Frequency and hydrogen bonding of nucleobase homopairs in small molecule crystals

We used the high resolution and accuracy of theCambridge Structural Database (CSD) to providedetailed information regarding base pairing inter-actions of selected nucleobases. We searched forbase pairs in which nucleobases interact with eachother through two or more hydrogen bonds andform more or less planar structures. The investigatedcompounds were either free forms or derivatives ofadenine, guanine, hypoxanthine, thymine, uracil andcytosine. We divided our findings into categoriesincluding types of pairs, protonation patterns andwhether they are formed by free bases or substitutedones. We found base pair types that are exclusiveto small molecule crystal structures, some that canbe found only in RNA containing crystal structuresand many that are native to both environments. Witha few exceptions, nucleobase protonation generallyfollowed a standard pattern governed by pKavalues.The lengths of hydrogen bonds did not depend onwhether the nucleobases forming a base pair werecharged or not. The reasons why particular nucle-obases formed base pairs in a certain way variedsignificantly.