The crystal and molecular structrue of 8-methyladenosine 3′-monophosphate dihydrate

Yasuniwa, Mayumi; Tokuoka, R.; Ogawa, Keizo; Yamagata, Yuriko; Fujii, Satoshi; Tomita, Ken; Limn, W.; Ikehara, Morio

doi:10.1016/0005-2787(79)90507-0

Cited by 13 publications

(6 citation statements)

References 14 publications

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“…A similar observation was made in the structure of 8-bromoxylofuranosyladenine (Birnbaum et al, 1982). On the other hand, in 8-(a-hydroxyisopropyl)adenosine (Birnbaum & Shugar, 1978) and in 8-methyladenosines (Yasuniwa et al, 1979;Silverton et al, 1982) the N(7)-C-(8)-N(9) angle is smaller than in unsubstituted adenosines. These changes presumably result from altered hybridization states of C(8) and depend on whether the substituent donates or withdraws electrons from the ring.…”

Section: Resultssupporting

confidence: 63%

8-Chloroguanosine: solid-state and solution conformations and their biological implications

Birnbaum¹,

Lassota²,

Shugar³

1984

Biochemistry

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The three-dimensional structure of 8-chloroguanosine dihydrate was determined by X-ray crystallography. The crystals belong to the orthorhombic space group P2(1)2(1)2(1), and the cell dimensions are a = 4.871 (1) A, b = 12.040 (1) A, and c = 24.506 (1) A. The structure was determined by direct methods, and least-squares refinement, which included all hydrogen atoms, converged at R = 0.031 for 1599 observed reflections. The conformation about the glycosidic bond is syn with chi CN = -131.1 degrees. The ribose ring has a C(2')-endo/C-(1')-exo (2T1) pucker, and the gauche+ conformation of the -CH2OH side chain is stabilized by an intramolecular O-(5')-H...N(3) hydrogen bond. Conformational analysis by means of 1H NMR spectroscopy showed that, in dimethyl sulfoxide, the sugar ring exhibits a marked preference for the C(2')-endo conformation (approximately 70%) and a conformation about the glycosidic bond predominantly syn (approximately 90%), hence similar to that in the solid state. However, the conformation of the exocyclic 5'-CH2OH group exhibits only a moderate preference for the gauche+ rotamer (approximately 40%), presumably due to the inability to form the intramolecular hydrogen bond to N(3) in a polar medium. The conformational features are examined in relation to the behavior of 8-substituted purine nucleosides in several enzymatic systems, with due account taken of the steric bulk and electronegativities of the 8-substituents.

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Section: Resultssupporting

confidence: 63%

8-Chloroguanosine: solid-state and solution conformations and their biological implications

Birnbaum¹,

Lassota²,

Shugar³

1984

Biochemistry

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“…Steric repulsion with the C8-substituent most significantly occurs between the damaged base and the sugar moiety in the anti conformation and thereby can result in the preferential adoption of the syn conformer. Indeed, even modified nucleotides with smaller substituents at the C8-position, such as 8-methyladenosine 65 and purines halogenated at the C8position, 66 mostly occur in the syn conformation in both the solid state and solution. However, a C8-substituent does not necessarily lock the purine nucleotide in the syn conformation.…”

Section: Chemical Research In Toxicologymentioning

confidence: 99%

Modeling the Conformational Preference of the Carbon-Bonded Covalent Adduct Formed upon Exposure of 2′-Deoxyguanosine to Ochratoxin A

Sharma

Manderville

Wetmore

2013

Chem. Res. Toxicol.

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The conformational flexibility of the C8-linked guanine adduct formed from attachment of ochratoxin A (OTA) was analyzed using a systematic computational approach and models ranging from the nucleobase to the adducted DNA helix. A focus was placed on the influence of the C8-modification of 2'-deoxyguanosine (dG) on the preferred relative arrangement of the nucleobase and the C8-substituent and, more importantly, the anti/syn conformational preference with respect to the glycosidic bond. Although OTA is twisted with respect to the base in the nucleobase model, addition of the deoxyribose sugar induces a further twist and restricts rotation about the C-C linkage due to close contacts between OTA and the sugar. The nucleoside model preferentially adpots a syn orientation (by 10-20 kJ mol(-1) depending on the OTA conformation) due to the presence of an O5'-H···N3 interaction. However, when this hydrogen bond is eliminated, which better mimics the DNA environment, a small (<5 kJ mol(-1)) anti/syn energy difference is predicted. Inclusion of the 5'-monophosphate group leads to an up to 20 kJ mol(-1) preference for the syn (nucleotide) conformation due to stabilizing base-phosphate interactions involving the amino group of guanine. Nevertheless, MD simulations and free energy analysis predict that both syn- and anti-conformations of OTB-dG are equally stable in helices when paired opposite cytosine. These results indicate that the adduct will likely adopt a syn conformation in an isolated nucleoside and nucleotide, while a mixture of syn and anti conformations will be observed in DNA duplexes. Since the syn conformation could stabilize base mismatches upon DNA replication or Z-DNA structures with varied biological outcomes, future computational and experimental work should elucidate the consequences of the conformational preference of this potentially harmful DNA lesion.

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“…This has been found in a number of crystal structures of such analogs (Yasuniwa et al, 1979;Birnbaum & Shugar, 1978).…”

Section: Introductionmentioning

confidence: 93%

The structure of 8-thioxoadenosine monohydrate

Mizuno¹,

Kitamura²,

Miyao³

et al. 1980

Acta Crystallogr Sect B

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The structure of 8-thioxoadenosine monohydrate, C10HtaNsOaS. H20 , has been determined. The crystals are monoclinic, space group P2~, with a = 8.758 (1), b = 6.717(1), c = 11.462 (2) A, /] = 95.22(1) °, Z = 2. The structure was refined to R = 0.048. The conformation about C (4')-C (5') is gauche-trans, and the puckering of the ribose is C(2')-endo-C(3')-exo. The molecule exhibits a syn conformation about the glycosyl bond in spite of the absence of an intramolecular O(5')-H... N(3) hydrogen bond. The bases are stacked into columns, overlapping mainly at the S substituents of adjacent molecules. All the donor atoms are involved in hydrogen bonds, while the S atom acts as a hydrogen-bond acceptor.

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The crystal and molecular structrue of 8-methyladenosine 3′-monophosphate dihydrate

Cited by 13 publications

References 14 publications

8-Chloroguanosine: solid-state and solution conformations and their biological implications

8-Chloroguanosine: solid-state and solution conformations and their biological implications

Modeling the Conformational Preference of the Carbon-Bonded Covalent Adduct Formed upon Exposure of 2′-Deoxyguanosine to Ochratoxin A

The structure of 8-thioxoadenosine monohydrate

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