Branched DNA (bDNA) Technology for Direct Quantification of Nucleic Acids: Design and Performance

1998 ◽  
pp. 205-223
Author(s):  
Mark L. Collins ◽  
Peter J. Dailey ◽  
Lu-Ping Shen ◽  
Mickey S. Urdea ◽  
Linda J. Wuestehube ◽  
...  
Keyword(s):  
Nucleic Acids ◽  
Branched Dna ◽  
And Performance ◽  
Direct Quantification

Branched DNA (bDNA) Technology for Direct Quantification of Nucleic Acids: Research and Clinical Applications

1998 ◽  
pp. 327-342
Author(s):  
Janice A. Kolberg ◽  
Douglas N. Ludtke ◽  
Lu-Ping Shen ◽  
Will Cao ◽  
Darrah O’Conner ◽  
...  
Keyword(s):  
Nucleic Acids ◽  
Clinical Applications ◽  
Branched Dna ◽  
Direct Quantification

Analysis of branched nucleic acid structure using comparative gel electrophoresis

2008 ◽  
Vol 41 (1) ◽  
pp. 1-39 ◽  
Author(s):  
David M. J. Lilley
Keyword(s):  
Nucleic Acids ◽  
Electrophoretic Mobility ◽  
Gel Electrophoresis ◽  
Holliday Junction ◽  
Dna And Rna ◽  
Dna Junctions ◽  
Branched Dna ◽  
Powerful Means ◽  
Crystallographic Structures ◽  
Acid Structure

AbstractElectrophoresis in polyacrylamide gels provides a simple yet powerful means of analyzing the relative disposition of helical arms in branched nucleic acids. The electrophoretic mobility of DNA or RNA with a central discontinuity is determined by the angle subtended between the arms radiating from the branchpoint. In a multi-helical branchpoint, comparative gel electrophoresis can provide a relative measure of all the inter-helical angles and thus the shape and symmetry of the molecule. Using the long–short arm approach, the electrophoretic mobility of all the species with two helical arms that are longer than all others is compared. This can be done as a function of conditions, allowing the analysis of ion-dependent folding of branched DNA and RNA species. Notable successes for the technique include the four-way (Holliday) junction in DNA and helical junctions in functionally significant RNA species such as ribozymes. Many of these structures have subsequently been proved correct by crystallography or other methods, up to 10 years later in the case of the Holliday junction. Just as important, the technique has not failed to date. Comparative gel electrophoresis can provide a window on both fast and slow conformational equilibria such as conformer exchange in four-way DNA junctions. But perhaps the biggest test of the approach has been to deduce the structures of complexes of four-way DNA junctions with proteins. Two recent crystallographic structures show that the global structures were correctly deduced by electrophoresis, proving the worth of the method even in these rather complex systems. Comparative gel electrophoresis is a robust method for the analysis of branched nucleic acids and their complexes.

Exploring the conformations of nucleic acids

1995 ◽  
Vol 5 (3) ◽  
pp. 443-460 ◽  
Author(s):  
Marcel Turcotte ◽  
Guy Lapalme ◽  
François Major
Keyword(s):  
Nucleic Acids ◽  
Functional Programming ◽  
Three Dimensional ◽  
Performance Criteria ◽  
Dimensional Structure ◽  
Pharmaceutical Companies ◽  
Experimental Development ◽  
Macromolecular Conformation ◽  
And Performance ◽  
Research Centres

AbstractThis paper presents an application of functional programming in the field of molecular biology: exploring the conformations of nucleic acids. TheNucleic Acid three-dimensional structure determination problem(NA3D) and a constraint satisfaction algorithm are formally described. Prototyping and experimental development using the Miranda functional programming language, over the last four years, are discussed. A Prolog implementation has been developed to evaluate software engineering and performance criteria between functional and logic programming. A C++ implementation has been developed for distribution purpose and to solve large practical problems. This system, called MC-SYM for ‘Macromolecular Conformation by SYMbolic generation’, is used in more than 50 laboratories, including academic and government research centres and pharmaceutical companies.

Effects of an organic acid mixture and methionine supplements on intestinal morphology, protein and nucleic acids content, microbial population and performance of broiler chickens

2011 ◽  
Vol 51 (11) ◽  
pp. 1025 ◽  
Author(s):  
A. A. Saki ◽  
S. M. Eftekhari ◽  
P. Zamani ◽  
H. Aliarabi ◽  
M. Abbasinezhad
Keyword(s):  
Nucleic Acids ◽  
Organic Acids ◽  
Organic Acid ◽  
Dna Content ◽  
Broiler Chickens ◽  
Microbial Population ◽  
Intestinal Morphology ◽  
Acid Mixture ◽  
Broiler Chicks ◽  
And Performance

A study was carried out to investigate the effects of dietary supplementation of an organic acids mixture and two methionine supplements on intestinal morphology, protein and nucleic acids content, microbial population and performance of broiler chickens. Six hundred unsexed day-old Ross 308 broiler chicks were used in a factorial arrangement (3 × 2) based on a completely randomised design by four replicates with 25 chicks in each. Experimental diets consisted of: 0% organic acid mixture + DL-methionine (Treatment 1), 0% organic acid mixture + Alimet (Treatment 2), 0.5% organic acid mixture + DL-methionine (Treatment 3), 0.5% organic acid mixture + Alimet (Treatment 4), 1% organic acid mixture + DL-methionine (Treatment 5) and 1% organic acid mixture + Alimet (Treatment 6). A significant increase in jejunum mucosal DNA content was found by using 1% of organic acid mixture compared with those by other levels of organic acids at 21 days of age (P < 0.05). Also Treatments 5 and 6 had a higher mucosal DNA content than other treatments (P < 0.05) in a similar period. While at grower stage, the results have shown that protein content, protein/DNA and protein/RNA ratio by 0.5 and 1% of organic acids mixture significantly increased compared with those in the 0% level (P < 0.05). The addition of 1% level of organic acid mixture significantly increased villus height compared with 0 and 0.5% level of organic acid mixture at 21 days of age (P < 0.05). Highest and lowest villus heights were obtained by Treatments 1 and 6 (P < 0.05). Crypt depth increased by 0.5 and 1% of organic acid at 21 and 42 days of age (P < 0.05). Villus surface was significantly increased by 1% of organic acid mixture compared with that by 0% level at 21 days of age. The use of organic acid levels especially 1% resulted in an increase in lactic acid bacteria and decreased Enterobacteriaceae counts in the ileum of broiler chicken (P < 0.05). Better bodyweight and feed conversion ratio were obtained (P < 0.05) by 0.5 and 1% of organic acids mixture, although no response was found in feed intake and mortality in this respect (P > 0.05). The results of this study have shown improved reactions on intestinal morphometrical parameters and microflora atmosphors, by using 1% organic acid mixture. In contrast no differences were found between Alimet and DL-methionine in all tested parameters.

scholarly journals Reproducibility and Performance of the Second-Generation Branched-DNA Assay in Routine Quantification of Human Immunodeficiency Virus Type 1 RNA in Plasma

1999 ◽  
Vol 37 (3) ◽  
pp. 812-814 ◽  
Author(s):  
Donald G. Murphy ◽  
Patrick Gonin ◽  
Micheline Fauvel
Keyword(s):  
Human Immunodeficiency Virus ◽  
Human Immunodeficiency Virus Type ◽  
Virus Type ◽  
Second Generation ◽  
Branched Dna ◽  
Efficient Test ◽  
Immunodeficiency Virus ◽  
And Performance ◽  
Hiv 1

We examined the reproducibility of a second-generation branched-DNA (bDNA) assay (Quantiplex HIV RNA 2.0) for quantification of human immunodeficiency virus type 1 (HIV-1) RNA in plasma by retesting 325 specimens on separate runs and on different lots. The performance of the bDNA test was also assessed by data analysis obtained during routine testing of 15,365 specimens. Upon retesting, 96 and 86% of specimens displaying RNA levels above 5,000 and between 500 and 5,000 copies/ml, respectively, showed less than a 0.3 log10(twofold) difference with their initial values. Assay variability was found to increase as viral load decreased. Overall, the bDNA version 2.0 assay was found to be a reproducible and efficient test for routine quantification of HIV-1 RNA in plasma.

scholarly journals Locked nucleic acids in PCR primers increase sensitivity and performance

Genomics ◽  
2008 ◽  
Vol 91 (3) ◽  
pp. 301-305 ◽  
Author(s):  
K.N. Ballantyne ◽  
R.A.H. van Oorschot ◽  
R.J. Mitchell
Keyword(s):  
Nucleic Acids ◽  
Pcr Primers ◽  
Locked Nucleic Acids ◽  
And Performance
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