Rearrangements and reconstitution of mononucleosomes as monitored by thermal denaturation measurements

1980 ◽  
Vol 58 (1) ◽  
pp. 73-81 ◽  
Author(s):  
Susan S. Chiu ◽  
Kay P. Lee ◽  
Peter N. Lewis
Keyword(s):  
Freeze Drying ◽  
Thermal Denaturation ◽  
Guanidine Hydrochloride ◽  
Melting Transition ◽  
Melting Profile ◽  
Base Pairs ◽  
Structural Domains ◽  
Calf Thymus ◽  
Dna Size ◽  
Histone Core

Derivative melting profiles of calf thymus mononucleosomes have been examined for changes resulting from variations in solvent pH and ionic strength, histone H1 content, and DNA size. Samples of mononucleosomes were found to rearrange during freeze-drying to form an altered monomer and a series of noncovalent multimers. The derivative melting profiles of these particles differ significantly from those for the untreated monomer and dimer. The noncovalent dimer exhibited a new melting transition at 66 °C involving approximately 18 base pairs of DNA normally associated with the highest melting transition. Mononucleosomes were reconstituted from 6 M guanidine hydrochloride to give particles with physical properties including melting profile which were virtually indistinguishable from those of the starting material. This result confirms the notion that no structural domains exist in the histone core that can be irreversibly denatured by noncovalent perturbations.

A thermal denaturation study of chromatin and nuclease-produced chromatin fragments

1977 ◽  
Vol 55 (7) ◽  
pp. 736-746 ◽  
Author(s):  
Peter N. Lewis
Keyword(s):  
Thermal Denaturation ◽  
Micrococcal Nuclease ◽  
Melting Transition ◽  
Cleavage Sites ◽  
Main Determinant ◽  
Calf Thymus ◽  
Sulfhydryl Oxidation ◽  
Thermal Denaturation Study ◽  
Lower Temperature ◽  
Mechanical Shearing

Calf thymus chromatin and nuclease-produced chromatin fragments have been examined by thermal denaturation measurements. Native chromatin gave a series of distinct melting transitions at 64, 73, 79, and 85 °C in 0.25 mM EDTA pH 8. Treatments such as dialysis, mechanical shearing, or sulfhydryl oxidation of histone H3 carried out on native chromatin significantly altered the derivative melting profiles by blurring the distinct transitions and shifting the highest melting transition to a lower temperature. Derivative melting profiles for electrophoretically purified chromatin fragments, monomer through hexamer, all resembled that obtained from dialyzed chromatin. These results suggest that higher order structures exist in chromatin that are easily disrupted. Since the products of micrococcal nuclease (EC 3.1.4.7) digestion of the altered chromatins did not exhibit any major electrophoretic differences from those obtained from nuclei, then most likely the primary arrangements of histones along the DNA are the main determinant for cleavage sites.

Torus Circumference and Thickness Parameters From a Linear DNA Size Series Suggest How Toruses Self-Assemble

1985 ◽  
Vol 43 ◽  
pp. 522-523
Author(s):  
George C. Ruben ◽  
Kenneth A. Marx
Keyword(s):  
Tertiary Structure ◽  
Dna Complexes ◽  
Tertiary Structures ◽  
Self Assembling ◽  
Double Stranded Dna ◽  
Calf Thymus ◽  
Dna Organization ◽  
Condensed Dna ◽  
Dna Size

Certain double stranded DNA bacteriophage and viruses are thought to have their DNA organized into large torus shaped structures. Morphologically, these poorly understood biological DNA tertiary structures resemble spermidine-condensed DNA complexes formed in vitro in the total absence of other macromolecules normally synthesized by the pathogens for the purpose of their own DNA packaging. Therefore, we have studied the tertiary structure of these self-assembling torus shaped spermidine- DNA complexes in a series of reports. Using freeze-etch, low Pt-C metal (10-15Å) replicas, we have visualized the microscopic DNA organization of both calf Thymus( CT) and linear 0X-174 RFII DNA toruses. In these structures DNA is circumferentially wound, continuously, around the torus into a semi-crystalline, hexagonal packed array of parallel DNA helix sections.

scholarly journals Dissociation of the AT-specific bifunctional intercalator [N-MeCys3,N-MeCys7]TANDEM from TpA sites in DNA

1995 ◽  
Vol 306 (1) ◽  
pp. 15-19 ◽  
Author(s):  
M C Fletcher ◽  
R K Olsen ◽  
K R Fox
Keyword(s):  
Dissociation Rate ◽  
Dnase I ◽  
Time Dependent ◽  
Base Pairs ◽  
Unusual Structure ◽  
Dnase I Footprinting ◽  
Calf Thymus ◽  
Stability Of Complexes ◽  
Dna Fragment ◽  
The Stability

We have examined the dissociation of [N-MeCys3,N-MeCys7]TANDEM, an AT-selective bifunctional intercalator, from TpA sites in mixed-sequence DNAs by a modification of the footprinting technique. Dissociation of complexes between the ligand and radiolabelled DNA fragments was initiated by adding a vast excess of unlabelled calf thymus DNA. Portions of this mixture were subjected to DNAse I footprinting at various times after adding the competitor DNA. Dissociation of the ligand from each site was seen by the time-dependent disappearance of the footprinting pattern. Within a natural DNA fragment (tyrT) the ligand dissociates from TTAT faster than from ATAT. We found that the stability of complexes with isolated TpA steps decreases in the order ATAT > TTAA > TATA. Dissociation from each of these sites is much faster than from longer regions of (AT)n. These results confirm the requirement for A and T base-pairs surrounding the TpA step and suggest that the interaction is strongest with regions of alternating AT, possibly as a result of its unusual structure. The ligand dissociates more slowly from the centre of (AT)n tracts than from the edges, suggesting that variations in dissociation rate arise from sequence-dependent variations in local DNA structure.

Folding of the SPKK Rich Peptide in the Presence of the Octa-Oligonucleotide

1997 ◽  
Vol 52 (1-2) ◽  
pp. 77-81 ◽  
Author(s):  
Igor Z. Zubrzycki ◽  
Lothar Bohm
Keyword(s):  
Thermal Denaturation ◽  
Helical Structure ◽  
Core Histone ◽  
Base Pairs ◽  
H1 Histone ◽  
Terminal Domain ◽  
Single Stranded Oligonucleotide

Abstract The nucleosome contains of 200 base pairs of DNA complexed with four core histone complex: H2A , H2B, H3, and H4. The fifth histone species, the H1 histone, interacts with linker DNA connecting neighbouring nucleosomes. We have studied the influence of the phosphorylation on the interactions of a repeating unit 15 residues long, containing the SPKK motif, the motif thought to induce turn along peptides sequences, enclosed within the trout testis H1 C-terminal domain with octanucleotide by means of the thermal denaturation and CD technique. The results indicate that the peptide preferentially binds to a single stranded oligonucleotide. It has been shown further that there is no β structure present but a distorted helical structure has been detected.

Influence of thermal denaturation on the electrophoretic mobility of calf thymus DNA

Biopolymers ◽  
1964 ◽  
Vol 2 (1) ◽  
pp. 1-8 ◽  
Author(s):  
L. Costaxtixo ◽  
A. M. Liquori ◽  
V. Vitagliaxo
Keyword(s):  
Electrophoretic Mobility ◽  
Thermal Denaturation ◽  
Calf Thymus Dna ◽  
Calf Thymus

scholarly journals Structural and evolutionary relationships among five members of the human gamma-crystallin gene family.

1985 ◽  
Vol 5 (6) ◽  
pp. 1408-1414 ◽  
Author(s):  
S O Meakin ◽  
M L Breitman ◽  
L C Tsui
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
The Other ◽  
Tata Box ◽  
Phage Library ◽  
Evolutionary Relationships ◽  
Base Pairs ◽  
Structural Domains ◽  
First Intron ◽  
Gamma Crystallin

We have characterized five human gamma-crystallin genes isolated from a genomic phage library. DNA sequencing of four of the genes revealed that two of them predict polypeptides of 174 residues showing 71% homology in their amino acid sequence; the other two correspond to closely related pseudogenes which contain the same in-frame termination codon at identical positions in the coding sequence. Two of the genes and one of the pseudogenes are oriented in a head-to-tail fashion clustered within 22.5 kilobases. All three contain a TATA box 60 to 80 base pairs upstream of the initiation codon and a highly conserved segment of 44 base pairs in length immediately preceding the TATA box. The two genes and the two pseudogenes are similar in structure: each contains a small 5' exon encoding three amino acids followed by two larger exons that correspond exactly to the two similar structural domains of the polypeptide. The first intron varies from 100 to 110 base pairs, and the second intron ranges from 1 to several kilobases, rendering an overall gene size of 1.7 to 4.5 kilobases. At least one of the two pseudogenes appears to have been functional before inactivation, suggesting that their identical mutation was generated by gene conversion.

A naproxen complex of dysprosium intercalates into calf thymus DNA base pairs

2014 ◽  
Vol 428 ◽  
pp. 1-5 ◽  
Author(s):  
Mengsi Yang ◽  
Jianhua Jin ◽  
Guiqing Xu ◽  
Fengling Cui ◽  
Hongxia Luo
Keyword(s):  
Calf Thymus Dna ◽  
Base Pairs ◽  
Dna Base ◽  
Calf Thymus ◽  
Dna Base Pairs

scholarly journals Ultracentrifuge studies of histone fractions from calf thymus deoxyribonucleoprotein

1969 ◽  
Vol 114 (2) ◽  
pp. 227-235 ◽  
Author(s):  
P A Edwards ◽  
K V Shooter
Keyword(s):  
Sodium Chloride ◽  
Guanidine Hydrochloride ◽  
Chloride Concentration ◽  
Sedimentation Coefficient ◽  
Apparent Molecular Weight ◽  
Concentrated Solutions ◽  
Molecular Weights ◽  
Sodium Chloride Solutions ◽  
Low Concentrations ◽  
Calf Thymus

Molecular weights and sedimentation coefficients of four major fractions of calf thymus histones were measured. The minimum molecular weights were determined in concentrated solutions of guanidine hydrochloride. The results indicate that, with the possible exception of fraction F3, the fractions are heterogeneous. Comparisons in 0·1m-sodium chloride suggest that fraction F1 does not aggregate and show that fractions F2(a) and F3 aggregate to form larger complexes than does fraction F2(b). The degree of aggregation of each fraction is independent of pH in the range pH1–7. Detailed studies with fraction F2(b) have confirmed that the change in sedimentation coefficient observed as the sodium chloride concentration of the solution is increased results from increases in the apparent molecular weight of the sedimenting units. It has been found that the molecules of fraction F2(b) are present as single molecules only in sodium chloride solutions of 33mm or less. At these low concentrations the effects of charge greatly increase the concentration dependence of the sedimentation rate; the results can, however, be interpreted by using the theory developed by Alexandrowicz & Daniel (1963) and Daniel & Alexandrowicz (1963).

The Role of DNA Concentration

1969 ◽  
Vol 24 (5) ◽  
pp. 511-514 ◽  
Author(s):  
Samarendra Basu
Keyword(s):  
Thermal Denaturation ◽  
Melting Profile ◽  
Dna Concentration ◽  
Melting Temperatures

Melting temperatures (Tm) of several DNA’s do not vary with the change of DNA concentration. However, at any temperature above Tm, the fractional hyperchromism was always greater at the lower concentration. This result was also evident in the presence of formaldehyde.Reversibility on renaturation decreased with the progress of thermal denaturation along the melting profile. The effect was much enhanced at low DNA concentration and for a DNA of low G—C content.The occurrence of some permanent changes on the dissociated molecules has been suspected to be the only cause for the observed effects.

scholarly journals Effects of Stability of Base Pairs Containing an Oxazolone on DNA Elongation

2014 ◽  
Vol 2014 ◽  
pp. 1-9 ◽  
Author(s):  
Masayo Suzuki ◽  
Kazuya Ohtsuki ◽  
Katsuhito Kino ◽  
Teruhiko Kobayashi ◽  
Masayuki Morikawa ◽  
...  
Keyword(s):  
Dna Replication ◽  
Oxidative Damage ◽  
Ab Initio ◽  
Base Pair ◽  
Thermal Denaturation ◽  
Primer Extension ◽  
Base Pairs ◽  
Nucleotide Incorporation ◽  
The Stability

The nucleoside 2,2,4-triamino-5(2H)-oxazolone (Oz) can result from oxidative damage to guanine residues in DNA. Despite differences among the three polymerases (Polβ, KF exo−, and Polη) regarding nucleotide incorporation patterns opposite Oz, all three polymerases can incorporate guanine opposite Oz. Based onab initiocalculations, we proposed a structure for a stable Oz:G base pair. Here, to assess the stability of each Oz-containing base pair (Oz:G, Oz:A, Oz:C, and Oz:T) upon DNA replication, we determined the efficiency of Polβ-, KF exo−-, or Polη-catalyzed primer extension beyond each base pair. With each polymerase, extension beyond Oz:G was more efficient than that beyond Oz:A, Oz:C, or Oz:T. Moreover, thermal denaturation studies revealed that theTmvalue for the duplex containing Oz:G was significantly higher than those obtained for duplexes containing Oz:A, Oz:C, or Oz:T. Therefore, the results fromab initiocalculations along with those from DNA replication assays and thermal denaturation experiments supported the conclusion that Oz:G is the most stable of the Oz-containing base pairs.

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