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 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.

The structural shift of a DNA template between a hairpin and a dimer tunes the emission color of DNA-templated AgNCs

Nanoscale ◽  
2018 ◽  
Vol 10 (44) ◽  
pp. 20717-20722 ◽  
Author(s):  
Pratik Shah ◽  
Suk Won Choi ◽  
Riddhi Nagda ◽  
Reka Geczy ◽  
Seok Keun Cho ◽  
...  
Keyword(s):  
Dna Sequence ◽  
Silver Nanoclusters ◽  
Dna Hairpin ◽  
Fluorescent Properties ◽  
Structural Shift ◽  
Emission Color ◽  
Dna Template

The structural shift of a DNA hairpin-dimer is as important as the DNA sequence in determining the fluorescent properties of DNA-stabilized silver nanoclusters (DNA/AgNCs).

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.

Tracking DNA and RNA Sequences at High Resolution

2013 ◽  
pp. 343-366 ◽  
Author(s):  
Dušan Cmarko ◽  
Anna Ligasová ◽  
Karel Koberna
Keyword(s):  
High Resolution ◽  
Rna Sequences ◽  
Dna And Rna

scholarly journals NADH:ubiquinone oxidoreductase from bovine heart mitochondria Complementary DNA sequence of the import precursor of the 10 kDa subunit of the flavoprotein fragment

FEBS Letters ◽  
1991 ◽  
Vol 282 (1) ◽  
pp. 135-138 ◽  
Author(s):  
J.Mark Skehel ◽  
Stephanie J. Pilkington ◽  
Michael J. Runswick ◽  
Ian M. Fearnley ◽  
John E. Walker
Keyword(s):  
Dna Sequence ◽  
Heart Mitochondria ◽  
Nadh:Ubiquinone Oxidoreductase ◽  
Complementary Dna ◽  
Bovine Heart

Partial characterization of an RNA component that copurifies with Saccharomyces cerevisiae RNase P

1989 ◽  
Vol 9 (6) ◽  
pp. 2536-2543
Author(s):  
J Y Lee ◽  
D R Engelke
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Secondary Structure ◽  
Schizosaccharomyces Pombe ◽  
Rnase P ◽  
Partial Characterization ◽  
Rna Sequences ◽  
Extensive Sequence ◽  
Sequence Similarities

Saccharomyces cerevisiae cellular RNase P is composed of both protein and RNA components that are essential for activity. The isolated holoenzyme contains a highly structured RNA of 369 nucleotides that has extensive sequence similarities to the 286-nucleotide RNA associated with Schizosaccharomyces pombe RNase P but bears little resemblance to the analogous RNA sequences in procaryotes or S. cerevisiae mitochondria. Even so, the predicted secondary structure of S. cerevisiae RNA is strikingly similar to the bacterial phylogenetic consensus rather than to previously predicted structures of other eucaryotic RNase P RNAs.

Complementary DNA sequence of rabbit CAP18—A unique lipopolysaccharide binding protein

1991 ◽  
Vol 179 (1) ◽  
pp. 170-175 ◽  
Author(s):  
James W. Larrick ◽  
John G. Morgan ◽  
Ilona Palings ◽  
Michimasa Hirata ◽  
Michael H. Yen
Keyword(s):  
Dna Sequence ◽  
Binding Protein ◽  
Lipopolysaccharide Binding Protein ◽  
Complementary Dna ◽  
Lipopolysaccharide Binding
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