The influence of Li+, Na+, Mg2+, Ca2+, and Zn2+ ions on the hydrogen bonds of the Watson-Crick base pairs

Biopolymers ◽  
1990 ◽  
Vol 29 (4-5) ◽  
pp. 757-769 ◽  
Author(s):  
Eugen H. S. Anwander ◽  
Michael M. Probst ◽  
Bernd M. Rode
Keyword(s):  
Hydrogen Bonds ◽  
Base Pairs

The Order of Phase Transition of Solvable DNA Melting Models

2003 ◽  
Vol 17 (16) ◽  
pp. 885-896 ◽  
Author(s):  
Su-Long Nyeo ◽  
I-Ching Yang
Keyword(s):  
Phase Transition ◽  
Hydrogen Bonds ◽  
Short Range ◽  
Scaling Laws ◽  
Dna Melting ◽  
Thermodynamic Quantities ◽  
Base Pairs ◽  
Order Of Phase Transition ◽  
Exactly Solvable ◽  
Dna Models

The phase transition of DNA molecules is studied in an exactly solvable formalism with the Morse and Deng–Fan potentials for the interstrand hydrogen bonds of nucleotide base pairs. It is shown that although the two potentials have different short-range behaviors, the thermodynamic quantities of the DNA system in these potentials enjoy the same scaling laws with the associated critical exponents, which are explicitly calculated. These exactly solvable DNA models are shown to exhibit a phase transition of the second order and the results of the analysis agree with previous studies.

Cooperative vibrational properties of hydrogen bonds in Watson–Crick DNA base pairs

2017 ◽  
Vol 41 (20) ◽  
pp. 12104-12109 ◽  
Author(s):  
Yulei Shi ◽  
Wanrun Jiang ◽  
Zhiyuan Zhang ◽  
Zhigang Wang
Keyword(s):  
Hydrogen Bonds ◽  
Vibrational Properties ◽  
Base Pairs ◽  
Dna Base ◽  
Dna Base Pairs

For the AT pair, Symst and Strech peaks further shift toward the red, giving the H-bonds an amplified effect (orange arrows).

Three-centre C—H...O hydrogen bonds in the DNA minor groove: analysis of oligonucleotide crystal structures

1999 ◽  
Vol 55 (12) ◽  
pp. 2005-2012 ◽  
Author(s):  
Anirban Ghosh ◽  
Manju Bansal
Keyword(s):  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Base Pair ◽  
Minor Groove ◽  
Local Geometry ◽  
Data Sets ◽  
Base Pairs ◽  
Dna Minor Groove ◽  
Close Proximity ◽  
Using Data

AA·TT and GA·TC dinucleotide steps in B-DNA-type oligomeric crystal structures and in protein-bound DNA fragments (solved using data with resolution <2.6 Å) show very small variations in their local dinucleotide geometries. A detailed analysis of these crystal structures reveals that in AA·TT and GA·TC steps the electropositive C2—H2 group of adenine is in very close proximity to the keto O atoms of both the pyrimidine bases in the antiparallel strand of the duplex structure, suggesting the possibility of intra-base pair as well as cross-strand inter-base pair C—H...O hydrogen bonds in the DNA minor groove. The C2—H2...O2 hydrogen bonds in the A·T base pairs could be a natural consequence of Watson–Crick pairing. However, the cross-strand interactions between the bases at the 3′-end of the AA·TT and GA·TC steps obviously arise owing to specific local geometry of these steps, since a majority of the H2...O2 distances in both data sets are considerably shorter than their values in the uniform fibre model (3.3 Å) and many are even smaller than the sum of the van der Waals radii. The analysis suggests that in addition to already documented features such as the large propeller twist of A·T base pairs and the hydration of the minor groove, these C2—H2...O2 cross-strand interactions may also play a role in the narrowing of the minor groove in A-tract regions of DNA and help explain the high structural rigidity and stability observed for poly(dA)·poly(dT).

scholarly journals Frequency and hydrogen bonding of nucleobase homopairs in small molecule crystals

2020 ◽  
Vol 48 (15) ◽  
pp. 8302-8319
Author(s):  
Małgorzata Katarzyna Cabaj ◽  
Paulina Maria Dominiak
Keyword(s):  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Small Molecule ◽  
Base Pair ◽  
Base Pairs ◽  
Standard Pattern ◽  
Planar Structures ◽  
Structural Database ◽  
Derivatives Of

Abstract We used the high resolution and accuracy of the Cambridge Structural Database (CSD) to provide detailed information regarding base pairing interactions of selected nucleobases. We searched for base pairs in which nucleobases interact with each other through two or more hydrogen bonds and form more or less planar structures. The investigated compounds were either free forms or derivatives of adenine, guanine, hypoxanthine, thymine, uracil and cytosine. We divided our findings into categories including types of pairs, protonation patterns and whether they are formed by free bases or substituted ones. We found base pair types that are exclusive to small molecule crystal structures, some that can be found only in RNA containing crystal structures and many that are native to both environments. With a few exceptions, nucleobase protonation generally followed a standard pattern governed by pKa values. The lengths of hydrogen bonds did not depend on whether the nucleobases forming a base pair were charged or not. The reasons why particular nucleobases formed base pairs in a certain way varied significantly.

Do C—H...O hydrogen bonds contribute to the stability of nucleic acid base pairs?

1995 ◽  
Vol 51 (2) ◽  
pp. 136-139 ◽  
Author(s):  
G. A. Leonard ◽  
K. McAuley-Hecht ◽  
T. Brown ◽  
W. N. Hunter
Keyword(s):  
Nucleic Acid ◽  
Hydrogen Bonds ◽  
Acid Base ◽  
Base Pairs ◽  
Nucleic Acid Base ◽  
The Stability

DBU induced formation of 8-bromoguanosine dimer with three hydrogen bonds between the GG− base pairs

Tetrahedron ◽  
2012 ◽  
Vol 68 (4) ◽  
pp. 1062-1070 ◽  
Author(s):  
Dijana Saftić ◽  
Biserka Žinić ◽  
Aleksandar Višnjevac
Keyword(s):  
Hydrogen Bonds ◽  
Base Pairs

Internucleotide J-couplings and chemical shifts of the NH···N hydrogen-bonds in the radiation-damaged guanine-cytosine base pairs

2010 ◽  
Vol 32 (6) ◽  
pp. 1159-1169 ◽  
Author(s):  
Huifang Li ◽  
Laibin Zhang ◽  
Li Han ◽  
Wenming Sun ◽  
Yuxiang Bu
Keyword(s):  
Hydrogen Bonds ◽  
Chemical Shifts ◽  
Base Pairs

Supramolecular architectures in two 1:1 cocrystals of 5-fluorouracil with 5-bromothiophene-2-carboxylic acid and thiophene-2-carboxylic acid

2017 ◽  
Vol 73 (6) ◽  
pp. 481-485 ◽  
Author(s):  
Marimuthu Mohana ◽  
Packianathan Thomas Muthiah ◽  
Colin D. McMillen
Keyword(s):  
Solid State ◽  
Carboxylic Acid ◽  
Hydrogen Bonds ◽  
Crystal Structures ◽  
X Ray Diffraction ◽  
Base Pairs ◽  
X Ray ◽  
Supramolecular Architectures ◽  
Acid Acid ◽  
Carboxylic Acid Dimer

In solid-state engineering, cocrystallization is a strategy actively pursued for pharmaceuticals. Two 1:1 cocrystals of 5-fluorouracil (5FU; systematic name: 5-fluoro-1,3-dihydropyrimidine-2,4-dione), namely 5-fluorouracil–5-bromothiophene-2-carboxylic acid (1/1), C5H3BrO2S·C4H3FN2O2, (I), and 5-fluorouracil–thiophene-2-carboxylic acid (1/1), C4H3FN2O2·C5H4O2S, (II), have been synthesized and characterized by single-crystal X-ray diffraction studies. In both cocrystals, carboxylic acid molecules are linked through an acid–acid R 2 2(8) homosynthon (O—H...O) to form a carboxylic acid dimer and 5FU molecules are connected through two types of base pairs [homosynthon, R 2 2(8) motif] via a pair of N—H...O hydrogen bonds. The crystal structures are further stabilized by C—H...O interactions in (II) and C—Br...O interactions in (I). In both crystal structures, π–π stacking and C—F...π interactions are also observed.

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