Frequency and hydrogen bonding of nucleobase homopairs in small molecule crystals.
Nucleic Acids Res
; 48(15): 8302-8319, 2020 09 04.
Article
en En
| MEDLINE
| ID: mdl-32725210
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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1
Colección:
01-internacional
Base de datos:
MEDLINE
Asunto principal:
Conformación Proteica
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Proteínas
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Bases de Datos de Proteínas
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Enlace de Hidrógeno
Idioma:
En
Revista:
Nucleic Acids Res
Año:
2020
Tipo del documento:
Article
País de afiliación:
Polonia