scholarly journals Characterization of genomic poly(dT-dG).poly(dC-dA) sequences: structure, organization, and conformation.

1984 ◽  
Vol 4 (12) ◽  
pp. 2610-2621 ◽  
Author(s):  
H Hamada ◽  
M G Petrino ◽  
T Kakunaga ◽  
M Seidman ◽  
B D Stollar
Keyword(s):  
Ionic Strength ◽  
Inverted Repeats ◽  
Actin Gene ◽  
Base Pairs ◽  
S1 Nuclease ◽  
Coding Sequences ◽  
Supercoiled Plasmid ◽  
Marked Preference ◽  
Low Ionic Strength

Hybridization studies suggest the abundant presence of poly(dT-dG).poly(dC-dA) (TG-element), a potential Z-DNA sequence, in eucaryotic genomes. We have isolated and characterized TG-elements from different locations in the human genome: from randomly isolated clones, associated with the actin gene family, and linked to another repeated element. The results indicate that the following features are typical of these TG-elements: the elements consist of 20 to 60 base pairs of (dT-dG)n.(dC-dA)n, the sequences characterized in our study were not flanked by direct or inverted repeats, the sequences are interspersed rather than in satellite blocks, the elements are not usually associated with other repeated elements, and some of the elements are found near coding sequences or in introns. Studies on the conformation of a genomic TG-element in a supercoiled plasmid indicate several distinct properties of the TG-element: it is in the Z-form only at low ionic strength, S1 nuclease recognizes its Z-form with a marked preference for one of the B-Z junctions, and the sensitive region extends for 20 base pairs near the B-Z junction. In contrast to the result with the supercoiled plasmid, S1 nuclease failed to recognize the TG-element in minichromosomes.

Characterization of genomic poly(dT-dG).poly(dC-dA) sequences: structure, organization, and conformation

1984 ◽  
Vol 4 (12) ◽  
pp. 2610-2621
Author(s):  
H Hamada ◽  
M G Petrino ◽  
T Kakunaga ◽  
M Seidman ◽  
B D Stollar
Keyword(s):  
Ionic Strength ◽  
Inverted Repeats ◽  
Actin Gene ◽  
Base Pairs ◽  
S1 Nuclease ◽  
Coding Sequences ◽  
Supercoiled Plasmid ◽  
Marked Preference ◽  
Low Ionic Strength

Hybridization studies suggest the abundant presence of poly(dT-dG).poly(dC-dA) (TG-element), a potential Z-DNA sequence, in eucaryotic genomes. We have isolated and characterized TG-elements from different locations in the human genome: from randomly isolated clones, associated with the actin gene family, and linked to another repeated element. The results indicate that the following features are typical of these TG-elements: the elements consist of 20 to 60 base pairs of (dT-dG)n.(dC-dA)n, the sequences characterized in our study were not flanked by direct or inverted repeats, the sequences are interspersed rather than in satellite blocks, the elements are not usually associated with other repeated elements, and some of the elements are found near coding sequences or in introns. Studies on the conformation of a genomic TG-element in a supercoiled plasmid indicate several distinct properties of the TG-element: it is in the Z-form only at low ionic strength, S1 nuclease recognizes its Z-form with a marked preference for one of the B-Z junctions, and the sensitive region extends for 20 base pairs near the B-Z junction. In contrast to the result with the supercoiled plasmid, S1 nuclease failed to recognize the TG-element in minichromosomes.

scholarly journals Sheep elastin genes. Isolation and preliminary characterization of a 9.9-kilobase genomic clone

1984 ◽  
Vol 220 (3) ◽  
pp. 643-652 ◽  
Author(s):  
J M Davidson ◽  
S Shibahara ◽  
M P Schafer ◽  
M Harrison ◽  
C Leach ◽  
...  
Keyword(s):  
Genomic Dna ◽  
Southern Blotting ◽  
Genomic Library ◽  
Base Pairs ◽  
Coding Sequences ◽  
Restriction Fragments ◽  
Sequence Elements ◽  
The Right ◽  
Elastin Gene

A sheep genomic library containing sheep DNA in the bacteriophage vector Charon 4A was screened for elastin-gene sequences with partially purified, 32P-labelled elastin mRNA (mRNAE). A recombinant containing a 9.9-kb (kilobase) insert was selected from several positive clones by secondary and tertiary screening for further characterization. Positive identification of this elastin clone, designated SE1, was made with radiolabelled mRNAE by hydridization-selected translation and Southern blotting of restriction-enzyme fragments of SE1 DNA. Hybridization of either mRNAE or elastin complementary DNA to restriction fragments of SE1 showed that most of these fragments of SE1 contained elastin-coding sequences. Orientation of the insert was established by preferential hybridization of a short complementary elastin DNA to restriction fragments adjacent to the right arm of Charon 4A. Reciprocal hybridizations of nick-translated SE1 and sheep genomic DNA on Southern blots showed that two restriction fragments of SE1 contained sequence elements which were repeated at high frequency in a restriction-endonuclease-EcoR1 digest of total sheep genomic DNA. In the accompanying paper [Davidson, Shibahara, Boyd, Mason, Tolstoshev & Crystal (1984) Biochem. J. 220, 653-663], it is shown that a subcloned fragment of this elastin gene quantitatively and specifically hybridized to mRNAE sequences in sheep tissue RNA. Electron microscopy of SE1-mRNAE hybrids indicated the presence of at least seven large R-loops. Measurements of these structures indicated that SE1 is likely to contain less than 2 kb of coding sequence and more than 8 kb of intervening sequence, with an average exon size of 120 base-pairs. Thus the elastin gene is distributed over an extended region of the sheep genome and contains numerous intervening and coding sequences.

scholarly journals The binding of echinomycin to deoxyribonucleic acid

1976 ◽  
Vol 157 (3) ◽  
pp. 721-740 ◽  
Author(s):  
L P G Wakelin ◽  
M J Waring
Keyword(s):  
Ionic Strength ◽  
Binding Constant ◽  
Buoyant Density ◽  
Specific Interaction ◽  
Effect Of Temperature ◽  
Heat Denaturation ◽  
Peptide Antibiotic ◽  
Base Pairs ◽  
Calf Thymus ◽  
Low Ionic Strength

Echinomycin is a peptide antibiotic which binds strongly to double-helical DNA up to a limit of approximately one molecule per five base-pairs. There is no detectable interaction with rRNA and only extremely feeble non-specific interaction with poly(rA)-poly(rU). Heat denaturation of DNA greatly decreases the binding, and similarly limited interaction is observed with naturally occurring single-stranded DNA. Association constants for binding to nine double-helical DNA species from different sources are presented; they vary by a factor of approximately 10, but are not simply related to the gross base composition. The interaction with DNA is ionic-strength-dependent, the binding constant falling by a factor of 4 when the ionic strength is raised from 0.01 to 0.10mol/litre. From the effect of temperature on the association constant for calf thymus DNA, the enthalpy of interaction is calculated to be about -13kJ/mol (-3kcal/mol). Binding of echinomycin persists in CsCl gradients and the buoyant density of nicked bacteriophage PM2 DNA is decreased by 25 mg/ml. Echinomycin interacts strongly with certain synthetic poly-deoxynucleotides, the binding constant decreasing in the order poly(dG)-poly(dC) greater than poly(dG-dC) greater than poly(dA-dT). For the latter two polymers the number of base-pairs occluded per bound antibiotic molecule is calculated to be three, whereas for poly(dG)-poly(dC) it is estimated to be four to five. Poly(dA)-poly(dT) and poly(dI)-poly(dC) interact only very weakly with the antibiotic. Poly(dI-dC) interacts to a slightly greater extent, but the binding curve is quite unlike that seen with the three strongly binding synthetic polynucleotides. Echinomycin affects the supercoiling of closed circular duplex bacteriophage PM2 DNA in the characteristic fashion of intercalating drugs. At low ionic strength the unwinding angle is almost twice that of ethidium. Likewise the extension of the helix, determined from changes in the viscosity of rod-like sonicated DNA fragments, is nearly double that expected for a simple (monofunctional) intercalation process. On this basis the interaction process is characterized as bifunctional intercalation. At higher ionic strength the unwinding angle relative to that of ethidium and the helix extension per bound echinomycin molecule fall, indicating a smooth progression towards more nearly monofunctional intercalation. Two simpler compounds which act as analogues of the quinoxaline chromophores of echinomycin, quinoxaline-2-carboxamide and the trypanocidal drug Bayer 7602, interact with DNA very much more weakly than does echinomycin, showing that the peptide portion of the antibiotic plays an essential role in determining the strength and specificity of the interaction.

Characterization of modified myosin at low ionic strength. Enzymic and spin-label studies

Biochemistry ◽  
1973 ◽  
Vol 12 (21) ◽  
pp. 4206-4211 ◽  
Author(s):  
Deborah Bennett Stone ◽  
Shirley C. Prevost
Keyword(s):  
Ionic Strength ◽  
Spin Label ◽  
Low Ionic Strength

scholarly journals Electrophorus acetylcholinesterase. Biochemical and electron microscope characterization of low ionic strength aggregates

1978 ◽  
Vol 77 (2) ◽  
pp. 315-322 ◽  
Author(s):  
J Cartaud ◽  
S Bon ◽  
J Massoulié
Keyword(s):  
Ionic Strength ◽  
High Resolution Electron Microscopy ◽  
Hydrodynamic Characteristics ◽  
Sedimentation Analysis ◽  
The Core ◽  
Resolution Electron ◽  
Electric Eel ◽  
Oxygen Oxidation ◽  
Low Ionic Strength

The "tailed" molecules of Electrophorus (electric eel) acetylcholinesterase aggregate under conditions of low ionic strength. These aggregates have been studied by sedimentation analysis and high-resolution electron microscopy. They consist of bundles of at least half a dozen molecules, the tails of which are packed side by side, to form the core of the structure. Although aggregation is normally fully reversible, aggregates were irreversibly stabilized by methylene blue-sensitized photo-oxidation. This process was shown to consist of a singlet oxygen oxidation reaction and probably involves methionine or histidine residues. It did not modify the structural or hydrodynamic characteristics of the aggregates.

Selection and characterization of DNAzymes with synthetically appended functionalities: A case of a synthetic RNAsea mimic

2004 ◽  
Vol 76 (7-8) ◽  
pp. 1571-1577 ◽  
Author(s):  
R. Ting ◽  
Leonard Lermer ◽  
J. Thomas ◽  
Y. Roupioz ◽  
D. M. Perrin
Keyword(s):  
Ionic Strength ◽  
Nucleic Acids ◽  
Rate Constants ◽  
Complex Chemical ◽  
Low Ionic Strength ◽  
Low Rate ◽  
Selection Of

We have been interested in merging synthetic nucleotide chemistry with combinatorial selection of DNAzymes to deliver a more complete (and complex) chemical complement to the catalytic repertoire of nucleic acids. Thus we ask, what do modified dNTPs really bring to nucleic acids in terms of an increased repertoire? In asking this question, we have looked first at conditions, and more recently for reaction classes where nucleic acids are found to be catalytically inefficient, deficient, or at least to date, seemingly incapable of certain functions. A case of this is M2+-independent ribophosphodiester hydrolysis at physiological pH and low ionic strength where nucleic acids exhibit especially low rate constants for self-cleavage and seem to be incapable of turnover.

scholarly journals Native Ion Mobility Mass Spectrometry: when Gas Phase Ion Structures Depend on the Electrospray Charging Process

2018 ◽  
Author(s):  
Nina A. Khristenko ◽  
Jussara Amato ◽  
Sandrine Livet ◽  
Bruno Pagano ◽  
Antonio Randazzo ◽  
...  
Keyword(s):  
Ionic Strength ◽  
Gas Phase ◽  
Ion Mobility ◽  
Droplet Surface ◽  
Dependent Manner ◽  
Base Pairs ◽  
Wide Range ◽  
A Chain ◽  
Gas Phase Ion ◽  
Low Ionic Strength

Ion mobility spectrometry (IMS) has become popular to characterize biomolecule folding. Numerous studies have shown that proteins that are folded in solution remain folded in the gas phase, whereas proteins that are unfolded in solution adopt more extended conformations in the gas phase. Here, we discuss how general this tenet is. We studied single-stranded DNAs (human telomeric cytosine-rich sequences with CCCTAA repeats), which fold into an intercalated motif (i-motif) structure in a pH-dependent manner, thanks to the formation of C‒H+‒C base pairs. As i-motif formation is favored at low ionic strength, we could investigate the ESI-IMS-MS behavior of i-motif structures at pH ~5.5 over a wide range of ammonium acetate concentrations (15 mM to 100 mM). The control experiments consisted of either the same sequence at pH ~7.5, wherein the sequence is unfolded, or sequence variants that cannot form i-motifs (CTCTAA repeats). The surprising results came from the control experiments. We found that the ionic strength of the solution had a greater effect on the compactness of the gas-phase structures than the solution folding state. This means that electrosprayed ions keep a memory of the charging process, which is influenced by the electrolyte concentration. We discuss these results in light of the analyte partitioning between the droplet interior and droplet surface, which in turn influences the probability of being ionized via a charged residue pathway or a chain extrusion pathway.<br>

scholarly journals Native Ion Mobility Mass Spectrometry: when Gas Phase Ion Structures Depend on the Electrospray Charging Process

2019 ◽  
Author(s):  
Nina A. Khristenko ◽  
Jussara Amato ◽  
Sandrine Livet ◽  
Bruno Pagano ◽  
Antonio Randazzo ◽  
...  
Keyword(s):  
Ionic Strength ◽  
Gas Phase ◽  
Ion Mobility ◽  
Droplet Surface ◽  
Dependent Manner ◽  
Base Pairs ◽  
Wide Range ◽  
A Chain ◽  
Gas Phase Ion ◽  
Low Ionic Strength

Ion mobility spectrometry (IMS) has become popular to characterize biomolecule folding. Numerous studies have shown that proteins that are folded in solution remain folded in the gas phase, whereas proteins that are unfolded in solution adopt more extended conformations in the gas phase. Here, we discuss how general this tenet is. We studied single-stranded DNAs (human telomeric cytosine-rich sequences with CCCTAA repeats), which fold into an intercalated motif (i-motif) structure in a pH-dependent manner, thanks to the formation of C‒H+‒C base pairs. As i-motif formation is favored at low ionic strength, we could investigate the ESI-IMS-MS behavior of i-motif structures at pH ~5.5 over a wide range of ammonium acetate concentrations (15 mM to 100 mM). The control experiments consisted of either the same sequence at pH ~7.5, wherein the sequence is unfolded, or sequence variants that cannot form i-motifs (CTCTAA repeats). The surprising results came from the control experiments. We found that the ionic strength of the solution had a greater effect on the compactness of the gas-phase structures than the solution folding state. This means that electrosprayed ions keep a memory of the charging process, which is influenced by the electrolyte concentration. We discuss these results in light of the analyte partitioning between the droplet interior and droplet surface, which in turn influences the probability of being ionized via a charged residue pathway or a chain extrusion pathway.<br>

Characterization of transcripts expressed from nitrogenase-3 structural genes of Azotobacter vinelandii

1992 ◽  
Vol 38 (9) ◽  
pp. 929-936 ◽  
Author(s):  
R. Premakumar ◽  
Marty R. Jacobson ◽  
Telisa M. Loveless ◽  
Paul E. Bishop
Keyword(s):  
Azotobacter Vinelandii ◽  
Coding Region ◽  
Base Pairs ◽  
S1 Nuclease ◽  
Mrna Species ◽  
Mutant Strains ◽  
S1 Nuclease Mapping ◽  
Alternative Nitrogenase ◽  
Nuclease Mapping

Five major anfH-hybridizing mRNA species accumulated in Azotobacter vinelandii cells derepressed for nitrogenase-3 (an alternative nitrogenase, which appears to lack Mo and V). Using anfH-, anfD-, anfG-, anfK-, and orf1orf2-specific probes and mutant strains of A. vinelandii these mRNA species have been identified as encoding anfHDGKorf1orf2 (6.0 kb), anfHDGK (4.3 kb), anfHD (2.6 kb), vnfHorfFd (1.3 kb), and vnfH and (or) anfH(1.0 kb). A 0.6-kb mRNA species, which hybridized only to the orf1orf2-specific probe, and a 3.5-kb mRNA species, which hybridized to anfD or anfK, also accumulated under these conditions. Northern blot analysis and S1 nuclease mapping indicate that transcription of the anf structural gene cluster initiates at a unique nif consensus promoter situated 127 base pairs upstream from the anfH coding region. Observation of anfH-hybridizing mRNA species that accumulate in strains derepressed for nitrogen fixation demonstrates that transcription of the anfHDGKorf1orf2 cluster is normally repressed by Mo, V, and NH4+, whereas transcription of the vnfHorfFd cluster does not require the presence of V and is repressed only by Mo, but not NH4+. Analysis of the accumulation of mRNAs in a tungsten-tolerant strain revealed that Mo and V repression of anf transcription must occur by different mechanisms. Key words: Azotobacter vinelandii, nitrogenase-3, transcripts, regulation, molybdenum, vanadium.

On the structure of cellular and viral chromatin

1978 ◽  
Vol 283 (997) ◽  
pp. 275-285 ◽  
Keyword(s):  
Ionic Strength ◽  
Simian Virus 40 ◽  
Histone H1 ◽  
Staphylococcal Nuclease ◽  
Dna Fragments ◽  
Base Pairs ◽  
Nuclease Digestion ◽  
Dna Fragment ◽  
Histone H5 ◽  
Low Ionic Strength

Some of the recent experimental data obtained in our laboratory are briefly reviewed. 1. A mild staphylococcal nuclease digestion of either chromatin or nuclei from mouse Ehrlich tumour cells results in chromatin subunits (mononucleosomes) of three discrete kinds. The smallest mononucleosome (MN 1 contains all histones except H1 and a DNA fragment 140 base pairs long. The intermediate mononucleosome (MN 2 ) contains all five histones and a DNA fragment 170 base pairs long. The third mononucleosome (MN 3 ) also contains all five histones, but its associated DNA is longer and somewhat heterogeneous in size (180-200 base pairs). Most of the MN 3 particles are rapidly converted to mononucleosomes MN 2 and MN 1 by nuclease digestion. However, there exists a relatively nuclease-resistant subpopulation of the MN 3 mononucleosomes. These 200 base-pair MN 3 particles contain not only histones but also non-histone proteins and are significantly more resistant to nuclease then even the smaller mononucleosomes MN 1 and MN 2 . 2. Nuclease digestion of hen erythrocyte nuclei or chromatin, in which histone H1 is partially replaced by histone H5 produces the mononucleosomes MN 1 and two electrophoretically resolvable kinds of MN 2 mononucleosomes, one containing histone H1 and the other one histone H5. A relatively nuclease-resistant subset of the mononucleosomes MN 3 is preferentially accumulated at later stages of the digestion. 3. Although pancreatic DNase (DNase I) and spleen acid DNase (DNase II) attack the DNA in chromatin in a manner different from that of staphylococcal nuclease, the deoxyribonucleoprotein (DNP) products of digestion are similar for all three enzymes under identical solvent conditions, as revealed by gel electrophoresis of the DNP at low ionic strength. 4. There are eight major kinds of staphylococcal nuclease-produced soluble subnucleosomes (i.e. particles smaller than the mononucleosomes). In particular, the subnucleosome SN 1 is a set of naked double-stranded DNA fragments ca. 20 base pairs long. Subnucleosome SN 2 is a complex of a specific highly basic non-histone protein and a DNA fragment ca. 27 base pairs long. Subnucleosomes SN 7 and SN 8 each contain all of the histones except H1 and DNA fragments ca. 100 and 120 base pairs long, respectively. 5. Nuclease digestion of isolated mono- and dinucleosomes does not produce all of the subnucleosomes. These and related findings indicate that the cleavages required to generate these subnucleosomes result from some aspect of chromatin structure which is lost upon digestion to mono- or dinucleosomes. Nuclease digestion of isolated minichromosomes of Simian virus 40 (SV40) (which contain all five histones including H1) produces mononucleosomes MN 1 and MN 2 but does not produce some of the subnucleosomes or the relatively nuclease-resistant subset of the MN 3 mononucleosomes. 6. The rate of sedimentation of the SV40 minichromosomes ( ca. 60 S ) under ‘physiological’ ionic conditions ( μ ≈ 0.15) is about two times higher than that in a low ionic strength buffer ( μ ≈ 0.005). Occurrence of the compact state of the minichromosome critically depends upon the presence of histone H1 and can be irreversibly fixed by treatment with formaldehyde.

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