scholarly journals New imidazopyridopyrimidine:naphthyridine base-pairing motif, ImNN:NaOO, consisting of a DAAD:ADDA hydrogen bonding pattern, markedly stabilize DNA duplexes

2011 ◽  
Vol 47 (38) ◽  
pp. 10818 ◽  
Author(s):  
Kazuyuki Kuramoto ◽  
Noriko Tarashima ◽  
Yasuyuki Hirama ◽  
Yusaku Kikuchi ◽  
Noriaki Minakawa ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Dna Duplexes ◽  
Base Pairing ◽  
Hydrogen Bonding Pattern

Evaluation of the 2 NH2A—T Pair in Hybridization, I Synthesis of the DNA/RNA Hybrid Oligomers Containing 2-Aminoadenosines

1988 ◽  
Vol 43 (5) ◽  
pp. 623-630 ◽  
Author(s):  
Kaeko Kikuchi ◽  
Yoshio Taniyama ◽  
Ryuji Marumoto
Keyword(s):  
Hydrogen Bonding ◽  
Dna Structure ◽  
Dna Duplexes ◽  
Cd Spectra ◽  
Base Pairing ◽  
Base Stacking ◽  
Base Pairs ◽  
Nuclease P1 ◽  
Rna Duplexes

Abstract DNA decamers containing 2-aminoadenosine were synthesized. Oligonucleotide duplexes including the 2 NH2A-T base pairs were prepared and their Tm profile examined. Contrary to expectation, elevation of the Tm value by the 2 NH2 group is very small in DNA/RNA duplexes. From the CD spectra measurement, we assume that the distortion of the B-DNA structure caused by scattered DNA/RNA base pairing diminishes the efficient hydrogen bonding and base stacking of the duplexes. It was also found that the DNA duplexes containing 2-aminoadenosine hybrids are considerably resistant to ribonuclease T2 or nuclease P1 digestion.

scholarly journals Probing the Hydrogen-Bonding Environment of Individual Bases in DNA Duplexes with Isotope-Edited Infrared Spectroscopy

2021 ◽  
Author(s):  
Robert J. Fick ◽  
Amy Y. Liu ◽  
Felix Nussbaumer ◽  
Christoph Kreutz ◽  
Atul Rangadurai ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Infrared Spectroscopy ◽  
Dna Duplexes

Studies on the thymine–mercury–thymine base pairing in parallel and anti-parallel DNA duplexes

2015 ◽  
Vol 39 (11) ◽  
pp. 8752-8762 ◽  
Author(s):  
Gaofeng Liu ◽  
Zhiwen Li ◽  
Junfei Zhu ◽  
Yang Liu ◽  
Ying Zhou ◽  
...  
Keyword(s):  
Dna Duplexes ◽  
Base Pairing ◽  
Dna Duplex ◽  
Base Pairs ◽  
Thermal Stabilities

Parallel and anti-parallel T–Hg–T base pairs have different thermal stabilities and conformational influences on DNA duplex structures.

scholarly journals Calculating Distortions of Short DNA Duplexes with Base Pairing Between an Oxidatively Damaged Guanine and a Guanine

Molecules ◽  
2014 ◽  
Vol 19 (8) ◽  
pp. 11030-11044 ◽  
Author(s):  
Masayo Suzuki ◽  
Katsuhito Kino ◽  
Masayuki Morikawa ◽  
Takanobu Kobayashi ◽  
Hiroshi Miyazawa
Keyword(s):  
Dna Duplexes ◽  
Base Pairing

Five pseudopolymorphs of 6-amino-2-thiouracil: absence of N—H...S hydrogen bonds

2012 ◽  
Vol 69 (1) ◽  
pp. 93-100 ◽  
Author(s):  
Wilhelm Maximilian Hützler ◽  
Michael Bolte
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Cambridge Structural Database ◽  
Hydrogen Bonding Pattern ◽  
Crystallization Experiments ◽  
Structural Database ◽  
Thiouracil Derivatives

In order to study the preferred hydrogen-bonding pattern of 6-amino-2-thiouracil, C4H5N3OS, (I), crystallization experiments yielded five different pseudopolymorphs of (I), namely the dimethylformamide disolvate, C4H5N3OS·2C3H7NO, (Ia), the dimethylacetamide monosolvate, C4H5N3OS·C4H9NO, (Ib), the dimethylacetamide sesquisolvate, C4H5N3OS·1.5C4H9NO, (Ic), and two different 1-methylpyrrolidin-2-one sesquisolvates, C4H5N3OS·1.5C5H9NO, (Id) and (Ie). All structures containR21(6) N—H...O hydrogen-bond motifs. In the latter four structures, additionalR22(8) N—H...O hydrogen-bond motifs are present stabilizing homodimers of (I). No type of hydrogen bond other than N—H...O is observed. According to a search of the Cambridge Structural Database, most 2-thiouracil derivatives form homodimers stabilized by anR22(8) hydrogen-bonding pattern, with (i) only N—H...O, (ii) only N—H...S or (iii) alternating pairs of N—H...O and N—H...S hydrogen bonds.

scholarly journals Crystal structures of butyl 2-amino-5-hydroxy-4-(4-nitrophenyl)benzofuran-3-carboxylate and 2-methoxyethyl 2-amino-5-hydroxy-4-(4-nitrophenyl)benzofuran-3-carboxylate

2019 ◽  
Vol 75 (6) ◽  
pp. 880-887 ◽  
Author(s):  
Rosita Diana ◽  
Angela Tuzi ◽  
Barbara Panunzi ◽  
Antonio Carella ◽  
Ugo Caruso
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Molecular Structures ◽  
Antitumoral Activity ◽  
Space Group ◽  
One Dimensional ◽  
Axis Direction ◽  
Hydrogen Bonding Pattern ◽  
Butyl Group

The title benzofuran derivatives 2-amino-5-hydroxy-4-(4-nitrophenyl)benzofuran-3-carboxylate (BF1), C19H18N2O6, and 2-methoxyethyl 2-amino-5-hydroxy-4-(4-nitrophenyl)benzofuran-3-carboxylate (BF2), C18H16N2O7, recently attracted attention because of their promising antitumoral activity. BF1 crystallizes in the space group P\overline{1}. BF2 in the space group P21/c. The nitrophenyl group is inclined to benzofuran moiety with a dihedral angle between their mean planes of 69.2 (2)° in BF1 and 60.20 (6)° in BF2. A common feature in the molecular structures of BF1 and BF2 is the intramolecular N—H...Ocarbonyl hydrogen bond. In the crystal of BF1, the molecules are linked head-to-tail into a one-dimensional hydrogen-bonding pattern along the a-axis direction. In BF2, pairs of head-to-tail hydrogen-bonded chains of molecules along the b-axis direction are linked by O—H...Omethoxy hydrogen bonds. In BF1, the butyl group is disordered over two orientations with occupancies of 0.557 (13) and 0.443 (13).

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