Structural stability of the photo-responsive DNA duplexes containing one azobenzene via a confined pore

2017 ◽  
Vol 53 (68) ◽  
pp. 9462-9465 ◽  
Author(s):  
Fu-Na Meng ◽  
Zi-Yuan Li ◽  
Yi-Lun Ying ◽  
Shao-Chuang Liu ◽  
Junji Zhang ◽  
...  
Keyword(s):  
Structural Stability ◽  
Dna Duplexes ◽  
Modified Dna

Herein, the structural stability of single azobenzene modified DNA duplexes, including the trans form and cis form, has been examined separately based on their distinguishable unzipping kinetics from the mixture by an α-hemolysin nanopore.

scholarly journals The use of BrCN for assembling modified DNA duplexes and DNA-RNA hybrids; comparison with water-soluble carbodiimide

1991 ◽  
Vol 19 (11) ◽  
pp. 3067-3072 ◽  
Author(s):  
Nina G. Dolinnaya ◽  
Nadejda I. Sokolova ◽  
Dana T. Ashirbekova ◽  
Zoe A. Shabarova
Keyword(s):  
Water Soluble ◽  
Dna Duplexes ◽  
Modified Dna

Efficient enzymatic synthesis of LNA-modified DNA duplexes using KOD DNA polymerase

2009 ◽  
Vol 7 (7) ◽  
pp. 1404 ◽  
Author(s):  
Rakesh N. Veedu ◽  
Birte Vester ◽  
Jesper Wengel
Keyword(s):  
Dna Polymerase ◽  
Enzymatic Synthesis ◽  
Dna Duplexes ◽  
Modified Dna

scholarly journals DNA Duplexes with Hydrophobic Modifications Inhibit Fusion between HIV-1 and Cell Membranes

2013 ◽  
Vol 57 (10) ◽  
pp. 4963-4970 ◽  
Author(s):  
Liang Xu ◽  
Lifeng Cai ◽  
Xueliang Chen ◽  
Xifeng Jiang ◽  
Huihui Chong ◽  
...  
Keyword(s):  
Lipid Bilayers ◽  
Cell Membranes ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
New Drugs ◽  
Heptad Repeat ◽  
Dna Duplexes ◽  
Dna Duplex ◽  
Modified Dna ◽  
Hiv 1

ABSTRACTDiscovery of new drugs for the treatment of AIDS typically possessing unique structures associated with novel mechanisms of action has been of great importance due to the quick drug-resistant mutations of HIV-1 strains. The work presented in this report describes a novel class of DNA duplex-based HIV-1 fusion inhibitors. Hydrophobic groups were introduced into a DNA duplex skeleton either at one end, at both ends, or in the middle. These modified DNA duplexes inhibited fusion between HIV-1 and human cell membranes at micro- or submicromolar concentrations. Respective inhibitors adopted an aptamer pattern instead of a base-pairing interaction pattern. Structure-activity relationship studies of the respective DNA duplexes showed that the rigid and negatively charged DNA skeletons, in addition to the presence of hydrophobic groups, were crucial to the anti-HIV-1 activity of these compounds. A fluorescent resonance energy transfer (FRET)-based inhibitory assay showed that these duplex inhibitors interacted with the primary pocket in the gp41 N-terminal heptad repeat (NHR) instead of interacting with the lipid bilayers.

Structure-Activity Relationships of Cytotoxic Cholesterol-Modified DNA Duplexes

1995 ◽  
Vol 38 (22) ◽  
pp. 4587-4596 ◽  
Author(s):  
Michael W. Reed ◽  
Eugeny Lukhtanov ◽  
Vladimir Gorn ◽  
Deborah D. Lucas ◽  
James H. Zhou ◽  
...  
Keyword(s):  
Dna Duplexes ◽  
Structure Activity Relationships ◽  
Structure Activity ◽  
Modified Dna

scholarly journals Covalently Functionalized DNA Duplexes and Quadruplexes as Hybrid Catalysts in an Enantioselective Friedel–Crafts Reaction

Molecules ◽  
2020 ◽  
Vol 25 (14) ◽  
pp. 3121
Author(s):  
Surjendu Dey ◽  
Andres Jäschke
Keyword(s):  
Secondary Structures ◽  
Catalytic Performance ◽  
Dna Duplexes ◽  
Quadruplex Dna ◽  
Hybrid Catalysts ◽  
Modified Dna ◽  
G Quadruplex ◽  
Dna Secondary Structures ◽  
Dna Strand

The precise site-specific positioning of metal–ligand complexes on various DNA structures through covalent linkages has gained importance in the development of hybrid catalysts for aqueous-phase homogeneous catalysis. Covalently modified double-stranded and G-quadruplex DNA-based hybrid catalysts have been investigated separately. To understand the role of different DNA secondary structures in enantioselective Friedel–Crafts alkylation, a well-known G-quadruplex-forming sequence was covalently modified at different positions. The catalytic performance of this modified DNA strand was studied in the presence and absence of a complementary DNA sequence, resulting in the formation of two different secondary structures, namely duplex and G-quadruplex. Indeed, the secondary structures had a tremendous effect on both the yield and stereoselectivity of the catalyzed reaction. In addition, the position of the modification, the topology of the DNA, the nature of the ligand, and the length of the linker between ligand and DNA were found to modulate the catalytic performance of the hybrid catalysts. Using the optimal linker length, the quadruplexes formed the (−)-enantiomer with up to 65% ee, while the duplex yielded the (+)-enantiomer with up to 62% ee. This study unveils a new and simple way to control the stereochemical outcome of a Friedel–Crafts reaction.

scholarly journals Enzymatic synthesis of hypermodified DNA polymers for sequence-specific display of four different hydrophobic groups

2020 ◽  
Vol 48 (21) ◽  
pp. 11982-11993
Author(s):  
Marek Ondruš ◽  
Veronika Sýkorová ◽  
Lucie Bednárová ◽  
Radek Pohl ◽  
Michal Hocek
Keyword(s):  
Phenyl Group ◽  
High Fidelity ◽  
Dna Duplexes ◽  
Asymmetric Pcr ◽  
Template Strand ◽  
Modified Dna ◽  
Specific Manner ◽  
Dna Backbone ◽  
Modified Oligonucleotide ◽  
Selection Of

Abstract A set of modified 2′-deoxyribonucleoside triphosphates (dNTPs) bearing a linear or branched alkane, indole or phenyl group linked through ethynyl or alkyl spacer were synthesized and used as substrates for polymerase synthesis of hypermodified DNA by primer extension (PEX). Using the alkyl-linked dNTPs, the polymerase synthesized up to 22-mer fully modified oligonucleotide (ON), whereas using the ethynyl-linked dNTPs, the enzyme was able to synthesize even long sequences of >100 modified nucleotides in a row. In PCR, the combinations of all four modified dNTPs showed only linear amplification. Asymmetric PCR or PEX with separation or digestion of the template strand can be used for synthesis of hypermodified single-stranded ONs, which are monodispersed polymers displaying four different substituents on DNA backbone in sequence-specific manner. The fully modified ONs hybridized with complementary strands and modified DNA duplexes were found to exist in B-type conformation (B- or C-DNA) according to CD spectral analysis. The modified DNA can be replicated with high fidelity to natural DNA through PCR and sequenced. Therefore, this approach has a promising potential in generation and selection of hypermodified aptamers and other functional polymers.

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