A duplex DNA model with regular inter-base-pair hydrogen bonds

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).

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Frequency and hydrogen bonding of nucleobase homopairs in small molecule crystals

Nucleic Acids Research ◽

10.1093/nar/gkaa629 ◽

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.

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Isosteric and fluorescent DNA base pair formed by 4-amino-phthalimide and 2,4-diaminopyrimidine: melting, structure, and THz polar solvation dynamics

Physical Chemistry Chemical Physics ◽

10.1039/c5cp06972f ◽

2016 ◽

Vol 18 (9) ◽

pp. 6813-6820 ◽

Cited By ~ 8

Author(s):

L. Dehmel ◽

F. Berndt ◽

M. Weinberger ◽

M. Sajadi ◽

I. Ioffe ◽

...

Keyword(s):

Base Pair ◽

Solvation Dynamics ◽

Duplex Dna ◽

Dna Base ◽

Dna Base Pair ◽

Polar Solvation

An artificial base pair in duplex DNA, formed by 2,4-diaminopyrimidine and fluorescent 4-aminophthalimide C-nucleosides, is characterized spectroscopically, for use in femtosecond solvation dynamics.

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