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At least 199 records · Page 11Linked to original sources
PubMed1999

Variant effects of non-native kissing-loop hairpin palindromes on HIV replication and HIV RNA dimerization: role of stem-loop B in HIV replication and HIV RNA dimerization.

The genome of all retroviruses consists of two identical RNAs noncovalently linked near their 5' end. In vitro synthesized RNAs from human immunodeficiency virus type 1 (HIV-1) can form loose or tight dimers depending on whether their respective kissing-loop hairpins (nts 248-270 in HIV-1Lai) bond via their hexameric autocomplementary sequences (ACS), also called palindromes, or via the ACS and stem sequences [Laughrea, M., and Jetté, L. (1996) Biochemistry 35, 1589-1598]. To understand the role of the ACS in HIV-1 replication and in the formation and stability of HIV-1 RNA dimers, we replaced the central CGCG261(or tetramer) of the HIV-1Lai ACS by two other HIV-1 tetramers (UGCA/UGCG), four non-HIV-1 tetramers [GUAC, UUAA (respectively found in HIV-2Rod and SIVmnd), GGCC and AGCU (absent from HIV and SIV viruses)], or GGCG, a nonpalindromic tetramer. The infectivity of GGCC, GUAC, and UGCA viruses was unchanged or insignificantly decreased; the infectivity of AGCU and UGCG viruses was decreased by 80%; the infectivity of UUAA and GGCG viruses was decreased by 92-98%. Thus, the four non-HIV-1 palindromes yielded phenotypes ranging from wild-type to as defective as a virus bearing a nonpalindrome. Studies of in vitro synthesized HIV-1 RNAs were generally consistent with in vivo results, specifically: (i) loose dimerization of GGCC and GUAC RNAs, but not of UUAA and AGCU RNAs, was influenced by the 3' DLS (a sequence located downstream of the 5' splice junction) in a way expected for a wild-type ACS; (ii) the 3' DLS strongly reduced tight dimerization of UUAA and AGCU RNAs, but not of GGCC and GUAC RNAs. We conclude that HIV-1 is sensitive to the ACS sequence without discriminating against all nonnative ACS: GGCC/GUAC, but not AGCU/UUAA, are good substitutes for the prevalent CGCG/UGCA native tetramers and better substitutes than the very rare UGCG native tetramer. The correlation between in vivo and in vitro results suggests that in vitro assays measure parameters of in vivo relevance. Deletion of CUCGG247 (the 5' strand of stem-loop B) decreased the replicative capacity by more than 99.9% and metamorphosed the 3' DLS into an inhibitor of the loose dimerization of HIV-1 RNA.

Base Composition↗
PubMed2001

Loop diuretics alter the diurnal rhythm of endogenous parathyroid hormone secretion. A randomized-controlled study on the effects of loop- and thiazide-diuretics on the diurnal rhythms of calcitropic hormones and biochemical bone markers in postmenopausal women.

BACKGROUND: Thiazide diuretics (TD) reduce urinary calcium, bone loss and fracture risk. Loop diuretics (LD) may have opposite effects. These effects could depend on induced rhythmic changes in bone and calcium homeostasis. DESIGN: After a run-in period of 7 days, we studied (in a factorial design) the diurnal rhythms of plasma levels of calcium, phosphate, parathyroid hormone (PTH), 1,25-dihydroxyvitamin D and osteocalcin, as well as renal excretions rates of calcium, phosphate, and cross-linked N-terminal telopeptide of type 1 collagen (NTx) in 50 postmenopausal women randomized to treatment with either a thiazide diuretic (TD; bendroflumethiazide, n = 14), a loop diuretic (LD; bumetanide, n = 13), LD plus TD (bendroflumethiazide plus bumetanide, n = 11), or placebo (n = 12). RESULTS: In all four groups, all measured quantities showed a diurnal variation. LD caused a steep increase, with a subsequent decrease, in urinary calcium and plasma PTH. The mean 24 h plasma PTH concentration was increased (8.5 +/- 0.9 mmol L-1) compared with placebo (4.4 +/- 0.4 mmol L-1), whereas net 24 h renal calcium excretion did not differ from that of the placebo group due to a rebound hypocalciuria. Compared with placebo, diurnal rhythms of plasma phosphate and osteocalcin were changed with an increase during daytime and a decrease during the night. TD did not alter the diurnal rhythm of any of the measured quantities. However, the 24-h renal calcium excretion decreased, whereas the mean 24-h plasma calcium concentration increased without PTH suppression. LD plus TD caused changes similar to those observed with LD alone. CONCLUSION: One daily dose of LD increases parathyroid activity with alterations in the diurnal pattern of osteocalcin. This could indicate a potential anabolic effect of LD.

Aged↗
PubMed2002

"Extracorporeal loop" (blind loop): an alternative microsurgical technique for prelaminated flap transfer.

Free tissue transfer is frequently used for reconstruction in the head and neck region. In patients who suffer tissue loss due to a high-energy trauma, the reconstructive surgeon is often faced with a large gap between the defect and the site of anastomosis outside the zone of injury. Utilization of long vein grafts for reestablishment of blood flow to the transferred tissue vessels is a common procedure. Arteriovenous fistula (AVF) formation on the side table is an alternative solution. In this paper, an "extracorporeal loop" (blind loop) technique is presented as an alternative microsurgical method for prelaminated flap transfer to two different traumatic recipient areas in the face (nose and ear).

Adolescent↗
PubMed1999

Role of the first extracellular loop in the functional activation of CCR2. The first extracellular loop contains distinct domains necessary for both agonist binding and transmembrane signaling.

The physiological cellular responses to monocyte chemoattractant protein-1 (MCP-1), a potent chemotactic and activating factor for mononuclear leukocytes, are mediated by specific binding to CCR2. The aim of this investigation is to identify receptor microdomains that are involved in high affinity agonist binding and receptor activation. The results from our functional studies in which we utilized neutralizing antisera against CCR2 are consistent with a multidomain binding model, previously proposed by others. The first extracellular loop was of particular interest, because in addition to a ligand-binding domain it contained also information for receptor activation, crucial for transmembrane signaling. Replacement of the first extracellular loop of CCR2 with the corresponding region of CCR1 decreased the MCP-1 binding affinity about 10-fold and prevented transmembrane signaling. A more detailed analysis by site-directed mutagenesis revealed that this receptor segment contains two distinct microdomains. The amino acid residues Asn(104) and Glu(105) are essential for high affinity agonist binding but are not involved in receptor activation. In contrast, the charged amino acid residue His(100) does not contribute to ligand binding but is vital for receptor activation and initiation of transmembrane signaling. We hypothesize that the interaction of agonist with this residue initiates the conformational switch that allows the formation of the functional CCR2-G protein complex.

Amino Acid Sequence↗
PubMed1993

The reactivities of HIV-1+ human sera with solid-phase V3 loop peptides can be poor predictors of their reactivities with V3 loops on native gp120 molecules.

The binding of HIV-1+ human serum antibodies to solid phase-adsorbed V3 loop peptides from the IIIB, SF-2, and MN isolates was compared with the abilities of the same peptides to inhibit binding of the sera to the homologous or heterologous native gp120 molecules. The reactivities of the sera with the solid-phase peptides were found to be poor predictors of the potencies of the peptides as competitors in solution for antibody binding to the V3 loop in situ. Furthermore, the extent of cross-reaction of HIV-1+ human serum antibodies with the three V3 peptides in solid-phase assays was potently influenced by the presence or absence of nonionic detergent. Because the use of solid-phase V3 peptide assays is widespread, and there is no consensus on the use or omission of detergent, there is considerable potential for confusion. These factors should be considered when interpreting data derived from V3 peptide serology when this method is used to dissect the human immune response to HIV-1 infection. It is also shown in quantitative studies of HIV-1+ serum antibody binding to homologous and heterologous gp120s that the general anti-gp120 antibody response is significantly "type specific" for the homologous gp120.

Amino Acid Sequence↗
PubMed2004

Double displacement loops (double d-loops) are templates for oligonucleotide-directed mutagenesis and gene repair.

Appreciable levels of gene repair result from the hybridization of two oligonucleotides at a specific site in a mutated gene and subsequent correction by a form of oligonucleotide-directed mutagenesis known as gene repair. The incorporation of the two oligonucleotides into superhelical plasmid DNA leads to the formation of double d-loops, structures shown to be templates for the repair of both frameshift and point mutations. Structural limitations placed on the template indicate that correction is influenced significantly by the positioning of the second oligonucleotide, known as the annealing oligonucleotide. Complexes constructed with two oligonucleotides directly opposite each other exhibit the highest levels of gene repair activity. Blocking the 3'-end of either oligonucleotide with an amino C7 group does not diminish the performance of the double d-loop as a template for correction of the point mutation, suggesting that primer extension does not play a pivotal role in the mechanism of gene repair.

DNA Repair↗
PubMed1976

Visual "closed-loop" and "open-loop" characteristics of voluntary movement in patients with Parkinsonism and intention tremor.

Normal voluntary movements are considered to be of two kinds, or to involve two components, (i) a ballistic or "open-loop" type, which are preprogrammed and executed without reference to current sensory information and (ii) a corrective or "closed-loop" type, whose course or termination are regulated by such information. In a previous paper it was suggested that Parkinsonism disrupted the first kind of movement, but intention tremor did not. In the present paper three experiments designed to test this hypothesis are described. Subjects were tested on an acquisition-tracking task using an oscilloscope display and joystick control, and measurements were made of the duration, velocity and error of their initial movements to acquire the target. Parkinsonian movements were found to be considerably different from normal in that (a) most movements by this group lasted longer than the reaction time for their initiation, as if including some secondary correction in their execution, (b) the rate of movement was not varied for different amplitudes (so keeping the duration fairly constant) as in normal subjects, but rather movements of all amplitudes were made at a constant slow rate, so that duration increased markedly with the larger steps, (c) error increased disproportionately as the velocity of movement increased; in particular any movements completed in one reaction time or less tended to be wildly inaccurate, (d) removing either the target or the response marker from the screen at the beginning of a movement had a significant effect, making it shorter in duration and smaller in amplitude than those usually produced with both markers visible all the time. Parkinsonian subjects showed no improvement in performance with repeated attempts at one movement over a whole sequence, so their deficit appears to be stable even after practice on a known fixed task. These results are interpreted as supporting the hypothesis that Parkinsonism interferes with the generation of accurate ballistic action which are characteristic of normal skilled movement. Tremor subjects in general resembled normal control subjects in their initial acquistion movements, but their accuracy was less with the larger steps.

Adult↗
PubMed2000

Progression of a loop-loop complex to a four-way junction is crucial for the activity of a regulatory antisense RNA.

The antisense RNA, CopA, regulates the replication frequency of plasmid R1 through inhibition of RepA translation by rapid and specific binding to its target RNA (CopT). The stable CopA-CopT complex is characterized by a four-way junction structure and a side-by-side alignment of two long intramolecular helices. The significance of this structure for binding in vitro and control in vivo was tested by mutations in both CopA and CopT. High rates of stable complex formation in vitro and efficient inhibition in vivo required initial loop-loop complexes to be rapidly converted to extended interactions. These interactions involve asymmetric helix progression and melting of the upper stems of both RNAs to promote the formation of two intermolecular helices. Data presented here delineate the boundaries of these helices and emphasize the need for unimpeded helix propagation. This process is directional, i.e. one of the two intermolecular helices (B) must form first to allow formation of the other (B'). A binding pathway, characterized by a hierarchy of intermediates leading to an irreversible and inhibitory RNA-RNA complex, is proposed.

Bacterial Proteins↗
PubMed2002

Structural variation and functional importance of a D-loop-T-loop interaction in valine-accepting tRNA-like structures of plant viral RNAs.

Valine-accepting tRNA-like structures (TLSs) are found at the 3' ends of the genomic RNAs of most plant viruses belonging to the genera Tymovirus, Furovirus, Pomovirus and Pecluvirus, and of one Tobamovirus species. Sequence alignment of these TLSs suggests the existence of a tertiary D-loop-T-loop interaction consisting of 2 bp, analogous to those in the elbow region of canonical tRNAs. The conserved G(18).Psi(55) pair of regular tRNAs is found to covary in these TLSs between G.U (possibly also modified to G.Psi) and A.G. We have mutated the relevant bases in turnip yellow mosaic virus (TYMV) and examined the mutants for symptom development on Chinese cabbage plants and for accumulation of genetic reversions. Development of symptoms is shown to rely on the presence of either A.G or G.U in the original mutants or in revertants. This finding supports the existence and functional importance of this tertiary interaction. The fact that only G.U and A.G are accepted at this position appears to result from steric and energetic limitations related to the highly compact nature of the elbow region. We discuss the implications of these findings for the various possible functions of the valine-accepting TLS.

Base Sequence↗
PubMed2003

DNA tri- and tetra-loops and RNA tetra-loops hairpins fold as elastic biopolymer chains in agreement with PDB coordinates.

The biopolymer chain elasticity (BCE) approach and the new molecular modelling methodology presented previously are used to predict the tri- dimensional backbones of DNA and RNA hairpin loops. The structures of eight remarkably stable DNA or RNA hairpin molecules closed by a mispair, recently determined in solution by NMR and deposited in the PDB, are shown to verify the predicted trajectories by an analysis automated for large numbers of PDB conformations. They encompass: one DNA tetraloop, -GTTA-; three DNA triloops, -AAA- or -GCA-; and four RNA tetraloops, -UUCG-. Folding generates no distortions and bond lengths and bond angles of main atoms of the sugar-phosphate backbone are well restored upon energy refinement. Three different methods (superpositions, distance of main chain atoms to the elastic line and RMSd) are used to show a very good agreement between the trajectories of sugar-phosphate backbones and between entire molecules of theoretical models and of PDB conformations. The geometry of end conditions imposed by the stem is sufficient to dictate the different characteristic DNA or RNA folding shapes. The reduced angular space, consisting of the new parameter, angle Omega, together with the chi angle offers a simple, coherent and quantitative description of hairpin loops.

Base Pair Mismatch↗
PubMed2006

A new NMR solution structure of the SL1 HIV-1Lai loop-loop dimer.

Dimerization of genomic RNA is directly related with the event of encapsidation and maturation of the virion. The initiating sequence of the dimerization is a short autocomplementary region in the hairpin loop SL1. We describe here a new solution structure of the RNA dimerization initiation site (DIS) of HIV-1(Lai). NMR pulsed field-gradient spin-echo techniques and multidimensional heteronuclear NMR spectroscopy indicate that this structure is formed by two hairpins linked by six Watson-Crick GC base pairs. Hinges between the stems and the loops are stabilized by intra and intermolecular interactions involving the A8, A9 and A16 adenines. The coaxial alignment of the three A-type helices present in the structure is supported by previous crystallography analysis but the A8 and A9 adenines are found in a bulged in position. These data suggest the existence of an equilibrium between bulged in and bulged out conformations in solution.

Base Sequence↗
PubMed2002

RNA LEGO: magnesium-dependent assembly of RNA building blocks through loop-loop interactions.

We describe the construction of nano-molecular assemblies using RNA building blocks the human immunodeficiency virus type 1 (HIV-1) dimerization initiation site (DIS) RNA, that forms stable base pairing through a magnesium-dependent loop-loop interaction ("kissing"). RNA building blocks containing two DIS or DIS-like hairpins connected by a two nucleotide linker self-assembled to form specific structures as observed by non-denaturing polyacrylamide gel electrophoresis (PAGE). Furthermore, observation of "real time" formation of the molecular assemblies by circular dichroism (CD) spectroscopy was attempted.

Base Sequence↗
PubMed2004

Formation of dendrimeric RNA assemblies though RNA loop-loop interactions.

We describe the construction of nano-scale dendritic assemblies using RNA building blocks based on dimerization initiation site (DIS) RNA of the human immunodeficiency virus type 1 (HIV-1) that forms stable base pairing through loop-loop ("kissing") interactions. RNA building blocks containing three DIS-like hairpins connected by a two nucleotide linker self-assembled in a magnesium-dependent manner to form dendrimeric structures as observed by non-denaturing polyacrylamide gel electrophoresis (PAGE).

Base Sequence↗
PubMed2005

DNA looping-mediated repression by histone-like protein H-NS: specific requirement of Esigma70 as a cofactor for looping.

Transcription initiation by RNA polymerase (RNP) carrying the house-keeping sigma subunit, sigma70 (Esigma70), is repressed by H-NS at a number of promoters including hdeABp in Escherichia coli, while initiation with RNP carrying the stationary phase sigma, sigma38 (Esigma38), is not. We investigated the molecular mechanism of selective repression by H-NS to identify the differences in transcription initiation by the two forms of RNPs, which show indistinguishable promoter selectivities in vitro. Using hdeABp as a model promoter, we observed with purified components that H-NS, acting at a sequence centered at -118, selectively repressed transcription by Esigma70. This selective repression is attributed to the differences in the interactions between hdeABp and the two forms of RNPs, since no other factor is required for the repression. We observed that the two forms of RNPs could form an open initiation complex (RP(O)) at hdeABp, but that Esigma70 failed to initiate transcription in the presence of H-NS. Interestingly, KMnO4 assays and high-resolution atomic force microscopy (AFM) revealed that hdeABp DNA wrapped around Esigma70 more tightly than around Esigma38, resulting in the potential crossing over of the DNA arms that project out of Esigma70 . RP(O) but not out of Esigma38 . RP(O). Based on these observations, we postulated that H-NS bound at -118 laterally extends by the cooperative recruitment of H-NS molecules to the promoter-downstream sequence joined by wrapping of the DNA around Esigma70 . RP(O), resulting in effective sealing of the DNA loop and trapping of Esigma70. Such a ternary complex of H-NS . Esigma70 hdeABp was demonstrated by AFM. In this case, therefore, Esigma70 acts as a cofactor for DNA looping. Expression of this class of genes by Esigma38 in the stationary phase is not due to its promoter specificity but to the architecture of the promoter . Esigma38 complex.

Bacterial Proteins↗
PubMed2001

Leading logarithmic contribution to the second-order lamb shift induced by the loop-after-loop diagram.

The contribution of order alpha(2)(Zalpha)(6)ln (3)(Zalpha)(-2) to the ground-state Lamb shift in hydrogen induced by the loop-after-loop diagram is evaluated analytically. An additional contribution of this order is found compared to the previous calculation by Karshenboim [Sov. Phys. JETP 76, 541 (1993)]. As a result, agreement is achieved for this correction between different numerical and analytical methods.

Journal Article↗
PubMed2006

Analysis of antibody response in humans to the type A OspC loop 5 domain and assessment of the potential utility of the loop 5 epitope in Lyme disease vaccine development.

The OspC protein of Borrelia burgdorferi is an immunodominant antigen. Here we demonstrate that the loop 5 domain of type A OspC is surface exposed, elicits bactericidal antibody in mice, and is antigenic in humans. The data suggest that loop 5 may be suitable for inclusion in a polyvalent, chimeric OspC vaccinogen.

Amino Acid Sequence↗
PubMed1998

Replacement of loop II of VP1 of the DA strain with loop II of the GDVII strain of Theiler's murine encephalomyelitis virus alters neurovirulence, viral persistence, and demyelination.

Theiler's murine encephalomyelitis viruses, which are murine picornaviruses, can cause central nervous system inflammatory disease. To study the role of loop II in capsid protein VP1, two mutant viruses of strain DA in which DA loop II amino acids were replaced with strain GDVII amino acids were constructed. Infection of mice with the two mutant viruses led to dramatically different patterns of disease.

Animals↗
PubMed2001

The nuclear matrix and chromosomal DNA loops: is their any correlation between partitioning of the genome into loops and functional domains?

In this paper we are presenting a critical analysis of the results of experiments aimed to elucidate the principles of the eukaryotic genome structural-functional organization. Although the DNA loops attached to the nuclear matrix (chromosomal scaffold) are frequently considered as independent functional domains, this supposition lack experimental proofs as far as the transcriptional domains are concerned. On the contrary, many observations indicate that organization of chromosomal DNA into loops is directly related to the replicon structure of the genome.

Animals↗