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At least 811 records · Page 45Linked to original sources
PubMed1992

Comparative molecular neuroanatomy of cloned GABAA receptor subunits in the rat CNS.

gamma-Aminobutyric acidA (GABAA) receptors in the mammalian central nervous system (CNS) are members of a family of ligand-gated ion channels consisting of heterooligomeric glycoprotein complexes in synaptic and extrasynaptic membranes. Although molecular cloning studies have identified 5 subunits (with approximately 40% amino acid homology) and isoforms thereof (approximately 70% homology), namely alpha 1-6, beta 1-4, gamma 1-3, delta, and rho, the subunit composition and stoichiometry of native receptors are not known. The regional distribution and cellular expression of GABAA receptor messenger RNAs (mRNAs) in the rat CNS have now been investigated by in situ hybridization histochemistry with subunit-specific 35S-labelled oligonucleotide probes on adjacent cryostat sections. Whereas alpha 1, beta 2, and gamma 2 transcripts were the most abundant and ubiquitous in the rat brain--correlating with the radioautographic distribution of GABAA receptors revealed by an ionophore ligand--others had a more restricted expression while often being abundant. For example, alpha 2 transcripts were found only in the olfactory bulb, cerebral cortex, caudate putamen, hippocampal formation, and certain lower brain stem nuclei; alpha 3 only in the olfactory bulb and cerebral cortex; alpha 5 in the hippocampal formation; and alpha 6 only in cerebellar granule cells. In addition, beta 1, beta 3, gamma 1, and delta mRNAs were also uniquely expressed in restricted brain regions. Moreover, in the spinal cord, alpha 1-3, beta 2,3, and gamma 2 mRNAs were differently expressed in Rexed layers 2-9, with alpha 2, beta 3, and gamma 2 transcripts most prominent in motoneurons of layer 9. Although differential protein trafficking could lead to the incorporation of some subunits into somatic membranes and others into dendritic membranes, some tentative conclusions as to the probable composition of native proteins in various regions of the CNS may be drawn.(ABSTRACT TRUNCATED AT 400 WORDS)

Animals↗
PubMed2003

Performance of capillary gel electrophoretic analysis of oligonucleotides coupled on-line with electrospray mass spectrometry.

Synthetic oligonucleotides (ODNs) are routinely analyzed using capillary gel electrophoresis (CGE) for size-sieving based separations as well as electrospray mass spectrometry (ESI-MS) for identification. On-line coupling of these methods is therefore desired in order to combine the analytical capabilities provided by both methods. Performance of on-line CGE-ESI-MS systems is influenced by various parameters, and choice of optimal conditions is crucial for successful coupling experiments. In this study, we explore characteristics of the on-line coupled CGE-ESI-MS system for ODN analysis. Effects of CGE buffer concentration, capillary length, separation and orifice voltage on CGE separation and MS detection of a phosphodiester ODN mixture were examined. Attention was paid to the influence of the interface, such as geometry of capillary alignment, sheath liquid flow-rate and sheath liquid composition on performance of the system.

Acetonitriles↗
PubMed2005

General method for modification of liposomes for encoded assembly on supported bilayers.

An amphiphilic oligonucleotide species ((C18)2-DNA) is presented as a generally useful reagent to display encoded tether sequences on the surface of phospholipid assemblies. (C18)2-DNA inserts into preformed vesicles and proteoliposomes of arbitrary composition, content, and origin using a simple and gentle procedure and is a significant improvement over the previously described method particularly since it allows postmodification of any phospholipid assembly without the need for special lipids carrying reactive headgroups. DNA-modified vesicles can then be tethered, via DNA hybridization, onto a supported phospholipid bilayer displaying the complementary sequence. The encoding capability of the tether can be exploited to form an array of tethered vesicles spatially defined by the DNA sequence displayed on the surface and demonstrates that (C18)2-DNA is stably associated with a membrane to allow sorting. Vesicles tethered in this way show two-dimensional mobility, reflecting the fluidity of the supporting bilayer, and promises to be a useful system with which to study vesicle-vesicle interactions.

DNA↗
PubMedDate not supplied

[Pyrimidine oligodeoxyxylonucleotides form triplexes with purine DNA in neutral media].

Interactions of oligonucleotides comprising (1-beta-D-2'-deoxy-threo-pentafuranosyl)thymine and (1-beta-D-2'-deoxy-threo-pentafuranosyl)cytosine residues (oligodeoxyxylonucleotides or OXNs) with complementary single-stranded DNA fragments were investigated. Using nondenaturing gel electrophoresis, footprinting, and melting assays, pyrimidine OXNs were shown to form triplexes with the purine DNA template, which are stable at neutral pH and comparable in heat stability with the corresponding natural polypurine-polypyrimidine DNA duplexes. In such triplexes, the N3 of cytosines in one of the OXNs are protonated. As revealed by CD spectroscopy in the 210-340 nm range, the form of the triple helix depends on the nucleotide composition and sequence of the DNA template, and is intermediate between A and B.

DNA↗
PubMed1986

B- to Z-DNA transition probed by oligonucleotides containing methylphosphonates.

The simulation of the B--Z-DNA transition by using space-filling models of the dimer d(C-G) shows the possibility of hydrogen-bond formation between the N-2 amino group of the partially rotated guanine and one of the 5'-phosphate oxygens of deoxyguanylic acid. To probe the importance of this postulated interaction, analogs of the hexamer d(C-G)3 were synthesized. These analogs contained a methylphosphonate linkage, of distinct stereochemistry, which replaced the first 5'-phosphate linkage of deoxyguanosine. The CD spectra in high salt concentration showed that the hexamer containing a methylphosphonate linkage with the RP stereochemistry formed Z-DNA to the same extent as d(C-G)3, whereas the hexamer containing a methylphosphonate linkage with the SP stereochemistry did not form Z-DNA. These results are consistent with a mechanism in which an interaction between the N-2 amino group of guanine and the prochiral SP oxygen of deoxyguanosine 5'-phosphate kinetically controls the formation of Z-DNA. A water bridge between the N-2 amino group of guanine and the 3'-phosphate oxygen of deoxyguanylic acid has been implicated in the stabilization of Z-DNA. To probe the importance of this water bridge, two additional analogs of the hexamer d(C-G)3 were synthesized. These analogs contained a methylphosphonate linkage, of distinct stereochemistry, that replaced the first deoxyguanosine 3'-phosphate. The CD spectra showed that the hexamer containing a methylphosphonate linkage of the RP stereochemistry underwent the transition to Z-DNA to the same extent as d(C-G)3, whereas the hexamer containing a methylphosphonate linkage of the SP stereochemistry underwent the transition to Z-DNA to a 35% lesser extent. Thus the water bridge involving the prochiral SP oxygen provides modest stabilization energy for Z-DNA. These studies, therefore, suggest that the B--Z-DNA transition is regulated both thermodynamically and kinetically through hydrogen-bond interactions involving phosphate oxygens and the N-2 amino group of guanine.

Base Composition↗
PubMed1991

Cloning and sequence analysis of cDNA encoding two crustacean hyperglycemic hormones from the lobster Homarus americanus.

Using the polymerase chain reaction with degenerated oligonucleotides, we have isolated cDNA clones that encode two structurally different (92% identity) crustacean hyperglycemic hormones (CHH) from the lobster Homarus americanus. The deduced amino acid sequences fully agree with previously published data on partial amino acid sequences, amino acid compositions and molecular masses of hyperglycemic peptides in the lobster. A comparative analysis between the deduced primary structure of two lobster CHH and the crab CHH sequence reveals a phylogenetic relationship and allows the prediction of biologically important regions within the structures of these novel neuropeptides.

Amino Acid Sequence↗
PubMed1987

The Greek A gamma beta+-HPFH observed in a large black family.

Several members of a Black family with a heterozygosity for an A gamma beta+-HPFH, shown in 1969 to have relatively low levels of Hb F and a low glycine to alanine ratio in the gamma chain of this Hb F, were reinvestigated. Thirteen of 30 available family members in two generations had the heterozygous form of this condition, which was characterized by a decreased level of Hb A2, an average Hb FAD value of 13.3%, an equal distribution of Hb F over the red cells, and normal hematological values. The gamma chain composition of isolated Hb F was determined by reversed phase high performance liquid chromatography for all 13 heterozygotes and showed an average A gamma value of 84.5%. Hybridization with synthetic oligonucleotides, specific for normal and mutant sequences at positions 111-129 5' to the A gamma globin gene, identified a G----A base substitution at position 117, similar to that seen in subjects with the Greek A gamma-HPFH. Our data support conclusions by others that this replacement is causative of the increased A gamma chain synthesis in this condition. Haplotype analysis supported the suggestion that the G----A substitution occurred as an independent event in this Black family.

Adenine↗
PubMed2000

From a short amino acidic sequence to the complete gene.

A useful strategy directed to the isolation of a required gene with a high GC content is reported. Using a degenerate oligonucleotide probe, deduced from the amino terminus of a protein, it is possible to obtain a fragment of DNA containing its encoding gene by PCR amplification. Furthermore, the cloning of a desired gene can be accomplished in two steps by using an oligonucleotide deduced (i) from an internal sequence, (ii) from a consensus sequence, or (iii) from a DNA sequence adjacent to a disrupting element (transposon, insertion sequence, cassette). This method, which could be applied to a bacteriophage, plasmid, or cosmid genomic library, has been successfully used for cloning several genes from different biological systems.

Amino Acid Sequence↗
PubMed1983

CpG frequency in large DNA segments.

The relationship between the deficiency of CpG dinucleotides and the coding-noncoding segments of DNA has been examined. Analysis of five human alpha-like globin DNA sequences and five human beta-like globin DNA sequences reveal that there is no apparent difference between protein coding and non-coding portions of DNA. Rather CpG deficiency appears to be a property of long contiguous segments of DNA consisting of several genes and their intergenic regions. Thus we propose that CpG deficiency is not involved with translation or transcription but rather is related to chromosomal constraints.

Adult↗
PubMed1985

Conformational microheterogeneity in a DNA double helix: structure of restriction endonuclease Bam H1 recognition site.

Structural studies using 500 MHz 1H NMR spectroscopy on Bam H1 recognition site d(GGATCC)2 in solution at 19 degrees is reported. The resonances from the sugar ring and base protons have been assigned from the 2D-COSY and NOESY spectra. Analyses of the NOESY cross-peaks between the base protons H8/H6 and sugar protons H2'/H2", H3' reveal that the nucleotide units G2, A3 and C6 adopt (C3'-endo, chi = 200 degrees-220 degrees) conformation while G1, T4 and C5 exhibit (C2'-endo, chi = 240 degrees-260 degrees) conformation. NMR data clearly suggest that the two strands of d(GGATCC)2 are conformationally equivalent and there is a structural two-fold between the two A-T pairs. The above information and the NOESY data are used to generate a structural model of d(GGATCC)2. The important features are: (i) G1-G2 stack, the site of cleavage, shows an alternation in sugar pucker i.e. C2'-endo, C3'-endo as in a B-A junction, (ii) G2-A3 stack adopts a mini A-DNA, both the sugars being C3'-endo, (iii) A3-T4 stack, the site of two-fold, displays an A-B junction with alternation in sugar pucker as C3'-endo, C2'-endo, (iv) T4-C5 stack adopts a mini B-DNA both the sugars being C2'-endo and (v) C5-C6 stack exhibits a B-A junction with C2'-endo, C3'-endo sugar puckers. Thus, our studies demonstrate that conformational microheterogeneity with a structural two fold, is present in the Bam H1 recognition site.

Base Composition↗
PubMed1989

Multiple splice forms of ribonuclease-inhibitor mRNA differ in the 5'-untranslated region.

We report the sequence of the cDNAs representing five independent splice forms of human placental RNase inhibitor (RI) mRNA. RI mRNAs differ principally in the 5'-untranslated region, which may include or lack a 68-nucleotide (nt) exon inserted at a splice site located only 20 nt upstream from the initiator AUG. At least three other exons may also abut the same splice site. This unusual and variable feature of the mRNA would suggest that secondary structure in the region of the start codon may differ among RI messages. A single copy of the RI gene exists in the human genome.

Amino Acid Sequence↗
PubMed2006

The mechanism of discrimination between cognate and non-specific DNA by dimeric b/HLH/LZ transcription factors.

The Myc/Max/Mad proteins are basic region-helix-loop-helix-leucine zipper (b/HLH/LZ) transcription factors that regulate the transcription of numerous genes involved in cell growth and proliferation. The Max protein is the obligate heterodimeric partner of the Myc and Mad proteins. Heterodimerization and DNA binding to target gene promoters are mediated by the b/HLH/LZ domains. Max can also form a homodimeric b/HLH/LZ. The enhanced expression of Myc and binding to promoters of target genes contribute to almost every aspect of tumor biology. However, the detailed mechanism by which dimeric and heterodimeric b/HLH/LZs discriminate cognate DNA (E-Box: CACGTG) from non-specific sequences in the target gene promoters is still unknown. Here, we use the Max b/HLH/LZ homodimer as a model for this class of transcription factors in the characterization and understanding of the mechanism of discrimination between the E-Box and non-specific DNA sequences. We report the characterization of a cognate and a non-specific Max b/HLH/LZ/DNA complex by EMSA, CD and NMR. Our results support a detailed mechanism by which dimeric b/HLH/LZ transcription factors can discriminate E-Box sequences from non-specific DNA. The mechanism proceeds via the conformational selection of fitting b/HLH/LZ homodimers with the basic region only partially helical. Next, the basic region undergoes a DNA-assisted folding or induced-fit. It is this step that provides the discrimination by stabilizing and destabilizing the alpha-helical conformation of the basic region in the cognate and non-specific complexes, respectively. This leads to a low affinity complex with a higher probability of being dissociated and hence to discrimination. A description of the side-chains and nucleotides proposed to be involved in the discrimination process is provided.

Amino Acid Sequence↗
PubMed2003

Effect of sequence on the conformation of DNA holliday junctions.

Structures of the DNA sequences d(CCGGCGCCGG) and d(CCAGTACbr(5)UGG) are presented here as four-way Holliday junctions in their compact stacked-X forms, with antiparallel alignment of the DNA strands. Thus, the ACC-trinucleotide motif, previously identified as important for stabilizing the junction, is now extended to PuCPy, where Pu is either an adenine or guanine, and Py is either a cytosine, 5-methylcytosine, or 5-bromouracil but not thymine nucleotide. We see that both sequence and base substituents affect the geometry of the junction in terms of the interduplex angle as well as the previously defined conformational variables, J(roll) (the rotation of the stacked duplexes about their respective helical axis) and J(slide) (the translational displacement of the stacked duplexes along their respective helical axis). The structures of the GCC and parent ACC containing junctions fall into a distinct conformational class that is relatively undistorted in terms of J(slide) and J(roll), with interduplex angles of 40-43 degrees. The substituted ACbr(5)U structure, however, is more akin to that of the distorted methylated ACm(5)C containing junction, with J(slide) (>or=2.3 A) and a similar J(roll) (164 degrees) opening the major groove-side of the junction, but shows a reduced interduplex angle. In contrast, the analogous d(CCAGTACTGG) sequence has to date been crystallized only as resolved B-DNA duplexes. This suggests that there is an electronic effect of substituents at the pyrimidine Py position on the stability of four-stranded junctions. The single-crystal structures presented here, therefore, show how sequence affects the detailed geometry, and subsequently, the associated stability and conformational dynamics of the Holliday junction.

Base Composition↗
PubMed1997

Deglycosylation susceptibility and base-pairing stability of 2'-deoxyoxanosine in oligodeoxynucleotide.

We have demonstrated recently that nitrous acid or nitric oxide converts 2'-deoxyguanosine (dGuo) into 2'-deoxyoxanosine (dOxo) [Suzuki, T., Yamaoka, R., Nishi, M., Ide, H., & Makino, K. (1996) J. Am. Chem. Soc. 118, 2515-2516]. In the present study, we have measured susceptibility of the N-glycosidic bond of dOxo to spontaneous hydrolysis and its base-pairing stability to evaluate the biological significance of dOxo as a new lesion in DNA. When oligodeoxynucleotide d(T5OT6) (O = dOxo), isolated from nitrous acid-treated d(T5GT6), was incubated at pH 4.0 and 70 degrees C, hydrolysis of the N-glycosidic bond of dOxo occurred with a first-order rate constant. Comparison of the rate constants with those of dGuo and dXao indicates that the N-glycosidic bond of dOxo was as stable as that of dGuo in d(T5GT6) and hydrolyzed 44-fold more slowly than that of 2'-deoxyxanthosine (dXao), a simultaneously generated damage by nitrous acid and nitric oxide. For the estimation of the base-pairing stability, UV melting curves were measured for the duplexes of d(T5OT6).d(A6NA5) (N = A, G, C, and T) at neutral pH. The Tm values obtained were 15.3, 14.1, 19.3, and 16. 3 degrees C for N = A, G, C, and T, respectively, which are much lower than that of the intact duplex containing a G.C pair at the same position [d(T5GT6).d(A6CA5), Tm = 32.8 degrees C] but comparable with those of d(T5XT6).d(A6NA5) (X = dXao, Tm = 14.8-22.3 degrees C). CD spectra of the four duplexes containing dOxo showed preservation of the structure of the intact duplex at low temperature. UV and NMR pH-titration studies indicated the pKa for the ring-opening and -closing equilibrium to be 9.4, implying that dOxo is in the ring-closed form at physiological pH. This structure appears to be not suitable geometrically for the hydrogen bond formation with a specific counter base, thus causing equally low Tm values for all the counter bases. Consequently, these results imply that dOxo, a novel DNA lesion, may have an important and unique role in mutagenic events in cells.

Acid-Base Equilibrium↗
PubMed1998

Sequence determinants of the intrinsic bend in the cyclic AMP response element.

The cyclic AMP response element (CRE site, ATGACGTCAT) is the DNA target for transcription factors whose activities are regulated by cyclic AMP (1). Recently, we discovered that the CRE site is bent by 10-13 degrees toward the major groove (2). Little or no bend is detected in the related AP-1 site (ATGACTCAT), which differs from the CRE site by loss of a single, central, C.G base pair (2, 3). Here we describe experiments designed to identify which base pairs within the CRE site induce the bent structure in an attempt to understand the origins of the dramatically different conformations of the CRE and AP-1 sites. Our data indicate that the intrinsic CRE bend results from distortion within the TGA sequence found in each CRE half site (ATGAC). These two TGA sequences are located in phase with one another in the CRE sequence but are not (completely) in phase in the AP-1 sequence. This difference in phasing leads to the overall difference in bend as detected by gel (2) and cyclization methods (S. C. Hockings, J. D. Kahn, and D. M. Crothers, unpublished results; M. A. Fabian and A. Schepartz, unpublished results). Our results confirm earlier predictions of altered structure within TG steps, provide insight into the structural reorganizations induced in DNA by bZIP proteins, and lead to a revision of the relationship between the structures of the free and bZIP-bound forms of the CRE and AP-1 sites.

Base Composition↗
PubMed2002

Plasmacytoid dendritic cells: a new cutaneous dendritic cell subset with distinct role in inflammatory skin diseases.

Epidermal dendritic cells found in inflamed skin include Langerhans cells and the recently identified population of inflammatory dendritic epidermal cells. Another subset of dendritic cells in humans is the plasmacytoid dendritic cell in peripheral blood, which is characterized by the production of large amounts of type I interferon (interferon-alpha and interferon-beta) upon viral infection. We hypothesized that plasmacytoid dendritic cells might be involved in anti-viral defense mechanisms of the skin. Here we investigated plasmacytoid dendritic cells, inflammatory dendritic epidermal cells, and Langerhans cells in epidermal single cell suspensions of normal looking skin from healthy volunteers and of lesional skin from patients with different inflammatory skin diseases. Langerhans cells were found in normal and in inflamed skin samples. In normal skin, plasmacytoid dendritic cells and inflammatory dendritic epidermal cells were low or absent. Lesional skin samples from patients with psoriasis vulgaris and contact dermatitis contained relatively high numbers of both inflammatory dendritic epidermal cells and plasmacytoid dendritic cells. In contrast, many inflammatory dendritic epidermal cells but only very few plasmacytoid dendritic cells could be detected in atopic dermatitis lesions. Lupus erythematosus was characterized by high numbers of plasmacytoid dendritic cells but low numbers of inflammatory dendritic epidermal cells. These results demonstrate that in addition to resident Langerhans cells, plasmacytoid dendritic cells and inflammatory dendritic epidermal cells are selectively recruited to the skin lesions depending on the type of skin disease. The lack of plasmacytoid dendritic cells in atopic dermatitis may predispose atopic dermatitis patients to viral infections such as eczema herpeticum, a secondary infection of atopic dermatitis lesions with herpes simplex virus. The composition of dendritic cell subsets may help to clarify the etiology of inflammatory skin diseases and forms the basis for therapeutic intervention with selective microbial molecules such as immunostimulatory CpG oligonucleotides.

Cell Lineage↗
PubMed1990

Single d(ApG)/cis-diamminedichloroplatinum(II) adduct-induced mutagenesis in Escherichia coli.

The mutation spectrum induced by the widely used antitumor drug cis-diamminedichloroplatinum(II) (cis-DDP) showed that cisDDP[d(ApG)] adducts, although they account for only 25% of the lesions formed, are approximately 5 times more mutagenic than the major GG adduct. We report the construction of vectors bearing a single cisDDP[d(ApG)] lesion and their use in mutagenesis experiments in Escherichia coli. The mutagenic processing of the lesion is found to depend strictly on induction of the SOS system of the bacterial host cells. In SOS-induced cells, mutation frequencies of 1-2% were detected. All these mutations are targeted to the 5' base of the adduct. Single A----T transversions are mainly observed (80%), whereas A----G transitions account for 10% of the total mutations. Tandem base-pair substitutions involving the adenine residue and the thymine residue immediately 5' to the adduct occur at a comparable frequency (10%). No selective loss of the strand bearing the platinum adduct was seen, suggesting that, in vivo, cisDDP[d(ApG)] adducts are not blocking lesions. The high mutation specificity of cisDDP[d(ApG)]-induced mutagenesis is discussed in relation to structural data.

Base Composition↗
PubMed2002

Long telomeric C-rich 5'-tails in human replicating cells.

Telomeres protect the ends of linear chromosomes from abnormal recombination events and buffer them against terminal DNA loss. Models of telomere replication predict that two daughter molecules have one end that is blunt, the product of leading-strand synthesis, and one end with a short G-rich 3'-overhang. However, experimental data from proliferating cells are not completely consistent with this model. For example, telomeres of human chromosomes have long G-rich 3'-overhangs, and the persistence of blunt ends is uncertain. Here we show that the product of leading-strand synthesis is not always blunt but can contain a long C-rich 5'-tail, the incompletely replicated template of the leading strand. We examined the presence of G-rich and C-rich single-strand DNA in fibroblasts and HeLa cells. Although there were no significant changes in the length distribution of the 3'-overhang, the 5'-overhangs were mostly present in S phase. Similar results were obtained using telomerase-negative fibroblasts. The amount and the length distribution of the 5' C-rich tails strongly correlate with the proliferative rate of the cell cultures. Our results suggest that, contrary to what has commonly been supposed, completion of leading-strand synthesis is inefficient and could well drive telomere shortening.

Base Composition↗