scholarly journals STUDIES ON NUCLEIC ACID METACHROMASY

1965 ◽  
Vol 27 (2) ◽  
pp. 313-326 ◽  
Author(s):  
Michael E. Lamm ◽  
Lillian Childers ◽  
Merrill K. Wolf
Keyword(s):  
Nucleic Acid ◽  
Toluidine Blue ◽  
Binding Sites ◽  
Heat Denaturation ◽  
Color Contrast ◽  
Fluid Absorption ◽  
Tissue Sections ◽  
Dna And Rna ◽  
Nucleic Acid Conformation ◽  
Intense Color

The stacking coefficients (K's) of nucleic acids have been thought to influence the color contrast between DNA and RNA in tissue sections stained with metachromatic dyes. This idea was tested by titrating toluidine blue (TB) and acridine orange (AO) in solution against DNA and RNA, native or treated with formaldehyde, acrolein, or Carnoy's fluid. Absorption spectra at varying polymer-dye ratios were used to compute K values by the methods of Bradley and colleagues. Results with both dyes fit Bradley's stacking equations. Fixatives did not block dye-binding sites but markedly altered K values. K of DNA was low, unaffected by aldehyde fixative, increased by Carnoy's fluid or heat denaturation. K of RNA was higher than that of DNA and was increased greatly by formaldehyde, almost as much by acrolein, considerably less by Carnoy's fluid. Aldehyde effects were partially reversed upon removal of aldehyde by dialysis. These observations accord with known effects of aldehydes and denaturation upon nucleic acid conformation. Differences between K's of DNA and RNA were greater after aldehyde treatment than after Carnoy's, and were greater with AO than with TB. This is generally consistent with the magnitude of the color contrasts observed in tissues. Additional factors must contribute to the intense color contrast observed in acrolein-fixed tissues stained with TB.

scholarly journals STUDIES ON NUCLEIC ACID METACHROMASY

1965 ◽  
Vol 27 (2) ◽  
pp. 327-336 ◽  
Author(s):  
Ned Feder ◽  
Merrill K. Wolf
Keyword(s):  
Nucleic Acid ◽  
Ribosomal Rna ◽  
Toluidine Blue ◽  
Color Contrast ◽  
Tissue Sections ◽  
Dna And Rna ◽  
Excellent Preservation ◽  
Structural Preservation ◽  
Intense Color

Acrolein-fixed, polyester wax-embedded tissue sections showed excellent preservation of light microscopic architecture and, when stained with toluidine blue, intense color contrast between DNA, which stained orthochromatically, and RNA, which stained metachromatically. This method has practical value for differentiating DNA from RNA in the same section. The color contrast was impaired by substituting formaldehyde for acrolein or paraffin for polyester wax, and was negligible in tissues fixed in formaldehyde or Carnoy's fluid and embedded in paraffin. Quality of structural preservation paralleled degree of color contrast. Metachromatic staining can be analysed, by the quantitative parameters of Bradley and colleagues, to provide inferences regarding the conformation of biopolymers in tissue sections. Comparison of the nucleic acid color contrasts in toluidine blue-stained sections with titrations of fixative-treated nucleic acids against toluidine blue in solution indicated a greater difference in conformation between DNA- and RNA-protein in acrolein-polyester sections than between acrolein-treated free DNA and RNA in solution. This is supported by recent evidence that the conformation of ribosomal RNA is quite different in whole ribosomes from that assumed by the same RNA free in solution. The acrolein-polyester method may enhance color contrast by providing superior preservation of ordered nucleoprotein conformations.

scholarly journals Polyamines and Their Role in Virus Infection

2017 ◽  
Vol 81 (4) ◽  
Author(s):  
Bryan C. Mounce ◽  
Michelle E. Olsen ◽  
Marco Vignuzzi ◽  
John H. Connor
Keyword(s):  
Protein Synthesis ◽  
Nucleic Acid ◽  
Mammalian Cells ◽  
Cellular Proliferation ◽  
Polyamine Synthesis ◽  
Host Interactions ◽  
Dna And Rna ◽  
Rna Polymerization ◽  
Nucleic Acid Conformation

SUMMARY Polyamines are small, abundant, aliphatic molecules present in all mammalian cells. Within the context of the cell, they play a myriad of roles, from modulating nucleic acid conformation to promoting cellular proliferation and signaling. In addition, polyamines have emerged as important molecules in virus-host interactions. Many viruses have been shown to require polyamines for one or more aspects of their replication cycle, including DNA and RNA polymerization, nucleic acid packaging, and protein synthesis. Understanding the role of polyamines has become easier with the application of small-molecule inhibitors of polyamine synthesis and the use of interferon-induced regulators of polyamines. Here we review the diverse mechanisms in which viruses require polyamines and investigate blocking polyamine synthesis as a potential broad-spectrum antiviral approach.

scholarly journals Dissecting and predicting different types of binding sites in nucleic acids based on structural information

2021 ◽  
Author(s):  
Zheng Jiang ◽  
Si-Rui Xiao ◽  
Rong Liu
Keyword(s):  
Nucleic Acid ◽  
Nucleic Acids ◽  
Binding Sites ◽  
Structural Information ◽  
Machine Learning Algorithms ◽  
Nucleic Acid Binding ◽  
Integrative Framework ◽  
Dna And Rna ◽  
Feature Spaces ◽  
Critical Binding

Abstract The biological functions of DNA and RNA generally depend on their interactions with other molecules, such as small ligands, proteins and nucleic acids. However, our knowledge of the nucleic acid binding sites for different interaction partners is very limited, and identification of these critical binding regions is not a trivial work. Herein, we performed a comprehensive comparison between binding and nonbinding sites and among different categories of binding sites in these two nucleic acid classes. From the structural perspective, RNA may interact with ligands through forming binding pockets and contact proteins and nucleic acids using protruding surfaces, while DNA may adopt regions closer to the middle of the chain to make contacts with other molecules. Based on structural information, we established a feature-based ensemble learning classifier to identify the binding sites by fully using the interplay among different machine learning algorithms, feature spaces and sample spaces. Meanwhile, we designed a template-based classifier by exploiting structural conservation. The complementarity between the two classifiers motivated us to build an integrative framework for improving prediction performance. Moreover, we utilized a post-processing procedure based on the random walk algorithm to further correct the integrative predictions. Our unified prediction framework yielded promising results for different binding sites and outperformed existing methods.

scholarly journals Novel cyanine dye as competitive ligand for probing the drug–nucleic acid interactions

2020 ◽  
Keyword(s):  
Nucleic Acid ◽  
Nucleic Acids ◽  
Binding Sites ◽  
Lanthanide Complexes ◽  
Rna Binding ◽  
Cyanine Dye ◽  
Dna And Rna ◽  
Dna And Rna Binding ◽  
Drug Displacement ◽  
Potential Antitumor

Background: During the past decades, increasing attention has been given to elucidating the molecular details of interactions between the pharmacological agents and nucleic acids since the drug–DNA complexation may lead to impairment of DNA replication, strand breaking and mutations. A variety of techniques have been developed to characterize the drug-nucleic acid binding, among which the fluorescence dye displacement assay is one of the most informative approaches. Recently, it was demonstrated that cyanine dyes can be successfully employed for the high throughput screening of the interactions between nucleic acids and drugs. To the best of our knowledge, so far, the potential application of cyanine dyes for the drug-displacement studies remains insufficiently evaluated. Objectives: The aim of the present study was to investigate the ability of a novel cyanine dye to serve as a competitor for the potential antitumor compounds, lanthanide complexes bearing europium (III) tris-β-diketonate (EC) for the DNA and RNA binding sites. Materials and methods: Calf thymus DNA, yeast RNA, trimethine cyanine dye and lanthanide complexes bearing europium (III) tris-β-diketonate were used for sample preparation. The fluorescence data were acquired using Perkin-Elmer LS-55 spectrofluorimeter. Results: Using the fluorescence spectroscopy technique we conducted the displacement reaction trimethine cyanine dye/europium coordination complexes in the presence of double stranded DNA and single-stranded RNA. An increase of the EC concentration in the systems AK3-5/DNA or AK3-5/RNA was followed by a gradual reduction in the AK3-5 fluorescence intensity, indicating that europium (III) tris-β-diketonate compounds can serve as competitors for the trimethine cyanine dye on the nucleic acids. Both the drug chemical structure and the type of nucleic acid proved to control the extent of EC-induced decrease of AK3-5 fluorescence in the presence of the DNA or RNA. Conclusion: By recruiting the potential antitumor agents europium chelate complexes as the competitive ligands for the cyanine dye for the DNA and RNA binding sites, we found that a novel trimethine compound can be effectively used in the fluorescence drug displacement assays.

How human serum albumin recognizes DNA and RNA

2018 ◽  
Vol 399 (4) ◽  
pp. 347-360 ◽  
Author(s):  
Ludmila I. Alinovskaya ◽  
Sergey E. Sedykh ◽  
Nikita V. Ivanisenko ◽  
Svetlana E. Soboleva ◽  
Georgy A. Nevinsky
Keyword(s):  
Nucleic Acid ◽  
Human Serum Albumin ◽  
Binding Sites ◽  
Sharp Increase ◽  
Lower Affinity ◽  
High Affinity ◽  
Dna And Rna ◽  
First Time ◽  
Additional Nucleotide ◽  
Specific Contribution

AbstractWe show here for the first time that HSA possesses two nucleic acid-(NA) binding sites and we estimated the relative contributions of the nucleotide links of (pN)nto their total affinity for these binding sites with higher and lower affinity for NAs. The minimal ligands of these binding sites areorthophosphate (Kd=3.0 and 20.0 mm), various dNMPs (5.6–400 μmand 0.063–18 mm) and different rNMPs (4.9–30 μmand 14–250 μm). Maximal contribution to the total affinity of all NAs to the first and second sites was observed for one nucleotide and was remarkably lower for three additional nucleotide units of (pN)n(n=1–4) with a significant decrease in the contribution at n=5–6, and at n≥7–8 all dependencies reached plateaus. For d(pA)nand r(pA)na relatively gradual decrease in the contribution to the affinity at n=1–6 was observed, while several d(pN)n, demonstrated a sharp increase in the contribution at n=2–4. Finally, all (pN)n>10demonstrated high affinity for the first (1.4–150 nm) and the second (80–2400 nm) sites of HSA. Double-stranded NAs showed significantly lower affinity comparing with single-stranded ligands. The thermodynamic parameters characterizing the specific contribution of every nucleotide link of all (pN)1−9(ΔG°) to their total affinity for HSA were estimated.

High-resolution nucleic acid sequence mapping via in situ hybridization at the Electron Microscope level

1995 ◽  
Vol 53 ◽  
pp. 752-753
Author(s):  
B.A. Hamkalo ◽  
S. Narayanswami ◽  
A.P. Kausch
Keyword(s):  
Nucleic Acid ◽  
Interphase Nucleus ◽  
Genome Mapping ◽  
Precise Location ◽  
Electron Microscope Level ◽  
Rna Sequences ◽  
Fundamental Interest ◽  
Whole Cells ◽  
Dna And Rna

The availability of nonradioactive methods to label nucleic acids an the resultant rapid and greater sensitivity of detection has catapulted the technique of in situ hybridization to become the method of choice to locate of specific DNA and RNA sequences on chromosomes and in whole cells in cytological preparations in many areas of biology. It is being applied to problems of fundamental interest to basic cell and molecular biologists such as the organization of the interphase nucleus in the context of putative functional domains; it is making major contributions to genome mapping efforts; and it is being applied to the analysis of clinical specimens. Although fluorescence detection of nucleic acid hybrids is routinely used, certain questions require greater resolution. For example, very closely linked sequences may not be separable using fluorescence; the precise location of sequences with respect to chromosome structures may be below the resolution of light microscopy(LM); and the relative positions of sequences on very small chromosomes may not be feasible.

scholarly journals Sulfur Modification in Natural RNA and Therapeutic Oligonucleotides

2021 ◽  
Author(s):  
Ya Ying Zheng ◽  
Ying Wu ◽  
Thomas Begley ◽  
Jia Sheng
Keyword(s):  
Nucleic Acid ◽  
Dna And Rna ◽  
Sulfur Modification ◽  
Oxygen Atoms

Sulfur modifications have been discovered on both DNA and RNA. Sulfur substitution of oxygen atoms at nucleobase or backbone locations in the nucleic acid framework led to a wide variety...

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