Functional characterization of a defense-responsive bulnesol/elemol synthase from potato.

Terpene synthases (TPSs) produce a variety of terpenoids that play numerous functional roles in primary and secondary metabolism, as well as in ecological interactions. Here, we report the functional characterization of an inducible potato TPS gene encoding bulnesol/elemol synthase (StBUS/ELS). The expression of StBUS/ELS in potato leaves was significantly induced in response to both bacterial (Pseudomonas syringae) and fungal (Alternaria solani) infection as well as methyl jasmonate treatment, indicating its role in defense. The leaves exhibited the highest StBUS/ELS expression followed by the stem with least and similar expression in tuber, sprout and root. Recombinant StBUS/ELS catalyzed the formation of different sesquiterpenes by utilizing farnesyl diphosphate as substrate, and the monoterpene geraniol from geranyl diphosphate. Among the sesquiterpenes formed by StBUS/ELS, elemol was the predominant product followed by α-bulnesene, bulnesol and ß-elemene. Further gas chromatography-mass spectrometry (GC-MS) analysis of StBUS/ELS assay products at different injection temperatures revealed elemol and bulnesol as the major products at 275 and 200/150°C, respectively, without much change in the levels of minor products. This indicated thermal rearrangement of bulnesol into elemol at higher temperatures. Transient overexpression of StBUS/ELS in potato leaves conferred tolerance against the growth of bacteria P. syringae and Ralstonia solanacearum, and the fungus A. solani. Further, expression analysis of pathogenesis-related (PR) genes in StBUS/ELS overexpressing leaves showed no significant change in comparison to control, indicating a direct involvement of StBUS/ELS enzymatic products against pathogens. Overall, our study suggested that StBUS/ELS is a pathogen-inducible TPS encoding bulnesol/elemol synthase and could provide a direct role in defense against biotic stress in potato.

Identification of Markers for Root Traits Related to Drought Tolerance Using Traditional Rice Germplasm.

Drought is one of the important constraints affecting rice productivity worldwide. The vigorous shoot and deep root system help to improve drought resistance. In present era, genome-wide association study (GWAS) is the preferred method for mapping of QTLs for complex traits such as root and drought tolerance traits. In the present study, 114 rice genotypes were evaluated for various root and shoot traits under water stress conditions. All genotypes showed a significant amount of variation for various root and shoot traits. Correlation analysis revealed that high dry shoot weight and fresh shoot weight is associated with root length, root volume, fresh root weight and dry root weight. A total of 11 significant marker-trait associations were detected for various root, shoot and drought tolerance traits with the coefficient of determination (R2) ranging from 18.99 to 53.41%. Marker RM252 and RM212 showed association with three root traits which suggests their scope for improvement of root system. In the present study, a novel QTL was detected for root length associated with RM127, explaining 19.30% of variation. The marker alleles with increasing phenotypic effects for root and drought-tolerant traits can be exploited for improvement of root and drought tolerance traits using marker-assisted selection.

Plant Metabolic Gene Clusters: Evolution, Organization, and Their Applications in Synthetic Biology.

Plants are a remarkable source of high-value specialized metabolites having significant physiological and ecological functions. Genes responsible for synthesizing specialized metabolites are often clustered together for a coordinated expression, which is commonly observed in bacteria and filamentous fungi. Similar to prokaryotic gene clustering, plants do have gene clusters encoding enzymes involved in the biosynthesis of specialized metabolites. More than 20 gene clusters involved in the biosynthesis of diverse metabolites have been identified across the plant kingdom. Recent studies demonstrate that gene clusters are evolved through gene duplications and neofunctionalization of primary metabolic pathway genes. Often, these clusters are tightly regulated at nucleosome level. The prevalence of gene clusters related to specialized metabolites offers an attractive possibility of an untapped source of highly useful biomolecules. Accordingly, the identification and functional characterization of novel biosynthetic pathways in plants need to be worked out. In this review, we summarize insights into the evolution of gene clusters and discuss the organization and importance of specific gene clusters in the biosynthesis of specialized metabolites. Regulatory mechanisms which operate in some of the important gene clusters have also been briefly described. Finally, we highlight the importance of gene clusters to develop future metabolic engineering or synthetic biology strategies for the heterologous production of novel metabolites.

Identification of clinical and psychosocial characteristics associated with perinatal depression in the south Indian population.

BACKGROUND: Longitudinal perinatal depression (PND) data is sparsely available in the Indian population. We have employed Edinburgh Postnatal Depression Scale (EPDS) to assess the prevalence and identify characteristics associated with PND in the south Indian population. PND was assessed longitudinally using EPDS scores with traditional cut-off approach as well as a novel method of latent class mixture modeling (LCMM). The LCMM method, to the best of our knowledge, has been used for the first time in the Indian population. METHODS: Three hundred and forty seven women, predominantly from economically-weaker sections of rural and urban South India were longitudinally assessed for antenatal depression (AD) and postnatal depression (PD) using EPDS cutoff-scores ≥13 and ≥10, respectively. Uni/multivariable analyses were used to identify PND associated characteristics. LCMM was then implemented, followed by risk characteristics identification. RESULTS: PND prevalence from traditional approach was 24.50 % (12.68 % AD; 18.16% PD). Characteristics associated with PND were urban-site and recent adverse life events. Irregular menstrual history and chronic health issues were associated with AD and PD, respectively. Three distinct PND trajectories were observed from LCMM-analysis: low-risk (76.08%), medium-risk (19.89%) and high-risk (4.04%). Urban-site, recent adverse life events, irregular menstrual history and pregnancy complications were associated with medium-risk/high-risk trajectories. LIMITATIONS: EPDS is a screening tool and not a diagnostic tool for depression. Since the study population included women from economically-weaker sections, the results need verification in other socio-economic groups. CONCLUSIONS: Both the traditional cut-off-based approach and LCMM provided very similar conclusions regarding the prevalence of PND and characteristics associated with it. Higher PND prevalence was observed in urban women compared to rural women. In low-income countries, identifying risk characteristics associated with PND is a critical component in designing prevention strategies for PND related conditions because of the limited access to mental health resources.

Variability Assessment for Root and Drought Tolerance Traits and Genetic Diversity Analysis of Rice Germplasm using SSR Markers.

The studies on genetic variation, diversity and population structure of rice germplasm of North East India could be an important step for improvements of abiotic and biotic stress tolerance in rice. Genetic diversity and genetic relatedness among 114 rice genotypes of North East India were assessed using genotypic data of 65 SSR markers and phenotypic data. The phenotypic diversity analysis showed the considerable variation across genotypes for root, shoot and drought tolerance traits. The principal component analysis (PCA) revealed the fresh shoot weight, root volume, dry shoot weight, fresh root weight and drought score as a major contributor to diversity. Genotyping of 114 rice genotypes using 65 SSR markers detected 147 alleles with the average polymorphic information content (PIC) value of 0.51. Population structure analysis using the Bayesian clustering model approach, distance-based neighbor-joining cluster and principal coordinate analysis using genotypic data grouped the accession into three sub-populations. Population structure analysis revealed that rice accession was moderately structured based on FST value estimates. Analysis of molecular variance (AMOVA) and pairwise FST values showed significant differentiation among all the pairs of sub-population ranging from 0.152 to 0.222 suggesting that all the three subpopulations were significantly different from each other. AMOVA revealed that most of the variation in rice accession mainly occurred among individuals. The present study suggests that diverse germplasm of NE India could be used for the improvement of root and drought tolerance in rice breeding programmes.

Terpene Moiety Enhancement by Overexpression of Geranyl(geranyl) Diphosphate Synthase and Geraniol Synthase Elevates Monomeric and Dimeric Monoterpene Indole Alkaloids in Transgenic Catharanthus roseus.

Catharanthus roseus is the sole source of two of the most important anticancer monoterpene indole alkaloids (MIAs), vinblastine and vincristine and their precursors, vindoline and catharanthine. The MIAs are produced from the condensation of precursors derived from indole and terpene secoiridoid pathways. It has been previously reported that the terpene moiety limits MIA biosynthesis in C. roseus. Here, to overcome this limitation and enhance MIAs levels in C. roseus, bifunctional geranyl(geranyl) diphosphate synthase [G(G)PPS] and geraniol synthase (GES) that provide precursors for early steps of terpene moiety (secologanin) formation, were overexpressed transiently by agroinfiltration and stably by Agrobacterium-mediated transformation. Both transient and stable overexpression of G(G)PPS and co-expression of G(G)PPS+GES significantly enhanced the accumulation of secologanin, which in turn elevated the levels of monomeric MIAs. In addition, transgenic C. roseus plants exhibited increased levels of root alkaloid ajmalicine. The dimeric alkaloid vinblastine was enhanced only in G(G)PPS but not in G(G)PPS+GES transgenic lines that correlated with transcript levels of peroxidase-1 (PRX1) involved in coupling of vindoline and catharanthine into 3',4'-anhydrovinblastine, the immediate precursor of vinblastine. Moreover, first generation (T1) lines exhibited comparable transcript and metabolite levels to that of T0 lines. In addition, transgenic lines displayed normal growth similar to wild-type plants indicating that the bifunctional G(G)PPS enhanced flux toward both primary and secondary metabolism. These results revealed that improved availability of early precursors for terpene moiety biosynthesis enhanced production of MIAs in C. roseus at the whole plant level. This is the first report demonstrating enhanced accumulation of monomeric and dimeric MIAs including root MIA ajmalicine in C. roseus through transgenic approaches.

The aqueous solution conformation of tubercidin and tubercidin 5'-phosphate.

The backbone of tubercidin and tubercidin 5'-phosphate in aqueous solution has a flexible molecular framework with preference for 2E-gg and 2E-gg-g'g' conformations, respectively. The glycosyl bond is unusually flexible and no definite preference for either anti or syn conformation could be detected. It is proposed that the incorporation of tubercidin 5'-phosphate into nucleic acids will disrupt the polymeric structure because of the high accessibility of syn conformation, and this might be related to the reported inhibition of nucleic acid and protein synthesis.

Redescription and Range Extension of Microhyla sholigari Dutta & Ray (Amphibia: Anura: Microhylidae) from South West India.

Microhyla sholigari is an endangered frog described in the year 2000. The original description was based on non-adult types and lacked information on several morphological characters, call structure, genetic material and photographs of the animal in life. The absence of such information posed challenges in field identification of this species. Since the original description, there is one other reported sighting of this species from Kerala in 2001. We encountered specimens that we confer to this species based on morphological similarity to the subadult holotype, from several new localities within and outside the Western Ghats of Karnataka. We here redescribe the species based on additional adult vouchers, provide molecular data, describe the advertisement call and report a range extension. Based on its current distribution, we assess the threat status of the species and suggest listing it as Least Concern according to IUCN Red List criteria. Our paper bridges an important gap in the knowledge of the genus Microhyla in India and highlights the importance of systematic surveys in documenting and understanding amphibian diversity in the region.

De Novo Sequencing and Analysis of Lemongrass Transcriptome Provide First Insights into the Essential Oil Biosynthesis of Aromatic Grasses.

Aromatic grasses of the genus Cymbopogon (Poaceae family) represent unique group of plants that produce diverse composition of monoterpene rich essential oils, which have great value in flavor, fragrance, cosmetic, and aromatherapy industries. Despite the commercial importance of these natural aromatic oils, their biosynthesis at the molecular level remains unexplored. As the first step toward understanding the essential oil biosynthesis, we performed de novo transcriptome assembly and analysis of C. flexuosus (lemongrass) by employing Illumina sequencing. Mining of transcriptome data and subsequent phylogenetic analysis led to identification of terpene synthases, pyrophosphatases, alcohol dehydrogenases, aldo-keto reductases, carotenoid cleavage dioxygenases, alcohol acetyltransferases, and aldehyde dehydrogenases, which are potentially involved in essential oil biosynthesis. Comparative essential oil profiling and mRNA expression analysis in three Cymbopogon species (C. flexuosus, aldehyde type; C. martinii, alcohol type; and C. winterianus, intermediate type) with varying essential oil composition indicated the involvement of identified candidate genes in the formation of alcohols, aldehydes, and acetates. Molecular modeling and docking further supported the role of identified protein sequences in aroma formation in Cymbopogon. Also, simple sequence repeats were found in the transcriptome with many linked to terpene pathway genes including the genes potentially involved in aroma biosynthesis. This work provides the first insights into the essential oil biosynthesis of aromatic grasses, and the identified candidate genes and markers can be a great resource for biotechnological and molecular breeding approaches to modulate the essential oil composition.

Stress-Induced Accumulation of DcAOX1 and DcAOX2a Transcripts Coincides with Critical Time Point for Structural Biomass Prediction in Carrot Primary Cultures (Daucus carota L.).

Stress-adaptive cell plasticity in target tissues and cells for plant biomass growth is important for yield stability. In vitro systems with reproducible cell plasticity can help to identify relevant metabolic and molecular events during early cell reprogramming. In carrot, regulation of the central root meristem is a critical target for yield-determining secondary growth. Calorespirometry, a tool previously identified as promising for predictive growth phenotyping has been applied to measure the respiration rate in carrot meristem. In a carrot primary culture system (PCS), this tool allowed identifying an early peak related with structural biomass formation during lag phase of growth, around the 4th day of culture. In the present study, we report a dynamic and correlated expression of carrot AOX genes (DcAOX1 and DcAOX2a) during PCS lag phase and during exponential growth. Both genes showed an increase in transcript levels until 36 h after explant inoculation, and a subsequent down-regulation, before the initiation of exponential growth. In PCS growing at two different temperatures (21°C and 28°C), DcAOX1 was also found to be more expressed in the highest temperature. DcAOX genes' were further explored in a plant pot experiment in response to chilling, which confirmed the early AOX transcript increase prior to the induction of a specific anti-freezing gene. Our findings point to DcAOX1 and DcAOX2a as being reasonable candidates for functional marker development related to early cell reprogramming. While the genomic sequence of DcAOX2a was previously described, we characterize here the complete genomic sequence of DcAOX1.

Phase II study of paclitaxel in patients with extensive-disease small-cell lung cancer: an Eastern Cooperative Oncology Group study.

PURPOSE: To evaluate the efficacy and safety of paclitaxel (Taxol; Bristol-Myers Squibb Co, Princeton, NJ), a novel diterpene plant product in the treatment of previously untreated patients with extensive-disease small-cell lung cancer (SCLC). PATIENTS AND METHODS: Patients with extensive-disease SCLC received paclitaxel 250 mg/m2 intravenously over 24 hours every 3 weeks. Nonresponders or partial responders, who received the maximum number of cycles (n = 4) of paclitaxel received salvage chemotherapy that consisted of etoposide (VP-16) 120 mg/m2 intravenously over 45 minutes on days 1, 2, and 3, and cisplatin 60 mg/m2 intravenously as a short infusion on day 1. Cycles were repeated every 3 weeks. RESULTS: Of 36 patients entered onto the study, 34 and 32 patients were assessable for toxicity and response, respectively. No complete responses (CRs) were observed. Eleven patients (34%) had a partial response (PR) and six (19%) had stable disease (SD). In three of six patients categorized as having SD, there was greater than 50% tumor shrinkage. However, no 4-week follow-up measurements were made, so these could not be considered PRs, in part because patients received salvage chemotherapy by study design. In this trial, induction and salvage chemotherapy resulted in a response (two CRs and 15 PRs) (53%) in 17 patients. The estimated median survival duration was 43 weeks. Dose-limiting toxicity was leukopenia, with 19 patients (56%) having grade 4 leukopenia. The numbers of patients who experienced other grade 4 toxicities were as follows: pulmonary, three (9%); liver, two (6%); cardiac, one (3%); thrombocytopenia, one (3%); metabolic, one (3%); stomatitis, one (3%); and allergic reaction, one (3%). Four additional patients had grade 3 leukopenia and one patient (3%) died of sepsis (grade 5 toxicity). CONCLUSION: Paclitaxel is an active new agent in the treatment of SCLC. Further investigation of this agent in combination with other active agents is appropriate.

Secondary structure of the hybrid poly(rA).poly(dT) in solution. Studies involving NOE at 500 MHz and stereochemical modelling within the constraints of NOE data.

One-dimensional nuclear Overhauser effect (NOE) in nuclear magnetic resonance spectroscopy along with stereochemically sound model building was employed to derive the structure of the hybrid poly(rA).poly(dT) in solution. Extremely strong NOE was observed at AH2' when AH8 was presaturated; strong NOEs were observed at TH2'TH2'' when TH6 was presaturated; in addition the observed NOEs at TH2' and TH2'' were nearly equal when TH6 was presaturated. There was no NOE transfer to AH3' from AH8 ruling out the possibility of (C-3'-endo, low anti chi approximately equal to 200 degrees to 220 degrees) conformation for the A residues. The observed NOE data suggest that the nucleotidyl units in both rA and dT strands have equivalent conformations: C-2'-endo/C-1'-exo, anti chi approximately equal to 240 degrees to 260 degrees. Such a nucleotide geometry for rA/dT is consistent with a right-handed B-DNA model for poly(rA).poly(dT) in solution in which the rA and dT strands are conformationally equivalent. Molecular models were generated for poly(rA).poly(dT) in the B-form based upon the geometrical constraints as obtained from the NOE data. Incorporation of (C-2'-endo pucker, chi congruent to 240 degrees to 260 degrees) into the classical B-form resulted in severe close contacts in the rA chain. By introducing base-displacement, tilt and twist along with concomitant changes in the backbone torsion angles, we were able to generate a B-form for the hybrid poly(rA).poly(dT) fully consistent with the observed NOE data. In the derived model the sugar pucker is C-1'-exo, a minor variant of C-2'-endo and the sugar base torsion is 243 degrees, the remaining torsion angles being: epsilon = 198 degrees, xi = 260 degrees, alpha = 286 degrees, beta = 161 degrees and gamma = 72 degrees; this structure is free of any steric compression and indicates that it is not necessary to switch to C-3'-endo pucker for rA residues in order to accommodate the 2'-OH group. The structure that we have proposed for the polynucleotide RNA-DNA hybrid in solution is in complete agreement with that proposed for a hexamer hybrid in solution from NOE data and is inconsistent with the heteronomous model proposed for the fibrous state.

Preliminary X-ray analysis of a truncated form of recombinant fructose-2,6-bisphosphatase.

The bisphosphatase domain of rat liver 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase and a C-terminal 30 amino acid truncated form were expressed in high yield in Escherichia coli and purified to homogeneity. The separately expressed bisphosphatase domain and its C-terminal truncated form had kinetic properties similar to the bisphosphatase of the intact bifunctional enzyme, but their turnover numbers were fourfold higher. The truncated enzyme crystallized in space group P1 with two molecules per asymmetric unit. The determined cell dimensions are: a = 41.9 A, b = 43.5 A, c = 57.6 A, alpha = 95.2 degrees, beta = 99.3 degrees, and gamma = 106.2 degrees. These crystals diffract to 2.0 A resolution when exposed to synchrotron radiation and are suitable for crystallographic structure analysis.

The relationship between cardiothoracic ratio and left ventricular ejection fraction in congestive heart failure. Digitalis Investigation Group.

BACKGROUND: Left ventricular ejection fraction (EF) is a valuable prognostic index in patients with congestive heart failure (CHF). Although EF can be readily measured, many clinicians use roentgenographic heart size as a clue to differentiate systolic from diastolic dysfunction, even in the absence of solid supportive data. OBJECTIVE: To test the hypothesis that the cardiothoracic ratio (CTR) measured from the chest roentgenogram can be used to estimate left ventricular EF in individuals with CHF. METHODS: To answer this question, the database of the Digitalis Investigation Group trial was used. The CTR, determined using the Danzer method, and quantitative EF, measured locally using angiographic, radionuclide, or 2-dimensional echocardiographic techniques, were compared in 7476 patients with clinical CHF (New York Heart Association functional classes I-IV) due to acquired left-sided cardiac disease of ischemic, hypertensive, idiopathic, and alcohol-related causes. RESULTS: Mean (+/-SD) CTR for the cohort was 0.53+/-.07. Mean (+/-SD) EF was 31.7%+/-12.2%. A weak, negative correlation between CTR and EF was observed (r=-0.176). Similar findings were obtained when the results were stratified by cause of CHF, presence of clinically defined right ventricular dysfunction, and method of EF measurement. Categorical analysis failed to yield a CTR cutoff point that facilitated useful segregation of individuals with an EF greater than 35% or 35% and below; greater than 40% or 40% and below; and greater than 45% or 45% and below in any patient group. CONCLUSIONS: Although a weak, negative correlation exists between CTR and EF, this relationship does not allow for accurate determination of systolic function in individual patients with CHF. Considering the morbidity and mortality associated with CHF, and the clinical implications of systolic function in this syndrome, direct measurement of EF is recommended.

PET brain mapping study of auditory verbal supraspan memory versus visual fixation in schizophrenia.

Changes in regional cerebral blood flow (rCBF), associated with performance of an auditory verbal supraspan memory task, were studied in eight remitted DSM-III-R schizophrenic patients and eight pair-wise matched normal controls. Four positron emission tomography (PET) scans, using the [15O]-H2O technique, were acquired: two while subjects fixated a cross hair and two while performing a verbal free-recall supraspan memory task. Task performance showed typical patterns of recency and primacy effects in both groups; however, patients performed more poorly than controls on the primary (working) memory aspect of the task. Regions showing rCBF changes overlapped in both groups and were similar to those seen in previous studies of normals; however, patients had smaller increases in rCBF than controls in frontal and superior temporal cortical regions bilaterally. Our results suggest that remitted patients with schizophrenia demonstrate impairments of capacity-limited information processing, which may be related to metabolic dysfunction within a distributed network of brain structures, including the prefrontal and temporal cortical regions; however, dysfunction limited to the frontal cortex cannot be ruled out by the results of this experiment.

A cytosine . cytosine base paired parallel DNA double helix with thymine . thymine bulges.

500 MHz 1H NMR studies using 2D-NOESY indicate that the oligonucleotide d(CTCTCT) at low pH forms a parallel double helix with cytosine . cytosine base pairs and thymine . thymine bulges. This unusual structure may explain the hypersensitivity of S1 nuclease at low pH towards supercoiled plasmids containing d(CT)n inserts.

GC rich DNA oligonucleotides with narrow minor groove width.

Investigation of the width of the minor groove using 500 MHz NMR spectroscopy in three closely related 11-mer B-DNA duplexes shows that the minor groove is narrow in a GC rich oligonucleotide, and that a narrow minor groove is not something endemic to DNAs with persistent repetitions of adenine nucleotides (A-tract DNA). The width of the groove is dictated by local sequence contexts and independent of neighboring A-tract DNA.

NMR study of self-paired parallel duplex of d(AAAAACCCCC) in solution.

The oligonucleotide d(A5C5) in solution forms a parallel self-duplex at neutral and low pH values. H2O NMR spectra at pH 5.1 indicate the presence of five imino resonances at lower temperatures; and the structure is stable up to 60 degrees C. These signals can arise only from the hemiprotonated C+.C pairs [Westhof, E. and Sundaralingham, M. (1980) Biochemistry 77, 1852-1856; Westhof, E. and Sundaralingham, M. (1980) J. Mol. Biol. 142, 331-361] and constitute the first direct observation of C+.C hemiprotonated pairs in solution. The cross peaks from H1's and more than five distinct AH8's in 500 MHz 1H 2D-NOESY spectra indicate that there are two conformationally different and energetically similar A-tracts. There is good qualitative agreement between NOESY data and two theoretically derived structures in which A-tracts are reverse Watson-Crick and reverse Hoogsteen base-paired, respectively.

NOE data at 500 MHz reveal the proximity of phenyl and tyrosine rings in enkephalin.

Met5-enkephalin-a pentapeptide (Tyr-Gly-Gly-Phe-Met)-can exist in two possible folded arrangements with a rigid two-hydrogen-bonded network. In one arrangement, a Gly 2-Gly 3 beta-bend is formed and in the other a Gly 3-Phe 4 beta-bend. The two conformations are distinguished by the spatial relation of Tyr 1 and Phe 4: in the Gly 2-Gly 3 beta-bend, Tyr 1 and Phe 4 can be brought close to each other while in the Gly 3-Phe 4 beta-bend they are far apart (greater than 5 A). We have utilized one-dimensional (1D) nuclear Overhauser effect (NOE) measurements between the ring protons of Tyr 1 and Phe 4 to determine their proximity. The NOE data clearly show that a pair protons, one each from Tyr 1 and Phe 4, are as close as 3.3 A while other inter-proton distances are beyond 4.5 A. Therefore, we propose the presence of a Gly 2-Gly 3 beta-bend (in which Tyr 1 and Phe 4 are spatially close) for Met5-enkephalin in solution. The structure of Met5-enkephalin in solution is very similar to the single crystal structure of Leu5-enkephalin and tends to explain the biological activity data of several modified enkephalins.

Secondary structure in solution of two anti-HIV-1 hammerhead ribozymes as investigated by two-dimensional 1H 500 MHz NMR spectroscopy in water.

Two hammerhead chimeric RNA/DNA ribozymes (HRz) were synthesized in pure form. Both were 30 nucleotides long, and the sequences were such that they could be targeted to cleave the HIV-1 gag RNA. Named HRz-W and HRz-M, the former had its invariable core region conserved, the latter had a uridine in the invariable region replaced by a guanine. Their secodary structures were determined by 2D NOESY 1H 500 MHz NMR spectroscopy in 90% water and 10% D2(0), following the imino protons. The data show that both HRz-M and HRz-W form identical secondary structures with stem regions consisting of continuous stacks of AT and GT pairs. An energy minimized computer model of this stem region is provided. The results suggest that the loss of catalytic activity that is known to result when an invariant core residue is replaced is not related to the secondary structure of the ribozymes in the absence of substrate.