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PubMed1981

Enzymatic synthesis of biotin-labeled polynucleotides: novel nucleic acid affinity probes.

Analogs of dUTP and UTP that contain a biotin molecule covalently bound to the C-5 position of the pyrimidine ring through an allylamine linker arm have been synthesized. These biotin-labeled nucleotides are efficient substrates for a variety of DNA and RNA polymerases in vitro. Polynucleotides containing low levels of biotin substitution (50 molecules or fewer per kilobase) have denaturation, reassociation, and hybridization characteristics similar to those of unsubstituted controls. Biotin-labeled polynucleotides, both single and double-stranded, are selectively and quantitatively retained on avidin-Sepharose, even after extensive washing with 8 M urea, 6 M guanidine hydrochloride, or 99% formamide. In addition, biotin-labeled polynucleotides can be selectively immunoprecipitated in the presence of antibiotin antibody and Staphylococcus aureus protein A. The unique features of biotin-labeled polynucleotides suggest that they will be useful affinity probes for the detection and isolation of specific DNA and RNA sequences.

Affinity Labels↗
PubMed1981

Systematic punctuation of eukaryotic DNA by A+T-rich sequences.

Isodenaturation of avian and mammalian DNA of Mr greater than 2.5 X 10(8) in 85% (vol/vol) formamide led to the observation by electron microscopy of A+T-rich zones ("AT-rich linkers") of 300-3000 base pairs which are distributed over the entire genome in a characteristic pattern. Linkers of mean length 800 base pairs are found either isolated or in clusters of about four to six linkers of more heterogeneous size separated on average by 2500 base pairs (in duck DNA). In between clusters, single linkers segment the DNA at distances of 10 to more than 100 kilobase pairs, with a majority in the range of 10-30 kilobase pairs. An analogous organization of linkers is found in rat and mouse DNA. The internal organization of the clusters varies, however, in a fashion that might be related to the large amount of light satellite DNA in the mouse and its apparent absence in rat and avian DNA. It is possible to fragment the DNA under appropriate conditions by the single-strand-specific nuclease S1 at the site of these A+T-rich zones and to obtain, on alkaline sucrose gradients, a bimodal pattern of DNA fragments of the size corresponding to the pattern observed by electron microscopy. The implications of this observation for DNA organization, chromatin structure, units of transcription and replication, and possible targets of A+T-specific drugs are discussed.

Adenine↗
PubMed1981

Identification of a population of bipotent stem cells in the HL60 human promyelocytic leukemia cell line.

HL60, the human promyelocytic leukemia cell line, consists of cells that resemble promyelocytes but are transformed into more mature myeloid forms (polymorphonuclear leukocytes) that express most of the functional characteristics of terminally differentiated myeloid forms when incubated in the presence of dimethyl formamide (HCONMe(2)). When HL60 cells are exposed to the phorbol diester 12-O-tetradecanoylphorbol 13-acetate [phorbol 12-myristate 13-acetate (PMA)], they shift from suspension to adherent on the surface of the tissue culture vessel, assume the appearance of macrophages, and acquire macrophage-associated surface markers, the enzyme-nonspecific esterase, the isozyme acid phosphatase, and the myeloid-specific esterase. Although data from other laboratories suggest that HL60 consists of stem cells that are bipotent with respect to myeloid or macrophage differentiation, unequivocal proof of bipotency or evidence that ruled out the presence of two different types of stem cells, each committed to different lines of hematopoietic differentiation, has been lacking. To resolve these two alternatives, we have developed a cloned population of HL60 cells and studied the properties of these cells when exposed to inducers of myeloid (HCONMe(2)) or macrophage (PMA) differentiation. After 120 hr of incubation with HCONMe(2), 95% of the cells acquire myeloid markers and lack specific macrophage markers, whereas the reverse is true in the presence of PMA, clearly establishing that HL60 is able to commit itself to the development of two different programs of hematopoietic differentiation. Moreover, the commitment to macrophage differentiation is irreversible after 6 hr of incubation in PMA whereas development of the myeloid program requires continuous exposure of the cells to HCONMe(2). Commitment of HL60 to macrophage differentiation by PMA is not affected by subsequent addition of HCONMe(2), whereas HCONMe(2)-induced myeloid differentiation is overridden by exposure of the cells to PMA. These data suggest that the HL60 cell may provide a model system for studying the process that generates several classes of precursor cells, each committed to different lines of hematopoietic differentiation, as well as the process that mediates the maturation of these committed precursor cells to their terminally differentiated state.

Cell Differentiation↗
PubMed1982

Cytochrome c gene-related sequences in mammalian genomes.

We use a rat cytochrome c gene that we previously isolated and determined the sequence of to estimate the number of related sequences present in the rat genome. Approximately 25 different EcoRI restriction endonuclease fragments from total rat DNA hybridize to the gene of known structure. Four of these correspond to homologous sequences present in four different lambda Charon 4A-rat cytochrome c recombinants previously isolated. Intact or nearly intact genes appear to reside on almost all of the genomic fragments, because they hybridize strongly to gene subfragments representing both 5' and 3' portions of the coding sequence as well as to 3' noncoding DNA that is found specifically associated with the coding region. A subgroup of about six of the fragments also shares homology within the 73 nucleotides immediately preceding the AUG codon. An intron-specific probe reveals only the EcoRI fragment from which it was derived and one other genomic fragment. On the basis of the temperature of complete dissociation of the coding region probe in 0.75 M NaCl/0.075 M Na3 citrate/50% (vol/vol) formamide, the 25 fragments are separable into three stringency classes of 40-50 degrees C, 50-55 degrees C, and 55-60 degrees C. The latter, high-stringency group of about seven fragments includes those cloned in the recombinant phage isolates, whose regions homologous to cytochrome c are shown to differ from the purified gene of known sequence by an amount equivalent to about 2% mismatched bases. Families of cytochrome c gene-related sequences are also found in the genomes of several other mammals, including humans.

Animals↗
PubMed1983

Perturbation of hydrogen bonds in the adenine . thymine base pair by Na+: A quantum chemical study.

Ab initio self-consistent field calculations with 4-31G and STO-3G basis sets show that Na+ are able to damage the H bonds in the formamidine . formamide complex, modeling the adenine . thymine base pair (both H bonds in the complex investigated are the same as in adenine . thymine). If a water molecule is placed between the complex and Na+, the H bonds of the model are fully protected. Covalent as well as noncovalent binding of polycyclic aromatic hydrocarbons to nucleic acids should decrease the local concentration of water as a result of the insertion of the hydrophobic hydrocarbon into the DNA and thereby increase the exposure of the DNA H bonds to Na+ attack. Thus, Na+ reaching the base pair could provoke or interfere with cell division.

Adenine↗
PubMed1984

Charge state of His-57-Asp-102 couple in a transition state analogue-trypsin complex: a molecular orbital study.

Ab initio molecular orbital studies have been made as a model for the deacylation step of trypsin. Ser-195 is modeled by H2O in which one H is replaced either by--PO2(OH)- (monoisopropyl phosphoryl, MIP) or by--CHO(OH)- (a transition state analogue, TSD). The quantum mechanical region includes imidazole+ and acetate- as models for His-57+ and Asp-102-, two hydrogen bonds from two formamide molecules to the oxyanion MIP or TSD, and three hydrogen bonds to Asp-102. The remainder of the enzyme is treated classically as a fractional charge model. The effect of proton transfer from His-57+ to Asp-102- is very similar for the MIP and TSD models, and the proton transfer is energetically unfavorable for all models that include at least the hydrogen bond from an H2O that models Ser-214. Thus, the several hydrogen bonds to the models of the catalytic unit (substrate, Ser-195, His-57, and Asp-102) stabilize the His-57+/Asp-102- salt link, and this indicates that proton transfer does not occur from His-57+ to Asp-102-. (Also, the similarities of energy of transfer of this proton transfer for the various models show that the model substrate analogue behaves very similarly to the MIP inhibitor.)

Aspartic Acid↗
PubMed1984

Quantitation of aflatoxin B1 adduction within the ribosomal RNA gene sequences of rat liver DNA.

The in vivo formation of covalent aflatoxin B1 (AFB1)-DNA adducts within the rRNA gene sequences of nuclear DNA has been studied in AFB1-treated rats. Liver nuclear DNA, enriched in ribosomal DNA (rDNA) by one round of cesium salt density gradient centrifugation, was treated under buffered alkaline conditions to convert unstable AFB1-N7-guanine adducts to stable AFB1-formamidopyrimidine derivatives. The alkali-treated DNA was hybridized to 18S and 28S rRNA in 70% formamide buffer to form rRNA X rDNA hybrids. These hybrids were separated from the bulk of nuclear DNA by two rounds of centrifugation in CsCl, and the level of AFB1 adduction to rDNA versus total nuclear DNA was compared as a function of dose 2 hr after AFB1 administration. Over an 8-fold dose range (0.25-2.0 mg of AFB1 per kg of body weight), rDNA contained 4- to 5-fold more AFB1 residues than nuclear DNA, indicating that rDNA is preferentially accessible to carcinogen modification in vivo. While aflatoxin B1 forms adducts with DNA principally at guanine residues, the guanine enrichment of rDNA was insufficient to explain the magnitude of observed preferential AFB1 modification of rDNA. These results support the hypothesis that rDNA regions are preferentially accessible to carcinogen modification because of the diffuse conformation maintained within transcribed genes. This experimental approach permits the quantitative description of carcinogen modification within a defined gene sequence; further refinement of this approach may be useful in defining the precise relationships between covalent chemical-DNA interactions and the alterations in gene expression that result.

Aflatoxin B1↗
PubMed1986

The nature of enzyme catalysis in trypsin.

We present a combined quantum/molecular mechanical study of the trypsin-catalyzed hydrolysis of a specific tripeptide substrate, including the entire enzyme in the calculation, as well as 200 H2O molecules. The results illustrate how the enzyme and nearby H2O molecules stabilize the ionic intermediates in peptide hydrolysis, such that the reaction is calculated to have a barrier that is significantly smaller than the calculated and experimental base-catalyzed barrier of formamide hydrolysis in aqueous solution. This enables us to understand how serine proteases increase the rates for reactions that take place in their active sites, compared to the corresponding rates for analogous solution reactions.

Binding Sites↗
PubMed1990

Distribution and self-organization of photosynthetic pigments in micelles: implication for the assembly of light-harvesting complexes and reaction centers in the photosynthetic membrane.

The addition of bacteriochlorophylls and bacteriopheophytins to formamide/water, 3:1 (vol/vol), (or water) containing small spherical micelles of Triton X-100 leads to the reorganization of the detergent into micelles that consist of 5000-40,000 amphiphilic molecules. The pigment distribution within the micelles was determined by modified Poisson statistics taking into consideration the various sizes of micelles. Pigment dimerization occurred in micelles with more than a single occupant and was driven by a free-energy change of -4.5 kcal/mol (1 cal = 4.184 J) for bacteriochlorophyll a in formamide/water, -7.6 kcal/mol for bacteriopheophytin a in formamide/water, and -6.6 kcal/mol for bacteriopheophytin a in water. These values correspond to the room temperature equilibrium constants 2.2 x 10(3) M-1, 3.9 x 10(5) M-1, and 7.5 x 10(4) M-1, respectively. The incorporation of bacteriochlorophylls with attached small formamide polymers and the subsequent dimerization of these pigments in the lipid phase provide a model for studying the synergetic organization of polypeptides and bacteriochlorophyll clusters in the photosynthetic membrane.

Journal Article↗
PubMed1993

Conformation-sensitive gel electrophoresis for rapid detection of single-base differences in double-stranded PCR products and DNA fragments: evidence for solvent-induced bends in DNA heteroduplexes.

Several techniques have recently been developed to detect single-base mismatches in DNA heteroduplexes that contain one strand of wild-type and one strand of mutated DNA. Here we tested the hypothesis that an appropriate system of mildly denaturing solvents can amplify the tendency of single-base mismatches to produce conformational changes, such as bends in the double helix, and thereby increase the differential migration of DNA heteroduplexes and homoduplexes during gel electrophoresis. The best separations of heteroduplexes and homoduplexes were obtained with a standard 6% polyacrylamide gel polymerized in 10% ethylene glycol/15% formamide/Tris-taurine buffer. As predicted by the hypothesis of solvent-induced bends, when the concentration of either ethylene glycol or formamide was increased, the differential migration decreased. Also, single-base mismatches within 50 bp of one end of a heteroduplex did not produce differential migration. Sixty of 68 single-base mismatches in a series of PCR products were detected in some 59 different sequence contexts. The eight mismatches not detected were either within 50 bp of the nearest end of the PCR product or in isolated high-melting-temperature domains. Therefore, it was possible to predict in advance the end regions and sequence contexts in which mismatches may be difficult to detect. The procedure can be applied to any PCR products of 200-800 bp and requires no special equipment or preparation of samples.

Bacteriophage M13↗
PubMed1993

Sequence-specific scission of DNA by the chemical nuclease activity of 1,10-phenanthroline-copper(I) targeted by RNA.

RNAs modified with the chemical nuclease 1,10-phenanthroline-copper(I) can achieve the sequence-specific scission of single- and double-stranded DNA targets. The RNAs are prepared in vitro by using 5-(3-aminoallyl)-UTP as the sole source of UTP and can be readily modified with 1,10-phenanthroline by using N-succinimidyl 3-(2-pyridyl-dithio)propionate (SPDP) to cross-link the ligand to the aminoallyl moiety. Single-stranded DNAs are efficiently cleaved at multiple sites because 1,10-phenanthroline is incorporated at several uridines in the sequence. Sequence-specific double-stranded scission of duplex DNA can also be accomplished with 1,10-phenanthroline-derivatized RNA within R loops. These triple-stranded structures form in 70% formamide and involve the displacement of one strand of DNA by the RNA of identical sequence. R loop-directed scission is the first method for DNA scission applicable to any sequence. A unique application of R loop-targeted nucleolytic scission, which relies on its ability to cut DNA at any sequence, is the determination of the distance between two marker DNA sequences within a target. In this case, 1,10-phenanthroline-linked RNAs are prepared from the two distinct sequences and used to cut the DNA fragment after R-loop formation. The size of the fragment liberated by these methods is a direct measure in base pairs of the distance between the two DNA sequences. For example, the distance separating two chicken delta crystallin (delta 1 and delta 2) genes has been confirmed as 24 kilobases by this method.

Animals↗
PubMed1996

Properties of a primer RNA-DNA hybrid at the mouse mitochondrial DNA leading-strand origin of replication.

Primers for vertebrate mitochondrial leading-strand DNA replication are products of transcription synthesized by mitochondrial RNA polymerase. The precursor primer RNA exists as a persistent RNA-DNA hybrid, known as an R-loop, formed during transcription through the replication origin (Xu, B., and Clayton, D. A. (1996) EMBO J. 15, 3135-3143). In an effort to examine the precise structure of this primer RNA intermediate, we have used two methods to reconstitute model R-loops containing the mouse mitochondrial DNA origin sequence. First, we demonstrate that bacteriophage SP6 RNA polymerase can efficiently catalyze the formation of an R-loop at the mouse mtDNA origin sequence. Second, the R-loop can be assembled by annealing presynthesized RNA and supercoiled DNA template in the presence of formamide. R-loop formation by either method is dependent on specific template sequences. The reconstituted R-loop is exceptionally stable and exhibits an unexpected structure. Structural studies indicate that the RNA strand is organized within the RNA-DNA base-paired region, suggesting that the heteroduplex interaction occurs through a specific conformation. We propose that the organized structure of the R-loop is critical for primer RNA function in vivo with important implications for the RNA processing and DNA replication machinery.

Animals↗
PubMed1997

Functional analysis of nodulin 26, an aquaporin in soybean root nodule symbiosomes.

Upon infection of soybean roots, nitrogen-fixing bacteria become enclosed in a specific organelle known as the symbiosome. The symbiosome membrane (SM) is a selectively permeable barrier that controls metabolite flux between the plant cytosol and the symbiotic bacterium inside. Nodulin 26 (NOD 26), a member of the aquaporin (AQP) water channel family, is a major protein component of the SM. Expression of NOD 26 in Xenopus oocytes gave a mercury-sensitive increase in osmotic water permeability (Pf). To define the biophysical properties of NOD 26 water channels in their native membranes, symbiosomes were isolated from soybean root nodules and the SM separated as vesicles from the bacteria. Permeabilities were measured using stopped-flow fluorimetry in SM vesicles with entrapped carboxyfluorescein. Osmotic water permeability (Pf) of SM was high, with a value of 0.05 +/- 0.003 cm/s observed at 20 degrees C (mean +/- S.E.; n = 15). Water flow exhibited a low activation energy, was inhibited by HgCl2 (0.1 mM), and exhibited a unit conductance of 3.2 +/- 1.3 x 10(-15) cm3/s, a value 30-fold lower than that of AQP 1, the red blood cell water channel. Diffusive water permeability (Pd) was 0.0024 +/- 0.0002 cm/s, and the resulting Pf to Pd ratio was 18.3, indicating that water crosses the SM in single file fashion via the NOD 26 water channel. In addition to high water permeability, SM vesicles also show high mercury-sensitive permeability to glycerol and formamide, but not urea, suggesting that NOD 26 also fluxes these solutes. Overall, we conclude that NOD 26 acts as a water channel with a single channel conductance that is 30-fold lower than AQP 1. Because the solutes that permeate NOD 26 are far larger than water, and water appears to cross the channel via a single file pathway, solute flux across NOD 26 appears to occur by a pathway that is distinct from that for water.

Animals↗
PubMed1998

Bidirectional water fluxes and specificity for small hydrophilic molecules in aquaporins 0-5.

The dimensions of the aqueous pore in aquaporins (AQP) 0, 1, 2, 3, 4, and 5 expressed in Xenopus laevis oocytes were probed by comparing the ability of various solutes to generate osmotic flow. By improved techniques, volume flows were determined from initial rates of changes. Identical values for the osmotic water permeability (Lp) were obtained in swelling as in shrinkage experiments demonstrating, for the first time, that aquaporins are bidirectional. The reflection coefficients (sigma) of urea, glycerol, acetamide, and formamide at 23 degreesC were: AQP0: 1, 1, 0.8, 0.6; AQP1: 1, 0.8, 1, 1; AQP2: 1, 0.8, 1, 1; AQP3: 1, 0.2, 0.7, 0.4; AQP4: 1, 0.9, 1, 1; and AQP5: 1, 1, 1, 0.8. As seen there is no clear connection between solute size and permeation. At 13 degreesC the sigmas for AQP3 were 1, 0.4, 1, and 0.5; functionally, this pore narrows at lower temperatures. HgCl2 reversibly reduced the Lp of AQP3 and increased sigmaglyc to 1 and sigmaform to 0.6. We conclude that the pore of the various aquaporins are structurally different and that a simple steric model is insufficient to explain solute-pore interactions.

Animals↗
PubMed2000

Characterization of the binding site on the formyl peptide receptor using three receptor mutants and analogs of Met-Leu-Phe and Met-Met-Trp-Leu-Leu.

The formyl peptide receptor (FPR) is a chemotactic G protein-coupled receptor found on the surface of phagocytes. We have previously shown that the formyl peptide binding site maps to the membrane-spanning region (Miettinen, H. M., Mills, J. S., Gripentrog, J. M., Dratz, E. A., Granger, B. L., and Jesaitis, A. J. (1997) J. Immunol. 159, 4045-4054). Recent reports have indicated that non-formylated peptides, such as MMWLL can also activate this receptor (Chen, J., Bernstein, H. S., Chen, M., Wang, L., Ishi, M., Turck, C. W., and Coughlin, S. R. (1995) J. Biol. Chem. 270, 23398-23401.) Here we show that the selectivity for the binding of different NH(2)-terminal analogs of MMWLL or MLF can be markedly altered by mutating Asp-106 to asparagine or Arg-201 to alanine. Both D106N and R201A produced a similar change in ligand specificity, including an enhanced ability to bind the HIV-1 peptide DP178. In contrast, the mutation R205A exhibited altered specificity at the COOH terminus of fMLF, with R205A binding fMLF-O-butyl > fMLF-O-methyl > fMLF, whereas wt FPR bound fMLF > fMLF-O-methyl approximately fMLF-O-butyl. These data, taken together with our previous finding that the leucine side chain of fMLF is probably bound to FPR near FPR (93)VRK(95) (Mills, J. S., Miettinen, H. M., Barnidge, D., Vlases, M. J., Wimer-Mackin, S., Dratz, E. A., and Jesaitis, A. J. (1998) J. Biol. Chem. 273, 10428-10435.), indicate that the most likely positioning of fMLF in the binding pocket of FPR is approximately parallel to the fifth transmembrane helix with the formamide group of fMLF hydrogen-bonded to both Asp-106 and Arg-201, the leucine side chain pointing toward the second transmembrane region, and the COOH-terminal carboxyl group of fMLF ion-paired with Arg-205.

Alanine↗
PubMed2002

Differential regulation of amidase- and formamidase-mediated ammonia production by the Helicobacter pylori fur repressor.

The production of high levels of ammonia allows the human gastric pathogen Helicobacter pylori to survive the acidic conditions in the human stomach. H. pylori produces ammonia through urease-mediated degradation of urea, but it is also able to convert a range of amide substrates into ammonia via its AmiE amidase and AmiF formamidase enzymes. Here data are provided that demonstrate that the iron-responsive regulatory protein Fur directly and indirectly regulates the activity of the two H. pylori amidases. In contrast to other amidase-positive bacteria, amidase and formamidase enzyme activities were not induced by medium supplementation with their respective substrates, acrylamide and formamide. AmiE protein expression and amidase enzyme activity were iron-repressed in H. pylori 26695 but constitutive in the isogenic fur mutant. This regulation was mediated at the transcriptional level via the binding of Fur to the amiE promoter region. In contrast, formamidase enzyme activity was not iron-repressed but was significantly higher in the fur mutant. This effect was not mediated at the transcriptional level, and Fur did not bind to the amiF promoter region. These roles of Fur in regulation of the H. pylori amidases suggest that the H. pylori Fur regulator may have acquired extra functions to compensate for the absence of other regulatory systems.

Amidohydrolases↗
PubMed2002

Isonitrile hydratase from Pseudomonas putida N19-2. Cloning, sequencing, gene expression, and identification of its active acid residue.

Isonitrile hydratase is a novel enzyme in Pseudomonas putida N19-2 that catalyzes the conversion of isonitriles to N-substituted formamides. Based on N-terminal and internal amino acid sequences, a 535-bp DNA fragment corresponding to a portion of the isonitrile hydratase gene was amplified, which was used as a probe to clone a 6.4-kb DNA fragment containing the whole gene. Sequence analysis of the 6.4-kb fragment revealed that the isonitrile hydratase gene (inhA) was 684 nucleotides long and encoded a protein with a molecular mass of 24,211 Da. Overexpression of inhA in Escherichia coli gave a large amount of soluble isonitrile hydratase exhibiting the same molecular and catalytic properties as the native enzyme from the Pseudomonas strain. The predicted amino acid sequence of inhA showed low similarity to that of an intracellular protease in Pyrococcus horikoshii (PH1704), and an active cysteine residue in the protease was conserved in the isonitrile hydratase at the corresponding position (Cys-101). A mutant enzyme containing Ala instead of Cys-101 did not exhibit isonitrile hydratase activity at all, demonstrating the essential role of this residue in the catalytic function.

Amino Acid Sequence↗
PubMed1998

Murine local lymph node assay for predictive testing of allergenicity: two irritants caused significant proliferation.

The murine local lymph node assay is a method for predictive testing of contact allergenicity, but its ability to discriminate between allergens and irritants has been questioned. To explain some of the conflicting results with irritants, the proliferation induced by methyl salicylate and nonanoic acid, both considered to be non-sensitisers, was further investigated. Both substances showed a dose--response relationship and clearly positive results when tested at higher concentrations (> or = 50%) and would thus be classified as potential sensitisers according to the present criteria for a positive assay result. In the case of methyl salicylate, the use of either dimethyl formamide or methyl ethyl ketone as vehicle did not significantly influence the results. The negative results obtained for methyl salicylate in some earlier reports were probably due to testing at too low concentrations. The proliferation induced by irritants such as methyl salicylate and nonanoic acid and inter alia sodium dodecyl sulfate, Triton X-100, oxalic acid, chloroform/methanol (2:1) must be better recognized and elucidated before the assay can be generally accepted as a predictive test method.

Allergens↗