Flexibility of the furanose ring in nucleic acids: a compilation of crystal data

A compilation of crystal structure data on deoxyribo- and ribonucleosides and their higher derivatives is presented. The aim of this paper is to highlight the flexibility of deoxyribose and ribose rings. So far, the conformational parameters of nucleic acids constituents of ribose and deoxyribose have not been analysed separately. This paper aims to correlate the conformational parameters with the nature and puckering of the sugar. Deoxyribose puckering occurs in the C2′ endo region while ribose puckering is observed both in the C3′ endo and C2′ endo regions. A few endocyclic and exocyclic bond angles depend on the puckering and the nature of the sugar. The majority of structures have an anti conformation about the glycosyl bond. There appears to be a puckering dependence on the torsion angle about the C4′C5′ bonds. Such stereochemical information is useful in model building studies of polynucleotides and nucleic acids.     

Correlated variations of bond lengths in pseudorotating furanose rings

Correlated variations of bond lengths in pseudorotating furanose rings are investigated by a theoretical method. At first, matrix equations are proposed to determine the spatial coordinates of the ring atoms from the bond lengths, the bond angles, and the pseudorotation parameters. Secondly, a necessary functional form of the variations of the bond lengths of five-membered rings is derived from a consideration of symmetry. Finally, demonstrations are performed on a furanose ring whose bond angle variations have been precisely determined by experimental analyses. The resulting bond length variations are: delta Ri = beta icos(8/5 pi.(i-2)+2P) where delta Ri is the variation of the bond length between atoms i and i+1, P is the pseudorotation phase, and beta i is a negative constant about -0.01 A. These bond length variations are balanced on the apparent strains of the bond lengths and the bond angles.     

Conformational studies of nucleic acids. I. A rapid and direct method for generating furanose coordinates from the pseudorotation angle

The greatest difficulty in modeling a nucleic acid is generating the coordinates of its furanoses. This difficulty arises from constraints imposed by the closed ring geometries of these sugars. We have developed a new method for modeling these furanose rings. Using this method, the coordinates of a sugar can be obtained quickly and unambiguously for any point on the pseudorotational pathway from one parameter: the phase angle of pseudorotation P. The significant difference between this and previous sugar modeling schemes is that here the endocyclic bond lengths of the five-membered sugar ring are allowed to vary a small amount according to simple, explicit, and experimentally reasonable analytic functions of P. The coefficients of these functions follow from the empirical behavior of the endocyclic bond angles and from geometrical constraints due to ring closure. The ability to model the sugars directly from one parameter greatly facilitates carrying out the global conformational studies on nucleic acid constituents which will be attempted in subsequent papers of this series.     

The nucleic acids of Drosophila melanogaster

1. Nucleic acids of whole Drosophila adults were prepared in good yield and substantially free from impurities by new modifications of the phenol method. 2. The average molar base compositions of the DNA (41% of guanine+cytosine) and transfer RNA (60% of guanine+cytosine) resemble those of mammalian nucleic acids; the ribosomal RNA has a DNA-like molar base composition (43% of guanine+cytosine), and it is considered that this is reflected in the lower stability of its secondary structure compared with mammalian ribosomal RNA. 3. The two main ribosomal forms were separated and average base compositions and sedimentation values determined.     

The geometry of the sugar radicals of nucleic acids

Geometric flexibility has been analyzed in nucleotides with 46 (deoxyribofuranose) and 74 (ribofuranose) conformers and tentatively (within most stable conformation of five-element ring in nucleic acids) 4 and 8 geometric isomers, respectively. Possible biological role of geometric isomers of deoxyribofuranose during DNA functioning has been discussed.     

G-四链体核酸的生物学功能

G-四链体是由富含鸟嘌呤的DNA或RNA折叠形成的高级结构。可形成G-四链体的序列在人基因组中广泛分布,涉及DNA复制、端粒维持、基因表达与调控以及遗传不稳定性等过程。研究发现有些化学合成的G-四链体序列也具有生物活性,如核仁素的核酸适体AS1411具有抑制恶性肿瘤增殖活性。G-四链体的生物学功能研究对于恶性疾病的发病机理和靶向治疗,以及设计开发核酸类抗癌药物有重要意义。     

The nucleic acids of some insect viruses

Purine and pyrimidine bases have been estimated from the desoxyribonucleic acids of eleven insect viruses. Their proportions vary in the different species in a balanced way so that the molar ratios adenine:thymine and guanine:cytosine are constant and close to unity, whereas adenine + thymine:guanine + cytosine ranges from 0.71 to 1.87. This ratio is identical for some biologically dissimilar viruses, and no general parallelism is evident between DNA composition and biological relationship. Two different viruses from one host have distinct DNA's.     

The interaction of chromium with nucleic acids

Native and denatured calf thymus DNA, and homopolyribonucleotides were compared with respect to chromium and protein binding after an in vitro incubation with rat liver microsomes, NADPH, and chromium(VI) or chromium(III). A significant amount of chromium bound to DNA when chromium(VI) was incubated with the native or the denatured form of DNA in the presence of microsomes and NADPH. For both native and denatured DNA the amount of protein bound to DNA increased with the amount of chromium bound to DNA. Denatured DNA had much higher amounts of chromium and protein bound than native DNA. There was no interaction between chromium(VI) and either form of DNA in the absence of the complete microsomal reducing system. The binding of chrornium(III) to native or denatured DNA was small and relatively unaffected by the presence of microsomes and NADPH. The binding of chromium and protein to polyriboadenylic acid (poly(A)), polyribocytidylic acid (poly(C), polyri-boguanylic acid (poly(G)) and polyribouridylic acid (poly(U)) was determined after incubation with chromium(VI) in the presence of microsomes and NADPH. The magnitude of chromium and protein binding to the ribo-polymers was found to be poly(G) ? poly(A) ? poly(C) ? poly(U). These results suggest that the metabolism of chromium(VI) is necessary in order for chromium to interact significantly with nucleic acids. The metabolically-produced chromium preferentially binds to the base guanine and results in DNA-protein cross-links. These findings are discussed with respect to the proposed scheme for the carcinogenicity of chromium(VI). Keywords: DNA-protein cross-links — Chromium-guanine interaction-Microsomal reduction of chromate