DNA and RNA: NMR studies of conformations and dynamics in solution

1987 ◽  
Vol 20 (1-2) ◽  
pp. 35-112 ◽  
Author(s):  
Dinshaw J. Patel ◽  
Lawrence Shapiro ◽  
Dennis Hare
Keyword(s):  
Aqueous Solution ◽  
Data Analysis ◽  
Nucleic Acids ◽  
Nmr Studies ◽  
Magnet Design ◽  
Dna And Rna ◽  
Qualitative Nature ◽  
Abundant Supply

The early NMR research on nucleic acids was of a qualitative nature and was restricted to partial characterization of short oligonucleotides in aqueous solution. Major advances in magnet design, spectrometer electronics, pulse techniques, data analysis and computational capabilities coupled with the availability of pure and abundant supply of long oligonucleotides have extended these studies towards the determination of the 3-D structure of nucleic acids in solution.

scholarly journals Polarization spectroscopy methods in the determination of interactions of small molecules with nucleic acids – tutorial

2018 ◽  
Vol 14 ◽  
pp. 84-105 ◽  
Author(s):  
Tamara Šmidlehner ◽  
Ivo Piantanida ◽  
Gennaro Pescitelli
Keyword(s):  
Nucleic Acids ◽  
Small Molecules ◽  
Helical Structure ◽  
Linear Dichroism ◽  
Research Field ◽  
X Ray Diffraction ◽  
Polarization Spectroscopy ◽  
Dna And Rna

The structural characterization of non-covalent complexes between nucleic acids and small molecules (ligands) is of a paramount significance to bioorganic research. Highly informative methods about nucleic acid/ligand complexes such as single crystal X-ray diffraction or NMR spectroscopy cannot be performed under biologically compatible conditions and are extensively time consuming. Therefore, in search for faster methods which can be applied to conditions that are at least similar to the naturally occurring ones, a set of polarization spectroscopy methods has shown highly promising results. Electronic circular dichroism (ECD) is the most commonly used method for the characterization of the helical structure of DNA and RNA and their complexes with ligands. Less common but complementary to ECD, is flow-oriented linear dichroism (LD). Other methods such as vibrational CD (VCD) and emission-based methods (FDCD, CPL), can also be used for suitable samples. Despite the popularity of polarization spectroscopy in biophysics, aside several highly focused reviews on the application of these methods to DNA/RNA research, there is no systematic tutorial covering all mentioned methods as a tool for the characterization of adducts between nucleic acids and small ligands. This tutorial aims to help researchers entering the research field to organize experiments accurately and to interpret the obtained data reliably.

Synthesis and characterization of 19F NMR chelators for measurement of cytosolic free Ca

1987 ◽  
Vol 252 (4) ◽  
pp. C441-C449 ◽  
Author(s):  
L. A. Levy ◽  
E. Murphy ◽  
R. E. London
Keyword(s):  
Chemical Shifts ◽  
Cell Types ◽  
Free Calcium ◽  
Tetraacetic Acid ◽  
Nmr Studies ◽  
Cytosolic Free Calcium ◽  
Fluorine Nmr ◽  
Dissociation Constant Kd

Fluorine 19 nuclear magnetic resonance (NMR) studies of intracellular fluorinated calcium chelators provide a useful strategy for the determination of cytosolic free calcium levels in cells and perfused organs. However, the fluorinated chelator with the highest affinity for calcium ions which has been described to date. 1,2-bis-(2-amino-5-fluorophenoxy)ethane-N,N,N',N'-tetraacetic acid (5FBAPTA), exhibits a dissociation constant (Kd) value 5- to 10-fold greater than the intracellular calcium concentration levels in most cell types, thus limiting the ability of fluorine NMR to report these concentrations reliably. We have consequently designed and synthesized several fluorinated calcium chelators with higher affinity for calcium. The best of these, 2-(2-amino-4-methyl-5-fluorophenoxy)-methyl-8 aminoquinidine-N,N,N',N'-tetraacetic acid (quinMF), has a Kd value approximately 10 times lower than that of 5FBAPTA. Several of the newly synthesized indicators have different chemical shifts for the calcium complexed and uncomplexed chelators to allow the simultaneous use of two indicators. In addition to providing information about the level of cytosolic free calcium, chelators containing a quinoline ring exhibit considerable sensitivity to magnesium levels and hence have potential application for the determination of cytosolic-magnesium concentrations. Application of these chelators is illustrated by determination of the cytosolic-free calcium level in erythrocytes. Use of quinMF, the chelator with the lowest Kd value, gives a calcium value of 25-30 nM.

Synthesis, Modification, and Characterization of Nanocarbon Electrodes for Determination of Nucleic Acids

2015 ◽  
pp. 241-281
Author(s):  
David Hynek ◽  
Katerina Tmejova ◽  
Jiri Kudr ◽  
Ondrej Zitka ◽  
Lukas Nejdl ◽  
...  
Keyword(s):  
Nucleic Acids

Synthesis, Modification and Characterization of Nanocarbon Electrodes for Determination of Nucleic Acids

2015 ◽  
pp. 1-35
Author(s):  
David Hynek ◽  
Katerina Tmejova ◽  
Jiri Kudr ◽  
Ondrej Zitka ◽  
Lukas Nejdl ◽  
...  
Keyword(s):  
Nucleic Acids

scholarly journals Highly specific enrichment of rare nucleic acids using Thermus thermophilus Argonaute

2018 ◽  
Author(s):  
Jinzhao Song ◽  
Jorrit W. Hegge ◽  
Michael G. Mauk ◽  
Neha Bhagwat ◽  
Jacob E. Till ◽  
...  
Keyword(s):  
Nucleic Acids ◽  
Thermus Thermophilus ◽  
Wild Type ◽  
Single Nucleotide ◽  
Blood Samples ◽  
Complementary Dna ◽  
Enzymatic Amplification ◽  
Dna And Rna ◽  
Rare Alleles

ABSTRACTCharacterization of disease-associated, cell-free nucleic acids (liquid biopsy) provides a powerful, minimally-invasive means for early detection, genotyping, and personalized therapy; but is challenged by alleles of interest differing by single nucleotide from and residing among large abundance of wild-type alleles. We describe a new multiplexed enrichment assay, dubbed NAVIGATER, that utilizes short nucleic acid-guided endonucleases Argonaute (Ago), derived from the bacterium Thermus thermophilus (TtAgo), to specifically cleave complementary DNA and RNA while sparing alleles having single nucleotide mismatches with the guides. NAVIGATER greatly increases the fractions of rare alleles of interest in samples and enhances sensitivity of downstream procedures such ddPCR, sequencing, and clamped enzymatic amplification. We demonstrate 60-fold enrichment of KRAS G12D in blood samples from pancreatic cancer patients and detection of KRAS, EGFR, and BRAF mutants with XNA-PCR at 0.01% fraction.

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