The A-rich sequence (A-loop) upstream of the PBS interacts with the anticodon loop of tRNA3(Lys) and has been proposed to be essential for conferring specificity to tRNA3(Lys) for priming the initiation of HIV-1 reverse transcription. We observed that polyamide nucleic acid targeted to the A-loop sequence (PNAAL) exhibits high binding specificity for its target sequence. The PNAAL pre-bound to the A-loop sequence prevents tRNA3(Lys) priming on the viral RNA consequently blocking in vitro initiation of reverse transcription. Further, PNAAL can efficiently disrupt the preformed [tRNA3(Lys)--viral RNA] complex thereby rendering it non-functional for reverse transcription. The endogenous reverse transcription in disrupted HIV-1 virions containing packaged tRNA3(Lys) and its replicating enzyme RT was significantly inhibited by PNAAL, thus providing direct evidence of the involvement of the A-loop region of viral RNA genome in tRNA3(Lys) priming process. These findings suggest the potential of the A-loop region as a critical target for blocking HIV-1 replication.

A survey of trinucleotide/tandem repeat-containing transcripts (TNRTs) isolated from human spinal cord to identify genes containing unstable DNA regions as candidates for disorders of motor function

Expansion of unstable DNA regions containing trinucleotide/tandem repeats (TNRs) represents a common genetic mutation in hereditary forms of neurological disorders. The spectrum of neurological diseases linked to TNR expansions has recently broadened to include conditions with both dominant and recessive inheritance and those with or without clinical anticipation. In view of the frequent involvement of the spinal cord in neurodegenerative disorders, we have analysed this key tissue to identify pathological TNRs. We have used two approaches to isolate a wide range of trinucleotide/tandem repeat-containing transcripts (TNRTs) from human spinal cord, firstly a polymerase chain reaction (PCR)-based method and secondly by screening a spinal cord cDNA library immobilised on a membrane. Overall, 97 TNRTs belonging to a number of key protein families, the most highly represented being transcription factors, intracellular signalling molecules and cytoskeletal proteins, have been isolated most of which have not previously been considered as potential disease-causing genes. The commonest repeat motifs found in our study were CAG (37%) and CCG (24%). Known genes involved in DNA repeat expansion-related neurological disorders (e.g., AAD10, Ataxin-3, Huntingtin) were detected which validated our methods. We have characterised homogeneous TNRs among the detected gene candidates in a search for potential pathological repeat expansions. The potential role of the gene candidates identified is discussed in terms of their contribution to neurodegenerative processes.

Insertion of a peptide from MuLV RT into the connection subdomain of HIV-1 RT results in a functionally active chimeric enzyme in monomeric conformation

The natural form of the human immunodeficiency virus type one reverse transcriptase (HIV-1 RT) found in virion particles is a heterodimer composed of the p66 and p51 subunits. The catalytic activity resides in the larger subunit in the heterodimeric (p66/p51) enzyme while in the monomeric form it is inactive. In contrast, Murine leukemia virus RT (MuLV RT) is functionally active in the monomeric form. In the primary amino acid sequence alignment of MuLV RT and HIV-1 RT, we have identified three specific regions in MuLV RT, that were missing in HIV-1 RT. In a separate study, we have shown that a chimeric RT construct comprising of the polymerase domain of HIV-1 RT and RNase-H domain of MuLV RT is functionally active as monomer [20]. In this communication, we demonstrate that insertion of a peptide (corresponding to amino acid residues 480-506) from the connection subdomain of MuLV RT into the connection subdomain of HIV-1 RT (between residues 429 and 430) results in a functionally active monomeric chimeric RT. Furthermore, this chimeric enzyme does not dimerize with exogenously added p51 subunit of HIV-1RT. Functional analysis of the chimeric RT revealed template specific variations in its catalytic activity. The chimeric enzyme catalyzes DNA synthesis on both heteropolymeric DNA and homopolymeric RNA (poly rA) template but curiously lacks reverse transcriptase ability on heteropolymeric RNA template. Similar to MuLV RT, the polymerase activity of the chimeric enzyme is not affected by acetonitrile, a reagent which dissociates dimeric HIV-1 RT into inactive monomers. These results together with a proposed 3-D molecular model of the chimeric enzyme suggests that the insertion of the missing region may induce a change in the spatial position of RNase H domain such that it is functionally active in monomeric conformation.

The beta7-beta8 loop of the p51 subunit in the heterodimeric (p66/p51) human immunodeficiency virus type 1 reverse transcriptase is essential for the catalytic function of the p66 subunit

The heterodimeric human immunodeficiency virus type 1 reverse transcriptase (HIV-1 RT) is composed of p66 and p51 subunits, p66 being the catalytic subunit. Our earlier investigation on the role of p51 in the catalytic process has shown that the p51 subunit facilitates the loading of the p66 subunit onto the template primer (TP). We had postulated that the beta7-beta8 loop of the p51 subunit may be involved in opening the polymerase cleft of p66 for DNA binding [Pandey, V. N., et al. (1996) Biochemistry 35, 2168]. We report here that deletion or alanine substitution of four residues of the beta7-beta8 loop results in severe impairment of the polymerase function of the heterodimeric enzyme. The enzyme activity was restored to the wild-type levels when the mutant p66 subunit was dimerized with the wild-type p51, suggesting that the intact beta7-beta8 loop in the p51 subunit is indispensable for the catalytic function of p66. Further, the template primer binding ability of the enzyme was significantly reduced upon deletion or alanine substitution in the beta7-beta8 loop. Interestingly, the loss of the TP binding ability of the mutant p66 was restored upon dimerization with wild-type p51. Examination of the glycerol gradient ultracentrifugation analysis revealed that while the wild-type HIV-1 RT sediments as a dimeric protein, the mutant enzymes carrying deletion or alanine substitution in both the subunits sediment predominantly as monomeric proteins, suggesting their inability to form stable dimers. In contrast, mutant p66 dimerized with wild-type p51 (p66delta/p51WT and p66Ala/p51WT) sedimented at the dimeric position. Taken together, these results clearly implicate the importance of the beta7-beta8 loop of p51 in the formation of stable functional heterodimers.

Metabolism of fluvalinate in chickpea plants under sub-tropical conditions of northern India

The metabolism of fluvalinate in chickpea plants in the field under sub-tropical climatic conditions has been investigated. Ten days after spraying with fluvalinate, leaves were collected and extracted in acetone. The extract was fractionated and the metabolites were identified by co-chromatography using TLC, GLC, and GC-MS. The anilino acid, a metabolite derived from ester cleavage, was the major metabolite present as both free and conjugated forms in chickpea leaves. 3-PBacid and 3-PBalc were minor metabolites. Glucose was found to be the major sugar conjugating with the metabolites.

Differential expression of 14 genes in amyotrophic lateral sclerosis spinal cord detected using gridded cDNA arrays

In order to obtain insight into the aetiology and pathogenesis of amyotrophic lateral sclerosis (ALS), high-density gene discovery arrays (GDA human version 1.2) containing 18 400 non-redundant EST cDNAs pooled from different tissue libraries have been used to monitor gene expression in lumbar spinal cord from ALS cases compared with controls. Quantitative filter analysis revealed differential expression of cDNAs normalized to internal standards. These candidates have been further investigated and their expression in spinal cord characterized in a panel of ALS and control subjects. Significant differential expression was obtained for 14 genes, 13 being elevated (up to six-fold) and one decreased (by 80%) in ALS. Amongst those elevated in ALS were thioredoxin and glial fibrilary acid protein, which have already been shown to be up-regulated in ALS, thus supporting the reliability of this approach. The other differentially regulated transcripts confirmed in the expression studies represent potential candidates in ALS pathogenesis being involved in antioxidant systems, neuroinflammation, the regulation of motor neurone function, lipid metabolism, protease inhibition and protection against apoptosis. The use of the GDA system has greatly facilitated the screening and retrieval of sequence information and has generated useful information on the cascade of molecular events occurring in ALS and potentially may highlight new candidates playing a role in the aetiology and progression of this disease.

GLC analysis of Indian rapeseed-mustard to study the variability of fatty acid composition

Rapeseed-mustard is one of the most economically important oilseed crops in India. Speciality oils having high amounts of a specific fatty acid are of immense importance for both nutritional and industrial purposes. Oil high in oleic acid has demand in commercial food-service applications due to a long shelf-life and cholesterol-reducing properties. Both linoleic and linolenic acids are essential fatty acids; however, less than 3% linolenic acid is preferred for oil stability. High erucic acid content is beneficial for the polymer industry, whereas low erucic acid is recommended for food purposes. Therefore, it is important to undertake systematic characterization of the available gene pool for its variable fatty acid profile to be utilized for specific purposes. In the present study the Indian rapeseed-mustard germplasm and some newly developed low-erucic-acid strains were analysed by GLC to study the fatty acid composition in these lines. The GLC analysis revealed that the rapeseed-mustard varieties being commonly grown in India are characterized by high erucic acid content (30-51%) in the oil with low levels of oleic acid (13-23%). However, from among the recently developed low-erucic-acid strains, several lines were identified with comparatively high oleic acid (60-70%), moderate to high linoleic acid (13-40%) and low linolenic acid (< 10%) contents. Work is in progress at TERI (New Delhi, India) to utilize these lines for development of strains with particular fatty acid compositions for specific purposes.

A 14-3-3 mRNA is up-regulated in amyotrophic lateral sclerosis spinal cord

We have recently isolated a 2.2-kb cDNA clone (1C5) from a human spinal cord cDNA library with partial identity to the 14-3-3 protein mRNA encoding the theta protein (YWHAQ). 14-3-3 protein transcripts are highly expressed in large projection neurones of the hippocampus, cerebellum, and spinal cord and have been found to be significantly up-regulated in rat motor neurones following hypoglossal nerve axotomy. In this study we investigated whether the 1C5 transcript (YWHAQ) isolated from spinal cord was involved in amyotrophic lateral sclerosis (ALS). We found a significant up-regulation of 1C5 (YWHAQ) in lumbar spinal cord from patients with sporadic ALS compared with controls, with the highest levels of expression being found in individuals with predominant lower motor neurone involvement. A 6-bp tandem repeat in the 5'-untranslated region of the gene was found to be polymorphic, but no significant association with disease was found following genomic analysis of this region. The localisation of 1C5 (YWHAQ) to chromosome 2 was determined and coincides with that reported for clone HS1 (EMBL accession no. X57347). These results show the marked up-regulation of the 14-3-3 isoform (YWHAQ) in ALS spinal cord and indicate the involvement of a potential 14-3-3-mediated survival pathway in the pathogenesis of ALS.

Variations in fatty acid composition of neem seeds collected from the Rajasthan state of India

Neem (Azadirachta indica) is a multipurpose tree native to the Indian subcontinent and South-East Asian countries. Products derived from neem have been used for centuries, particularly in India, for medicinal and pest-management purposes. Azadirachtin and neem oil are the two major commercially important products derived from the tree. The oil contains palmitic, stearic, oleic and linoleic acids in good proportion. Although there is growing demand for quality planting material for plantation of neem, efforts are lacking for the selection of neem trees based on their biochemical composition. In the present study, 60 Neem seed samples were collected from different provinances of the Rajasthan state in India. These samples were analysed by GLC to study the variability of fatty acid composition. Significant variability in individual fatty acids was observed. The palmitic acid ranged from 16 to 34%, stearic acid from 6 to 24%, oleic acid from 25 to 58% and linoleic acid from 6 to 17%. This variability can be exploited for selection of trees and for studying the genetic variability in neem. These selections can also be utilized for genetic improvement of the tree.

Mesenteric leiomyoma in infancy

Leiomyoma of the mesentery is an uncommon tumor. This has been documented in adults and children. However, there is no such case reported in an infant, which is being presented in this report.

Inhibition of Tat-mediated transactivation of HIV-1 LTR transcription by polyamide nucleic acid targeted to TAR hairpin element

Tat, an essential human immunodeficiency virus type 1 protein interacts with the transactivation response element (TAR) and stimulates transcription from the viral long-terminal repeat (LTR). Blockage of Tat-TAR interaction halts viral transcription and hence replication. We have found that polyamide nucleic acid (PNA), targeted to the TAR sequences of viral RNA genome is able to prevent Tat-TAR interaction by efficient sequestration of the TAR. Anti-TAR PNA competes for TAR and prevents Tat-mediated stimulation of HIV-1 LTR transcription in vitro but has no influence on the basal level of transcription in the absence of Tat. Using a reporter gene construct pHIV LTR-CAT and pCMV-Tat in cell culture, we have further shown that anti-TAR PNA is able to block Tat-mediated transactivation of HIV-1 LTR transcription in vivo as judged by the extent of LTR driven CAT gene expression in the absence and presence of anti-TAR PNA. Supplementation of 100 nM of anti-TAR PNA into the culture medium further enhances the suppression of transactivation. Nonspecific scrambled PNA had no influence on Tat-TAR interaction and LTR-driven CAT gene expression in cell culture. These results suggest that PNA targeted to the TAR sequence of the viral genome may be a potential inhibitor of HIV-1 gene expression.

Role of Q190 of MuLV RT in ddNTP resistance and fidelity of DNA synthesis: a molecular model of interactions with substrates

Gln190 of MuLV reverse transcriptase (RT) plays an important role in the catalytic mechanism of MuLV RT for its conservative and non-conservative mutant derivatives exhibit low catalytic activity. We now report that both Q190N and Q190A MuLV RTs are more efficient in their activity to incorporate ddNTPs and exhibit higher fidelity than the wild-type (WT) enzyme of DNA synthesis in both RNA- and DNA-directed reactions. To obtain some insight into the structural basis for the differential utilization of dNTP and ddNTP by the mutant enzymes, we modeled the binary and the ternary complexes of MuLV RT using corresponding HIV-1 RT structures and available structure of the fragment of MuLV RT. Q190 of MuLV RT appears to be essential for the interaction with 3'OH of dNTP. The lack of a 3'OH moiety in ddNTP does not permit the binding of ddNTPs to WT MuLV RT. However, the shorter side chain of Q190N (or A) mutant MuLV RT and the absence of 3'OH in ddNTP result in the rearrangement of hydrophobic interactions favoring the binding and limited incorporation of ddNTPs. In addition, while modeling the binary and ternary complexes of MuLV RT, we noted that in the formation of the ternary complex, an interaction of Q190 with dNTP substrate requires a shift from its interaction with the template base. This may be achieved by a small conformational change or motion of the loop between beta9 and alphaH containing Q190, which may correspond to the conformational change step requiring participation of Q190 during the catalytic reaction as reported in an earlier biochemical investigation.

The J-helix of Escherichia coli DNA polymerase I (Klenow fragment) regulates polymerase and 3'- 5'-exonuclease functions

To assess the functional importance of the J-helix region of Escherichia coli DNA polymerase I, we performed site-directed mutagenesis of the following five residues: Asn-675, Gln-677, Asn-678, Ile-679, and Pro-680. Of these, the Q677A mutant is polymerase-defective with no change in its exonuclease activity. In contrast, the N678A mutant has unchanged polymerase activity but shows increased mismatch-directed exonuclease activity. Interestingly, mutation of Pro-680 has a Q677A-like effect on polymerase activity and an N678A-like effect on the exonuclease activity. Mutation of Pro-680 to Gly or Gln results in a 10-30-fold reduction in k(cat) on homo- and heteropolymeric template-primers, with no significant change in relative DNA binding affinity or K(m)((dNTP)). The mutants P680G and P680Q also showed a nearly complete loss in the processive mode of DNA synthesis. Since the side chain of proline is generally non-reactive, mutation of Pro-680 may be expected to alter the physical form of the J-helix itself. The biochemical properties of P680G/P680Q together with the structural observation that J-helix assumes helical or coiled secondary structure in the polymerase or exonuclease mode-bound DNA complexes suggest that the structural alteration in the J-helix region may be responsible for the controlled shuttling of DNA between the polymerase and the exonuclease sites.

A carboxylate triad is essential for the polymerase activity of Escherichia coli DNA polymerase I (Klenow fragment). Presence of two functional triads at the catalytic center

The catalytic roles of two essential active-site aspartates at positions 705 and 882 of Escherichia coli DNA polymerase I have been well established (Steitz, T. A. (1998) Nature 391, 231-232). We now demonstrate that the participation of at least one additional carboxylate, a glutamate at position 710 or 883, is obligatory for catalysis. This conclusion has been drawn from our investigation of the properties of single (E710D, E710A, E883D, and E883A) and double (E710D/E883D and E710A/E883A) substitutions of residues Glu(710) and Glu(883). While single substitutions of either of the glutamates resulted in some reduction in polymerase activity, the mutant enzyme with simultaneous substitution of both glutamates with alanine exhibited a nearly complete loss of activity. Interestingly, substitution with two aspartates in place of the glutamates resulted in an enzyme species that catalyzed DNA synthesis in a strictly distributive mode. Pyrophosphorolytic activity of the mutant enzymes reflected their polymerase activity profiles, with markedly reduced pyrophosphorolysis by the double mutant enzymes. Moreover, an evaluation of Mg(2+) and salt optima for all mutant enzymes of Glu(710) and Glu(883) revealed significant deviations from that for the wild type, implying a possible role of these glutamates in metal coordination as well as in maintaining the structural integrity of the active site.

Mutational analysis of Lys65 of HIV-1 reverse transcriptase

Amino acid Lys(65) is part of the highly flexible beta3-beta4 loop in the fingers domain of the 66 kDa subunit of human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT). Recent crystal data show that the epsilon-amino group of Lys(65) interacts with the gamma-phosphate of the bound deoxynucleoside triphosphate ('dNTP') substrate [Huang, Chopra, Verdine and Harrison (1998) Science 282, 1669-1675]. In order to biochemically define the function of RT Lys(65), we have used site-specific mutagenesis to generate RT with a variety of substitutions at this position, including K65E, K65Q, K65A and K65R. Kinetic analyses demonstrate that if Lys(65) in RT is substituted with an amino acid other than arginine the enzyme exhibits dramatic decreases in the binding affinity (K(m)) for all dNTP substrates, in RT catalytic efficiency (k(cat)/K(m)) and in the mutant enzyme's ability to carry out pyrophosphorolysis, the reverse reaction of DNA synthesis. The pH optimum for the DNA polymerase activity of K65E RT was 6.5, compared to 7.5 for the wild-type enzyme, and 8.0 for the K65R, K65A and K65Q mutants. Molecular modelling studies show that mutations of Lys(65) do not affect the geometry of the loop's alpha-carbon backbone, but rather lead to changes in positioning of the side chains of residues Lys(70) and Arg(72). In particular, Glu in K65E can form a salt bridge with Arg(72), leading to the diminution of the latter residue's interaction with the alpha-phosphate of the dNTP residue. This alteration in dNTP-binding may explain the large pH-dependent changes in both dNTP-binding and catalytic efficiency noted with the enzyme. Furthermore, the K65A, K65Q and K65E mutant enzymes are 100-fold less sensitive to all dideoxynucleoside triphosphate ('ddNTP') inhibitors, whereas the K65R mutation results in a selective 10-fold decrease in binding of ddCTP and ddATP only. This implies that mutations at position 65 in HIV-1 RT influence the nucleotide-binding specificity of the enzyme.

Valine of the YVDD motif of moloney murine leukemia virus reverse transcriptase: role in the fidelity of DNA synthesis

The YXDD motif is highly conserved in the reverse transcriptase family. The variable X residue is occupied by valine and methionine in MuLV RT and HIV-1 RT, respectively. Previous studies have shown that Tyr 222, the Y residue of the YXDD motif in MuLV RT, constitutes a major component of the fidelity center of the enzyme [Kaushik, N., Singh, K., Alluru, I., and Modak, M. J. (1999) Biochemistry 38, 2617-2627]. In this work, we present evidence that reverse transcriptases containing valine in the "X" position of the YXDD motif generally catalyze DNA synthesis with greater fidelity than those containing methionine or alanine. In the MuLV RT system, the two mutants V223M and V223A exhibited an overall reduced fidelity of DNA synthesis, specifically for RNA-templated reactions. Further analysis revealed that these mutants exhibit a higher efficiency of misinsertion on MS2 RNA than the wild-type enzyme for every mispair tested. However, unlike HIV-1 RT, the insensitivity of the wild-type MuLV RT to all four ddNTPs remained unchanged by mutation of V223 to Met or Ala. A 3D molecular model of the ternary complex of MuLV RT, template primer, and dNTP suggests that Val 223 along with its neighboring Tyr 222 stabilizes the substrate binding pocket via hydrophobic interactions with the dNTP substrate and template-primer.

Characterization of trinucleotide- and tandem repeat-containing transcripts obtained from human spinal cord cDNA library by high-density filter hybridization

In order to identify trinucleotide- and tandem repeat-containing transcripts in human spinal cord, hybridization of a high-density spinal cord cDNA library filter was carried out using a radioactively labeled degenerate oligonucleotide designed to detect different trinucleotide repeats including those known to occur in disease-associated expansions, in a single step. The sequence analysis of the trinucleotide repeat-containing transcripts (TNRTs) revealed 23 known mammalian genes with trinucleotide repeat-containing regions (TNRs), some of which were not previously reported to contain TNRs, and 18 cDNA clones with no or insignificant sequence homology to known genes. Amongst the known genes detected was the fragile X gene (FMR-1) containing (CGG)30. Other genes containing extended TNRs of 9 to 21 repeats were calcium-dependent protease, ATBF1-A, ferritin H chain, and the G protein Gsalpha2. Ten sequences containing perfect TNRs and two sequences containing perfect tandem repeats (derived from 11 TNRTs) were further analyzed for allelic variation using primers flanking the TNR, and five were shown to exhibit two to five alleles per TNR. These transcripts were further investigated for their chromosomal localization where unknown or only partially characterized. The transcripts that were polymorphic in the TNR region were ATBF1-A (a homeodomain protein), clone 390013 on chromosome Xp11, a member of the family of the 14.3.3 protein kinase C regulators, a human translation initiation factor (an isolog of the yeast Suilisol gene 1), and a novel sequence (TR21). Only the first two transcripts showed the presence of rare expanded alleles. Characterization of polymorphic TNRs in novel and even known genes expressed in human spinal cord is likely to help in the identification of new candidates for genes involved in neurodegenerative disorders.

Role of glutamine 151 of human immunodeficiency virus type-1 reverse transcriptase in substrate selection as assessed by site-directed mutagenesis

A natural mutation at codon 151 (Gln --> Met; Q151M) of HIV-1 RT has been shown to confer resistance to the virus against dideoxy nucleoside analogues [Shirasaka, T., et al. (1995) Proc. Natl. Acad. Sci. U.S.A. 92, 2398], suggesting that Gln 151 may be involved in conferring sensitivity to nucleoside analogues. To understand its functional implication, we generated two mutant derivatives of this residue (Q151M and Q151N) and examined their sensitivities to ddNTPs and their ability to discriminate against rNTPs versus dNTP substrates on natural U5-PBS HIV-1 RNA template. We found that Q151M was highly discriminatory against all four ddNTPs but was able to incorporate rNTPs as efficiently as the wild type enzyme. In contrast, the Q151N mutant was only moderately resistant to ddNTPs but exhibited a higher level of discrimination against rNTPs. The fidelity of misinsertion was found to be highest for the Q151N mutant followed by Q151M and the wild type enzyme. These results point toward the importance of the amino acid side chain at position 151 in influencing the ability of the enzyme in recognition and discrimination against the sugar moieties of nucleotide substrates.

Analysis of the role of glutamine 190 in the catalytic mechanism of murine leukemia virus reverse transcriptase

To determine the catalytic role of Gln(190), a member of the highly conserved LPQG motif in Moloney murine leukemia virus reverse transcriptase, we carried out site-directed mutagenesis of this residue to generate Q190N and Q190A. Both mutant proteins exhibited a significant loss in their polymerase and pyrophosphorolysis activities with a more pronounced effect noted with the Gln --> Asn substitution. The catalytic efficiencies of the mutants exhibited a 40-70-fold reduction with poly(rC) and poly(dC) templates in the presence of Mg(2+) and a 10-20-fold reduction with poly(rA) template in the presence of Mn(2+). Interestingly, the K(m) for NTP exhibited only a moderate 3-10-fold increase irrespective of the template-primer and the metal ion. Photoaffinity labeling of both the mutant and the WT enzymes exhibited an identical affinity for RNA.DNA and DNA.DNA template-primers. However, unlike the WT enzyme, the mutant enzymes exhibited a significantly reduced ability to catalyze the nucleotidyltransferase reaction on the covalently immobilized template-primer. An examination of the rate constants for the first and the second nucleotide for the mutant enzymes indicated dissimilar rates, indicating that Gln(190) may be involved in a rate-limiting, conformational change step both before and after the phosphodiester bond formation. Furthermore, the processivity of DNA synthesis by the mutant enzymes was decreased severely, which may result from the lower catalytic efficiency as well as translocation defect.

Rapunzel syndrome--a case report

The gastric trichobezoars usually occur in young girls, often those with psychiatric disorders. Rarely these are known to extend from the stomach to the small intestine as a tail, when they are termed the Rapunzel syndrome. Until 1997, only 10 such cases have been reported in the literature. We report another case in which we could extract the trichobezoar by gastrotomy and enterotomy.

Tyrosine 222, a member of the YXDD motif of MuLV RT, is catalytically essential and is a major component of the fidelity center

Tyrosine 222 of MuLV RT is an invariant residue of the highly conserved YXDD motif in the reverse transcriptase class of enzymes. The residue X is Met 184 in HIV-1 RT and Val 223 in MuLV RT. This residue has been implicated in the fidelity of DNA synthesis, whereas the role of the preceding tyrosine in this aspect, as well as in the catalytic mechanism of MuLV RT, remains to be elucidated. We have substituted Tyr 222 with Phe, Ser, and Ala by site-directed mutagenesis and have characterized the properties of the individual mutant enzymes. The results show that Tyr-->Phe substitution did not affect the polymerase activity of the enzyme, while Tyr-->Ser and Tyr-->Ala substitutions significantly reduced the polymerase activity. The pyrophosphorolysis activities of these mutants showed the same trend as the polymerase activities, suggesting an essential role for Y222 in the catalytic mechanism of MuLV RT. One of the most interesting observations of Y-->F substitution was the significantly increased fidelity of DNA synthesis on RNA templates. In addition, a limited extent of ribonucleotide incorporation on RNA template that was consistently noted with the wild-type enzyme was reduced with the Y222F mutant. The resistance to all four ddNTPs, however, persisted in the wild type and Y222 mutants on the RNA template. A ternary complex model of MuLV RT shows that (a) the aromatic ring of Tyr/Phe is positioned between the terminal and penultimate primer bases and (b) the phenolic OH group is seen within hydrogen bonding distance with the base moieties of two template and penultimate primer nucleotides. We propose that the base stacking interaction of Tyr 222 stabilizes the primer terminus position which is essential for the catalytic reaction. However, the weaker stacking interaction of Y compared to F, due to polarization of the pi-charge toward the phenoxyl-OH as well as the resonating character of its H-bond center, may provide slight flexibility to the position of the template base which may be responsible for the error-proneness of MuLV RT.

Functional analysis of amino acid residues constituting the dNTP binding pocket of HIV-1 reverse transcriptase

In order to understand the functional implication of residues constituting the dNTP-binding pocket of human immunodeficiency virus type 1 reverse transcriptase, we performed site-directed mutagenesis at positions 65, 72, 113, 115, 151, 183, 184, and 219, and the resulting mutant enzymes were examined for their biochemical properties and nucleotide selectivity on RNA and DNA templates. Mutations at positions 65, 115, 183, 184, and 219 had negligible to moderate influence on the polymerase activity, while Ala substitution at positions 72 and 151 as well as substitution with Ala or Glu at position 113 severely impaired the polymerase function of the enzyme. The K219A, Y115F, and Q151M mutants had no influence on the fidelity; Y183A, Y183F, K65A, and Q151N mutants exhibited higher fidelity on both RNA and DNA templates, while Y115A was less error-prone selectively on a DNA template. Analysis of the three-dimensional model of the enzyme-template primer-dNTP ternary complex suggests that residues Tyr-183, Lys-65, and Gln-151 may have impact on the flexibility of the dNTP-binding pocket by virtue of their multiple interactions with the dNTP, template, primer, and other neighboring residues constituting the pocket. Recruitment of the correct versus incorrect nucleotides may be a function of the flexibility of this pocket. A relatively rigid pocket would provide greater stringency, resulting in higher fidelity of DNA synthesis in contrast to a flexible pocket. Substitution of a residue having multiple interactions with a residue having reduced interaction capability will alter the internal geometry of the pocket, thus directly influencing the fidelity.

Phenotypic mechanism of HIV-1 resistance to 3'-azido-3'-deoxythymidine (AZT): increased polymerization processivity and enhanced sensitivity to pyrophosphate of the mutant viral reverse transcriptase

The multiple mutations associated with high-level AZT resistance (D67N, K70R, T215F, K219Q) arise in two separate subdomains of the viral reverse transcriptase (RT), suggesting that these mutations may contribute differently to overall resistance. We compared wild-type RT with the D67N/K70R/T215F/K219Q, D67N/K70R, and T215F/K219Q mutant enzymes. The D67N/K70R/T215F/K219Q mutant showed increased DNA polymerase processivity; this resulted from decreased template/primer dissociation from RT, and was due to the T215F/K219Q mutations. The D67N/K70R/T215F/K219Q mutant was less sensitive to AZTTP (IC50 approximately 300 nM) than wt RT (IC50 approximately 100 nM) in the presence of 0.5 mM pyrophosphate. This change in pyrophosphate-mediated sensitivity of the mutant enzyme was selective for AZTTP, since similar Km values for TTP and inhibition by ddCTP and ddGTP were noted with wt and mutant RT in the absence or in the presence of pyrophosphate. The D67N/K70R/T215F/K219Q mutant showed an increased rate of pyrophosphorolysis (the reverse reaction of DNA synthesis) of chain-terminated DNA; this enhanced pyrophosphorolysis was due to the D67N/K70R mutations. However, the processivity of pyrophosphorolysis was similar for the wild-type and mutant enzymes. We propose that HIV-1 resistance to AZT results from the selectively decreased binding of AZTTP and the increased pyrophosphorolytic cleavage of chain-terminated viral DNA by the mutant RT at physiological pyrophosphate levels, resulting in a net decrease in chain termination. The increased processivity of viral DNA synthesis may be important to enable facile HIV replication in the presence of AZT, by compensating for the increased reverse reaction rate.

Isolation and characterization of trinucleotide repeat containing partial transcripts in human spinal cord

We report the isolation of 41 partial transcripts containing trinucleotide repeats (TNRs) (CAG/CCG or CAA) from human spinal cord using a polymerase chain reaction-based method. The sequence analysis and database search at the nucleic acid and protein level revealed several classes of TNR-containing partial transcripts (TNRPTs). The TNRPTs included 16 known genes and 10 contained or partially overlapped with 13 expressed sequence tags (ESTs), some of which are known to contain TNRs and others which have previously not been shown to contain these repeats (e.g., clone 54 with homology for the homeobox protein HOX-A5). A further 15 partial transcripts showed no homologies in the databases and therefore may be unique. The validity of this approach is supported by the detection of nervous system-specific genes (e.g., glial fibrillary acid protein) and genes known to show trinucleotide expansions in disease (e.g., AAD10 associated with spino cerebellar ataxia type 2). This method provides a simple approach for the isolation of TNRPTs, from which full-length transcripts can be obtained and the discovery of TNR-containing genes may be facilitated. TNRPTs can also be used to study quantitative gene expression at the transcriptional level, to construct TNR-enriched cDNA libraries, and to make larger contigs from ESTs.

Polyamide nucleic acid targeted to the primer binding site of the HIV-1 RNA genome blocks in vitro HIV-1 reverse transcription

We report here that polyamide nucleic acid (PNA) as well as a polyamide nucleic acid-DNA chimera complementary to the primer binding site of the HIV-1 genome can completely block priming by tRNA3Lys and consequently the in vitro initiation of reverse transcription by HIV-1 RT. Conventional heating and cooling is not required for annealing PNA analogs to the complementary nucleotide sequence as effective blockage of reverse transcription results from their invasion in the duplex region of preprimed U5-PBS HIV-1 RNA template-primer and was seen even at ambient temperature. Further, the extension of the initiated nascent (-) strand DNA can also be blocked by inclusion of another PNA, targeted to upstream sequences in the U5 region of the viral RNA. Interestingly, a PNA chimera having only two DNA nucleotides annealed with the U5-PBS RNA is recognized as a bonafide primer by HIV-1 RT, as the 3'OH end of the chimeric molecule is extended by the enzyme in the presence of dNTPs. A significant observation was that RNA/PNA or RNA/(PNA-DNA) hybrids were entirely resistant to the RNase H activity of HIV-1 RT. Furthermore, PNA invasion into the RNA/DNA hybrid completely prevented the cleavage of the RNA strand, suggesting that the RNase H activity of HIV-1 RT which was required in reverse transcription may also be inhibited by the PNA oligomer. These observations suggest that oligomeric PNAs targeted to various critical regions of the viral genome are likely to have strong therapeutic potential for interrupting multiple steps involved in the replication of HIV-1 and warrant serious investigation especially in the area of an effective delivery system.

Role of glutamine-151 of human immunodeficiency virus type-1 reverse transcriptase in RNA-directed DNA synthesis

Glutamine-151 of HIV-1 RT has been shown to be a catalytically important residue through the characterization of its mutant phenotype Glu151Ala (Sarafianos et al., 1995a). To further understand the role of this residue, we have extended this analysis to include polymerization on natural RNA template in addition to DNA template. We find that Q151A mutant exhibited a severe reduction in the polymerase activity without any significant effect on the affinity for dNTP substrate. Unlike DNA-directed reactions, the rate-limiting step for RNA-directed reactions does not appear to be either at the dNTP binding step or the chemical step. Analysis of the products formed on natural heteromeric HIV-genomic RNA template annealed with an 18-mer DNA primer with a sequence complementary to the primer binding site (PBS) has shown that addition of nucleotides is nonlinear with time since the enzyme appears to stall on the RNA template following the incorporation of the first nucleotide. The Q151A mutant was found to be nearly devoid of pyrophosphorolytic activity on a RNA-PBS template-primer. Similar properties have been previously reported for a mutant of R72 (R72A) of HIV-1 RT (Sarafianos et al., 1995b). However, R72 was implicated in stabilizing the transition state ternary complex before and after the phosphodiester bond formation (Kaushik et al., 1996; Sarafianos et al., 1995b). Our results with Q151A suggest that the side chain of Q151 may help stabilize the side chain of R72, and the loss of pyrophosphorolysis activity observed with the Q151 mutant may be the indirect manifestation of this stabilizing effect on R72. These observations point to the functional interdependence of residues Q151 and R72 in the polymerase function of the enzyme. An analysis of the 3D model structure of HIV-1 RT bound to DNA-DNA and RNA-DNA template-primer reveals that the guanidine hydrogen of R72 seems to stabilize Q151 by hydrogen bonding with its amide oxygen. A systematic conformational search of the side chain of Q151 also suggests a stable orientation where its specific interaction with the base of the RNA template may aid in stabilizing it.

Elucidation of the role of Arg 110 of murine leukemia virus reverse transcriptase in the catalytic mechanism: biochemical characterization of its mutant enzymes

Based on the projected three-dimensional equivalence of conserved amino acids in the catalytic domains of DNA polymerases, we propose Arg 110 of MuLV RT to be an important participant in the catalytic mechanism of MuLV RT. In order to obtain evidence to support this proposition and to assess the functional importance of Arg 110, we carried out site directed mutagenesis of Arg 110 and replaced it with Lys, Ala, and Glu. The mutant enzymes were characterized with respect to their kinetic parameters, ability to bind template-primers, and the mode of DNA synthesis. All the three substitutions at 110 position resulted in severe loss of polymerase activity without any significant effect on the RNase H function. In spite of an approximately 1000-fold reduction in kcat of polymerase activity with three mutant enzymes, no significant reduction in the affinities for either template-primer or dNTP substrates was apparent. Mutant enzymes also did not exhibit significant sulfur elemental effect, implying that the chemical step, i.e., phosphodiester bond formation, was not defective. Examination of the mode of DNA synthesis by the mutant enzymes indicated a shift from processive to the distributive mode of synthesis. The mutants of R110 also displayed significant loss of pyrophosphorolysis activity. Furthermore, the time course of primer extension with mutant enzymes indicated severe reduction in the rates of addition of the first nucleotide and even further reduction in the addition of the second nucleotide. These results suggest that the rate limiting step for the mutant enzymes may be before and after the phosphodiester bond formation. Based on these results, we propose that Arg 110 of MuLV RT participates in the conformational change steps prior to and after the chemical step of polymerase reaction.

Biochemical analysis of catalytically crucial aspartate mutants of human immunodeficiency virus type 1 reverse transcriptase

In order to clarify the role(s) of the individual member of the carboxylate triad in the catalytic mechanism of human immunodeficiency virus type 1 (HIV-1) reverse transcriptase, we carried out site-directed mutagenesis of D185, D186, and D110, followed by the extensive characterization of the properties of the individual mutant enzymes. We find that all three residues participate at or prior to the chemical step of bond formation. The incorporation pattern seen with phosphorothioate analogs of dNTP on both RNA-DNA and DNA-DNA template-primers indicated that D186 may be the residue that coordinates with the alpha-phosphate group of dNTP in the transition-state ternary complex. Further support for the role assigned to D186 was obtained by examination of the ability of the individual carboxylate mutants to catalyze the reverse of the polymerase reaction (pyrophosphorolysis). Mutants of D185 exhibited near-normal pyrophosphorolysis activity, while those of D186 were completely devoid of this activity. Thus, D185 appears to participate only in the forward reaction, probably required for the generation of nucleophile by interacting with the 3'-OH of the primer terminus, while D186 seems to be involved in both the forward and the reverse reactions, presumably by participating in the pentavalent intermediate transition state. Lack of any elemental effects during polymerization with mutant enzymes of residue D110, together with their inability to catalyze pyrophosphorolysis, suggest its probable participation in the metal-coordinated binding to the beta-gamma-phosphate of dNTP or PPi in the forward and reverse reactions, respectively. A molecular model of the ternary complex based on these results is also presented.

Significance of the O-helix residues of Escherichia coli DNA polymerase I in DNA synthesis: dynamics of the dNTP binding pocket

In order to identify functionally important residues in the O and O1 helices of Escherichia coli DNA polymerase I, we mutated 9 residues of this region to alanine. The alanine substitutions result in moderate to severe effects on the polymerase activity of the individual mutant enzymes. Severe loss of activity is associated with R754A, K758A, F762A, and Y766A. However, the loss of polymerase activity with different template primers exhibited a rather unique pattern implying differential participation of the individual residue in the synthesis directed by poly(rA), poly(dA), and poly(dC) templates. The ability of all mutants to form E-DNA binary complex was found to be unaffected with the exception of Y766A and F771A, where significant reduction in the cross-linking of both the template and the primer strand was noted. Most interestingly, the catalytic activity of all inactive mutant enzymes, with the exception of K758A, could be restored by substituting Mn2+ in place of Mg2+ as a divalent cation. Based on these results and associated changes in the kinetic parameters and other properties of the individual mutant enzyme, we conclude the following: (a) Tyr 766 and Phe 771 are either involved in the binding of template-primer or are in the vicinity of the DNA binding track. (b) Residues Arg 754, Lys 758, Phe 762, and Tyr 766 appear to be required for the binding of Mg.dTTP, while only Arg 754 and Lys 758 are utilized in the polymerization of Mn.dTTP. (c) In the polymerization of dGTP, only Lys 758 appears essential regardless of the type of divalent cation. (d) Phe 762 participates only in the binding of Mg.dTTP. Finally, (e) based on the analysis of the time course of nucleotide incorporation, processivity, and pyrophosphorolysis reaction, we suggest that Lys 758 is probably involved in a conformational change of the ternary complexes preceding and following the chemical step. In summary, our results suggest that the formation of the dNTP binding pocket is a dynamic process which requires the participation of different residues depending on the type of dNTP and the divalent cation.

Role of methionine 184 of human immunodeficiency virus type-1 reverse transcriptase in the polymerase function and fidelity of DNA synthesis

Methionine 184 of HIV-1 RT is a constituent of the catalytically crucial and highly conserved YXDD motif in the reverse transcriptase class of enzymes. We investigated the role of this residue by substituting it with Ala and Val by site-directed mutagenesis followed by extensive characterization of the two mutant enzymes. The kinetic parameters governing DNA synthesis directed by RNA and DNA templates indicated that both M184A and M184V mutants are catalytically as efficient as the wild type enzyme. Photoaffinity labeling of both the mutant and the wild type enzyme exhibited an identical affinity for RNA-DNA and DNA-DNA template primers. We further demonstrate that M-->V substitution at 184 position significantly increases the fidelity of DNA synthesis while M-->A substitution results in a highly error-prone enzyme without having compromised its efficiency of DNA synthesis. The M184V mutant exhibited a 25-45-fold increase in mismatch selectivity (ratio of k(cat)/K(m) of correct versus incorrect nucleotides) as compared to the WT enzyme. This pattern of error-prone synthesis is also confirmed by examining the abilities of the enzyme-(template-primer) covalent complexes to incorporate correct versus incorrect nucleotide onto the immobilized template-primer. The nature of error-prone synthesis by the M184A mutant shows an increase in both the mismatch synthesis and extension of the mismatched primer termini. Using a three-dimensional molecular model of the ternary complex of HIV-1 RT, template-primer, and dNTP, we observe that the strategic location of M184 may allow it to interact with the sugar moiety of either the primer nucleotide or the dNTP substrate.

Site-directed mutagenesis of arginine 72 of HIV-1 reverse transcriptase. Catalytic role and inhibitor sensitivity

In order to determine the catalytic role of Arg72 of HIV-1 reverse transcriptase (RT), we carried out site-directed mutagenesis at codon 72. Two mutant proteins (R72A and R72K) were purified and characterized. With Arg to Ala substitution the kcat of the polymerase reaction was reduced by nearly 100-fold with poly(rA) template, but only about 5-15-fold with poly(rC) and poly(dC) templates. The Arg to Lys substitution exhibited a qualitatively similar pattern, although the overall reduction in kcat was less severe. Most interestingly, we noted a large difference in the rate constant of the first and second nucleotide incorporation by R72A, suggesting that Arg72 participates in the reaction after the formation of the first phosphodiester bond. We propose this step to be the pyrophosphate binding and removal step following the nucleotidyltransferase reaction. Support for this proposal is obtained from the observation that the R72A mutant (i) exhibited a pronounced translocation defect in the processivity analysis, (ii) lacked the ability to catalyze pyrophosphorolysis, and (iii) showed complete resistance to phosphonoformate, an analog of PPi.Arg72 is the first residue of HIV-1 RT proposed to be involved in the pyrophosphate binding/removal function of RT.