Modified components of RNA. The molecular and crystal structure of 5-carboxymethylaminomethyl-2-thiouridine (S2cmnm5U)

Structural significance of hypermodified nucleoside 5-carboxymethylaminomethyluridine (cmnm5U) from 'wobble' (34th) position of mitochondrial tRNAs: Molecular modeling and Markov state model studies

A quantum chemical semi-empirical RM1 approach was used to deduce the structural role of hypermodified nucleoside 5-carboxymethylaminomethyluridine 5'-monophosphate (pcmnm⁵U) from 'wobble' (34th) position of mitochondrial tRNAs. The energetically preferred pcmnm⁵U₍₃₄₎ adopted a 'skew' conformation for C5-substituted side chain (-CH₂-NH₂⁺-CH₂-COO^-) moiety that orient towards the 5'-ribose-phosphate backbone, which support 'anti' orientation of glycosyl (χ₃₄) torsion angle. Preferred conformation of pcmnm⁵U₍₃₄₎ was stabilized by O(4) … HC(10), O1P⋯HN(11), O(15) … HN(11), O(15) … HC(10), O4' … HC(6) and O(2) … HC2' hydrogen bonding interactions. The high flexibility of side chain moiety displayed different structural properties for pcmnm⁵U₍₃₄₎. Three different conformations of pcmnm⁵U₍₃₄₎ were observed in molecular dynamics simulations and Markov state model studies. The unmodified uracil revealed 'syn' and 'anti' orientations for glycosyl (χ₃₄) torsion angle that substantiate the role of "-CH₂-NH₂⁺-CH₂-COO^-" moiety in maintaining the 'anti' orientation of pcmnm⁵U₍₃₄₎. The preferred conformation of pcmnm⁵U₍₃₄₎ helps to recognize Guanosine more proficiently than Adenosine from the third position of codons. The role of pcmnm⁵U₍₃₄₎ in tRNA biogenesis paves the way to understand its structural significance in usual mitochondrial metabolism and respiration.

Site-selected incorporation of 5-carboxymethylaminomethyl(-2-thio)uridine into RNA sequences by phosphoramidite chemistry

5-Carboxymethylaminomethyluridine (cmnm(5)U) and 5-carboxymethylaminomethyl-2-thiouridine (cmnm(5)s(2)U) are located at the wobble position in several cytosolic and mitochondrial tRNA sequences. In this paper, we report the first site-selected incorporation of cmnm(5)U and cmnm(5)s(2)U into RNA sequences by phosphoramidite chemistry on a CPG solid support. Trifluoroacetyl and 2-(trimethylsilyl)ethyl were selected for the protection of the amine and carboxyl functions, respectively.

2,4-Dithiouracil: the reproducible H-bonded structural motifs in the complexes with 18-membered crown ethers

2,4-dithiouracil (DTU) forms in the crystals the H-bonded monohydrates of a 1:1:1 ratio with 18-crown-6 (18C6) 1, cis,syn,cis-isomer of dicyclohexano-18-crown-6 (DCH6A) 2, and benzo-18-crown-6 (B18C6) 3, while the anhydrous adduct with cis,anti,cis-isomer of dicyclohexano-18-crown-6 (DCH6B) 4 is of a 2:1 ratio. In 1-3 the components reproducibly alternate in the chains, while in 4 the chains are built of the alternative centrosymmetric dimers of 2,4-dithiouracil and the molecules of the cis,anti,cis-isomer of dicyclohexano-18-crown-6.

Pyrimidinethione nucleosides and their deaza analogues

The methods of preparation, structure, chemical properties and synthetic potentiality of pyrimidinethione nucleosides and their deaza analogues are reported.