scholarly journals Structural characterization of DNA and RNA sequences recognized by the gene 5 protein of bacteriophage fd

1999 ◽  
Vol 339 (3) ◽  
pp. 525-531 ◽  
Author(s):  
Antony W. OLIVER ◽  
G. Geoff KNEALE
Keyword(s):  
Dna Sequence ◽  
Rna Structure ◽  
Gel Filtration ◽  
Rna Sequences ◽  
Rna Translation ◽  
Translational Repressor ◽  
Dna And Rna ◽  
Gene 5 Protein ◽  
Na Ions

The single-stranded DNA sequence d(GT5G4CT4C) occurs close to the origin of replication within the intergenic region of the viral strand of bacteriophage fd. The RNA analogue of this sequence r(GU5G4CU4C) forms part of the untranslated leader sequence of the gene 2 mRNA and is specifically bound by the fd gene 5 protein in its role as a translational repressor. The structure of these sequences is likely to have an important role in the control of both DNA replication and RNA translation in the phage. We show that this 16 nt sequence, in both a DNA and an RNA context, can exist in a structured and unstructured form as determined by high-resolution gel filtration and non-denaturing gel electrophoresis. The CD spectrum of the structured form is characteristic of parallel guanine tetraplexes. The structured form of the DNA sequence melts at approx. 47 °C in the presence of Na+ ions but the structure is stabilized up to 75 °C in the presence of K+ ions. The RNA structure is more stable than the equivalent DNA structure (melting temperature approx. 62 °C), and its stability is further enhanced in the presence of K+ ions. Two of the central guanine residues are fully protected from cleavage as determined by dimethyl sulphate protection experiments, whereas methylation interference studies show that methylation of any of the four central guanine residues inhibits structure formation. Our results demonstrate that the structured form of the nucleic acid is mediated through the formation of a guanine-tetraplex core region, in RNA this might be further stabilized by the presence of weaker uracil quartets.

scholarly journals Studies on the interactions of Ag(i) with DNA and their implication on the DNA-templated synthesis of silver nanoclusters and on the interaction with complementary DNA and RNA sequences

RSC Advances ◽  
2021 ◽  
Vol 11 (15) ◽  
pp. 9029-9042
Author(s):  
Alejandra de la Hoz ◽  
Alba Navarro ◽  
Anna Aviñó ◽  
Ramon Eritja ◽  
Raimundo Gargallo
Keyword(s):  
Secondary Structure ◽  
Dna Sequence ◽  
Analytical Signal ◽  
Silver Nanoclusters ◽  
Fluorescent Properties ◽  
Rna Sequences ◽  
Complementary Dna ◽  
Templated Synthesis ◽  
Dna And Rna ◽  
Hybridization Reaction

Variables affecting the fluorescent properties of DNA-stabilized silver nanoclusters are studied. The secondary structure of the AgNC-stabilizing DNA sequence dramatically affects the analytical signal behind the hybridization reaction.

scholarly journals Purification and characterization of an α-l-arabinofuranosidase from Streptomyces lividans 66 and DNA sequence of the gene (abfA)

1994 ◽  
Vol 302 (2) ◽  
pp. 443-449 ◽  
Author(s):  
C Manin ◽  
F Shareek ◽  
R Morosoli ◽  
D Kluepfel
Keyword(s):  
Dna Sequence ◽  
Avena Sativa ◽  
Specific Activity ◽  
Gel Filtration ◽  
Streptomyces Lividans ◽  
Native Protein ◽  
Purification And Characterization ◽  
Gene Encoding ◽  
Sds Page

The gene encoding an alpha-L-arabinofuranosidase (abfA) was homologously cloned in Streptomyces lividans and its DNA sequence was determined. The enzyme was purified from the cytoplasm of the hyperproducing clone S. lividans IAF116. Its M(r) was estimated by gel filtration and found to be approx. 380,000. Since SDS/PAGE indicated a native protein of M(r) 69,000, it can be concluded that the native protein consists of several subunits of that size. The pI value was 4.6. The kinetic constants determined with p-nitrophenyl alpha-L-arabinofuranoside as substrate were a Vmax of 180 units/mg of protein and a Km of 0.6 mM. The specific activity of the purified enzyme on this substrate was 153 units/mg of protein. Optimal enzyme activity was obtained at 60 degrees C and pH 6.0. The enzyme cleaved p-nitrophenyl alpha-L-arabinofuranoside, but had no activity on a variety of other p-nitrophenyl glycosides, except on p-nitrophenyl beta-D-xylopyranoside. The enzyme showed no activity on oat-spelts (Avena sativa) xylan or arabinogalactan, but acted on beet (Beta) arabinan or arabinoxylan. Hydrolysis occurred on arabino-oligoxylosides obtained from oat-splets xylan after digestion with xylanases. Since S. lividans normally does not secrete arabinofuranosidase, this enzyme may play a role in the assimilation of arabinose moieties from arabinose-containing xylo-oligosaccharides generated by beta-xylosidases or xylanases.

scholarly journals Spectroscopic Characterization of Mitochondrial G-Quadruplexes

2022 ◽  
Vol 23 (2) ◽  
pp. 925
Author(s):  
Sara Illodo ◽  
Cibrán Pérez-González ◽  
Ramiro Barcia ◽  
Flor Rodríguez-Prieto ◽  
Wajih Al-Soufi ◽  
...  
Keyword(s):  
Crucial Role ◽  
Spectroscopic Characterization ◽  
Rna Sequences ◽  
Conserved Sequence ◽  
Dna And Rna ◽  
Sodium Cations ◽  
Topology Changes ◽  
Spectroscopy Studies ◽  
Rna Transcript

Guanine quadruplexes (G4s) are highly polymorphic four-stranded structures formed within guanine-rich DNA and RNA sequences that play a crucial role in biological processes. The recent discovery of the first G4 structures within mitochondrial DNA has led to a small revolution in the field. In particular, the G-rich conserved sequence block II (CSB II) can form different types of G4s that are thought to play a crucial role in replication. In this study, we decipher the most relevant G4 structures that can be formed within CSB II: RNA G4 at the RNA transcript, DNA G4 within the non-transcribed strand and DNA:RNA hybrid between the RNA transcript and the non-transcribed strand. We show that the more abundant, but unexplored, G6AG7 (37%) and G6AG8 (35%) sequences in CSB II yield more stable G4s than the less profuse G5AG7 sequence. Moreover, the existence of a guanine located 1 bp upstream promotes G4 formation. In all cases, parallel G4s are formed, but their topology changes from a less ordered to a highly ordered G4 when adding small amounts of potassium or sodium cations. Circular dichroism was used due to discriminate different conformations and topologies of nucleic acids and was complemented with gel electrophoresis and fluorescence spectroscopy studies.

scholarly journals An Approach to Analyze the Ambiguity in RNA Structure

2010 ◽  
Vol 15 ◽  
pp. 1
Author(s):  
Shailendra Singh ◽  
Amardeep Singh
Keyword(s):  
Rna Structure ◽  
Rna Secondary Structure ◽  
Probabilistic Approach ◽  
Functional Protein ◽  
Rna Sequences ◽  
Structure Representation ◽  
Dna And Rna ◽  
Different Types ◽  
Intermediary Role ◽  
First Time

DNA and RNA are two very important bio-molecules of the human cell. RNA is the second major form of nucleic acid in human cells that plays an intermediary role between DNA and functional protein. Several classes of RNA’s are found in cells, each with a / its distinct function. Understanding of storage and utilization of a cell’s genetic information is based on the structure of RNA.  However,  Many  many experimental results have shown that RNA plays a another greater role in the cells. RNA sequences contains  which contain signals at the structure level can be exploited to detect functional motifs common to all, or a portion of, those sequences. Different types of analysis of a structure can provide functional information in different degrees of detail. In this This paper discusses various types of RNA secondary structure representation has been discussed and in which appropriate structure has been adopted  or ‘can be adopted’ if this is for the first time as appropriate for a probabilistic approach that shows un-ambiguity avoids ambiguity.  

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.

Isolation and Characterization of Plasminogen Activator from Pig Leucocytes

1974 ◽  
Vol 31 (01) ◽  
pp. 072-085 ◽  
Author(s):  
M Kopitar ◽  
M Stegnar ◽  
B Accetto ◽  
D Lebez
Keyword(s):  
Molecular Weight ◽  
Plasminogen Activator ◽  
Gel Electrophoresis ◽  
Gel Filtration ◽  
Ph Optimum ◽  
Isolation And Characterization ◽  
Ph Range ◽  
Inhibition Studies ◽  
Final Purification

SummaryPlasminogen activator was isolated from disrupted pig leucocytes by the aid of DEAE chromatography, gel filtration on Sephadex G-100 and final purification on CM cellulose, or by preparative gel electrophoresis.Isolated plasminogen activator corresponds No. 3 band of the starting sample of leucocyte cells (that is composed from 10 gel electrophoretic bands).pH optimum was found to be in pH range 8.0–8.5 and the highest pH stability is between pH range 5.0–8.0.Inhibition studies of isolated plasminogen activator were performed with EACA, AMCHA, PAMBA and Trasylol, using Anson and Astrup method. By Astrup method 100% inhibition was found with EACA and Trasylol and 30% with AMCHA. PAMBA gave 60% inhibition already at concentration 10–3 M/ml. Molecular weight of plasminogen activator was determined by gel filtration on Sephadex G-100. The value obtained from 4 different samples was found to be 28000–30500.

The Immunological Characterization of Human Antibodies to Factor VIII Isolated by Immuno-Affinity Chromatography

1981 ◽  
Vol 45 (01) ◽  
pp. 060-064 ◽  
Author(s):  
M L Kavanagh ◽  
C N Wood ◽  
J F Davidson
Keyword(s):  
Factor Viii ◽  
Affinity Chromatography ◽  
Gel Filtration ◽  
Immunological Characterization ◽  
Human Antibodies ◽  
Heavy Chains ◽  
Light Chain Type ◽  
Antibody Preparations ◽  
Chain Type

SummaryNine human antibodies to factor VIII were isolated from haemophilic plasmas by affinity chromatography and gel filtration and six were subsequently subjected to immunological characterization. Three partially purified preparations were similarly characterized. Eight of the antibodies were characterized as being exclusively IgG and one preparation was found to contain IgM. Seven of the antibodies contained only a single light chain type, four being of type lambda and three of type kappa. Two antibody preparations contained both kappa and lambda light chains. In four of the preparations, only a single heavy chain sub-class could be demonstrated, three of IgG3 and one of IgG4. Of the remainder, three were a mixture of IgG3 and IgG4 sub-classes and one contained both IgG2 and IgG4. IgG sub-classification could not be achieved with the IgM-containing preparation. These results demonstrate a restricted heterogeneity of light and heavy chains in human antibodies to factor VIII.

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