NMR studies of DNA duplexes containing alpha-anomeric nucleotides and polarity reversals

1998 ◽  
Vol 76 (2-3) ◽  
pp. 403-410 ◽  
Author(s):  
James M Aramini ◽  
Markus W Germann
Keyword(s):  
Nucleic Acid ◽  
Dynamic Properties ◽  
Dna Duplexes ◽  
Nmr Studies ◽  
Complementary Dna ◽  
Nmr Techniques ◽  
Polarity Reversals ◽  
Alpha Beta ◽  
Shed Light ◽  
Medical Relevance

We present a summary of our research to date on a family of self-complementary DNA decamers containing single alpha-anomeric nucleotides flanked by 3'-3' and 5'-5' phosphodiester linkages from the perspective of the salient NMR techniques employed to shed light on the structural and dynamic properties of these sequences. Research into this class of synthetic alpha-/ beta-oligonucleotides containing mixed strand disposition may have medical relevance given their recently documented efficacy as antisense therapeutics.Key words: nucleic acid NMR, alpha anomeric, polarity reversals.

scholarly journals Synthesis and Physicochemical Properties of [(1R,2S,5R)-2-isopropyl-5-methylcyclohexyloxy]-thiophen-5-yl-substituted Tetrapyrazinoporphyrazine with Magnesium(II) Ion

2021 ◽  
Vol 11 (6) ◽  
pp. 2576
Author(s):  
Sebastian Lijewski ◽  
Jiří Tydlitát ◽  
Beata Czarczynska-Goslinska ◽  
Milan Klikar ◽  
Jadwiga Mielcarek ◽  
...  
Keyword(s):  
Quantum Yield ◽  
Singlet Oxygen ◽  
2D Nmr ◽  
Nmr Studies ◽  
Oxygen Formation ◽  
Nmr Techniques ◽  
Flash Column Chromatography ◽  
Photochemical Stability ◽  
Singlet Oxygen Formation ◽  
Very High

Tetrapyrazinoporphyrazine with peripheral menthol-thiophenyl substituents was synthesized using Linstead conditions and purified by flash column chromatography. The optimized synthetic and purification procedures allowed us to obtain a new macrocycle with 36% yield. Tetrapyrazinoporphyrazine derivative was characterized by UV–Vis and NMR spectroscopy, as well as MS spectrometry. Complex NMR studies using 1D and 2D NMR techniques allowed the analysis of the bulky menthol-thiophenyl substituted periphery of the new macrocycle. Further, photochemical stability and singlet oxygen quantum yield were determined by indirect method with diphenylisobenzofuran. The new tetrapyrazinoporphyrazine revealed low generation of singlet oxygen with a quantum yield of singlet oxygen formation at 2.3% in dimethylformamide. In turn, the macrocycle under irradiation with visible light presented very high stability with quantum yield for photostability of 9.59 × 10−6 in dimethylformamide, which figures significantly exceed the border for its classification as a stable porphyrinoid (10−4–10−5).

NMR studies of exocyclic 1,N2-propanodeoxyguanosine adducts (X) opposite purines in DNA duplexes: protonated X(syn).cntdot.A(anti) pairing (acidic pH) and X(syn).cntdot.G(anti) pairing (neutral pH) at the lesion site

Biochemistry ◽  
1989 ◽  
Vol 28 (13) ◽  
pp. 5647-5657 ◽  
Author(s):  
Michael Kouchakdjian ◽  
Edmund Marinelli ◽  
Xiaolian Gao ◽  
Francis Johnson ◽  
Arthur Grollman ◽  
...  
Keyword(s):  
Acidic Ph ◽  
Dna Duplexes ◽  
Lesion Site ◽  
Nmr Studies ◽  
Neutral Ph

17O-nmr studies of the conformational and dynamic properties of enkephalins in aqueous and organic solutions using selectively labeled analogues

Biopolymers ◽  
1989 ◽  
Vol 28 (1) ◽  
pp. 15-26 ◽  
Author(s):  
Constantinos Sakarellos ◽  
Ioannis P. Gerothanassis ◽  
Nicolaos Birlirakis ◽  
Theodoros Karayannis ◽  
Maria Sakarellos-Daitsiotis ◽  
...  
Keyword(s):  
Dynamic Properties ◽  
Nmr Studies ◽  
17O Nmr ◽  
Organic Solutions

scholarly journals Metal-mediated base pairs in parallel-stranded DNA

2017 ◽  
Vol 13 ◽  
pp. 2671-2681 ◽  
Author(s):  
Jens Müller
Keyword(s):  
Nucleic Acid ◽  
Complex Formation ◽  
Transition Metal Ions ◽  
Dna Duplexes ◽  
Base Pairs ◽  
Experimental Conditions ◽  
Site Specific ◽  
Glycosidic Bonds ◽  
Double Helices ◽  
Significant Extension

In nucleic acid chemistry, metal-mediated base pairs represent a versatile method for the site-specific introduction of metal-based functionality. In metal-mediated base pairs, the hydrogen bonds between complementary nucleobases are replaced by coordinate bonds to one or two transition metal ions located in the helical core. In recent years, the concept of metal-mediated base pairing has found a significant extension by applying it to parallel-stranded DNA duplexes. The antiparallel-stranded orientation of the complementary strands as found in natural B-DNA double helices enforces a cisoid orientation of the glycosidic bonds. To enable the formation of metal-mediated base pairs preferring a transoid orientation of the glycosidic bonds, parallel-stranded duplexes have been investigated. In many cases, such as the well-established cytosine–Ag(I)–cytosine base pair, metal complex formation is more stabilizing in parallel-stranded DNA than in antiparallel-stranded DNA. This review presents an overview of all metal-mediated base pairs reported as yet in parallel-stranded DNA, compares them with their counterparts in regular DNA (where available), and explains the experimental conditions used to stabilize the respective parallel-stranded duplexes.

scholarly journals How can novel microscopic approaches shed light on the function of nucleic acid-based drugs?

2015 ◽  
Vol 7 (13) ◽  
pp. 1623-1625 ◽  
Author(s):  
Daniel Vocelle ◽  
Christina Chan ◽  
S Patrick Walton
Keyword(s):  
Nucleic Acid ◽  
Shed Light

Solid State NMR Studies of the Adsorbed States of Formic Acid on Y Zeolites

1980 ◽  
Vol 3 ◽  
Author(s):  
T. Michael Duncan ◽  
Robert W. Vaughan
Keyword(s):  
Solid State ◽  
Formic Acid ◽  
Solid State Nmr ◽  
Double Resonance ◽  
Chemical Shift Anisotropy ◽  
Surface States ◽  
Cross Polarization ◽  
Nmr Studies ◽  
Y Zeolites ◽  
Nmr Techniques

ABSTRACTSeveral multiple-pulse double-resonance NMR techniques have been applied to isolate and characterize the spectra of the adsorbed states of formic acid on two Y zeolites. The two surface states, bidentatT3 and ynidentate, possess different motional properties and 13C - H cross-polarization techniques may be used to separate the spectra. The 13C chemical shift anisotropy is founa to iorrelate with the symmetry of the formate species. The H spectrum of the carbonyl hydrogen, selectively observed with the dipolardifference method, indicates that this hydrogen becomes more acidic upon adsorption.

scholarly journals NMR studies of DNA duplexes singly cross-linked by different synthetic linkers

1995 ◽  
Vol 23 (23) ◽  
pp. 4827-4835 ◽  
Author(s):  
Serge Altmann ◽  
Alexander M. Labhardt ◽  
Daniel Bur ◽  
Christain Lehmann ◽  
Willi Bannwarth ◽  
...  
Keyword(s):  
Dna Duplexes ◽  
Nmr Studies
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