M. Sundaralingam

CH…O hydrogen bonding in biology

Abstract Observations of short CH…O contacts in biological macromolecules, including nucleic acids, proteins and carbohydrates, suggest that these unconventional hydrogen bonds have both a structurally and functionally important role.

Stereochemistry of nucleic acids and their constituents: XIX. Copper binding sites and mechanism of G·C selective denaturation of DNA. Crystal and molecular structures of guanine·copper(II) chloride and cytosine·copper(II) chloride complexes☆☆☆★

Abstract The crystal and molecular structures of the copper(II) chloride complexes of guanine (C5H6N5O·CuCl3·H2O) and cytosine (C4N3H5O·CuCl2) have been determined by the heavy-atom technique and refined by the method of least-squares to R values of 0.052 and 0.078, respectively, using three-dimensional diffractometric data and copper Kα radiation. Crystals of guanine copper(II) chloride are monoclinic space group C2/c, with unit cell constants a = 16.952 A , b = 10.183 A , c = 13.185 A , β = 99.97 °. The calculated and observed densities are 2.015 and 2.024 g cm−3, respectively. Crystals of cytosine copper(II) chloride are monoclinic space group P21/c with unit cell constants a = 8.349 A , b = 13.744 A , c = 13.660 A , β = 128.0 °. Calculated and observed densities are, respectively, 1.90 and 1.96 g cm−3. The preferred copper binding sites were found to be N(3) and O(2) (weak) for cytosine and N(9) for guanine. It is significant that the copper binding to cytosine involves two of the three sites which are normally involved in hydrogen bonding to guanine in the Watson-Crick base pairing scheme. The known preference of copper(II) for binding to G·C pairs rather than A · T pairs is shown to be related to the observed copper(II) binding scheme. From other physico-chemical evidence implicating copper binding to N(7) of guanine, probable complexes of copper and cytosine and/or guanine are suggested which can affect denaturation of DNA.

X-ray analysis of an RNA tetraplex (UGGGGU)(4) with divalent Sr(2+) ions at subatomic resolution (0.61 A).

Four-stranded guanine tetraplexes in RNA have been identified to be involved in crucial biological functions, such as dimerization of retroviral RNA, translational repression, and mRNA turnover. However, the structural basis for these biological processes is still largely unknown. Here we report the RNA tetraplex structure (UGGGGU)4 at ultra-high resolution (0.61 Å). The space group is P4212, and cell constants are a = b = 36.16 Å and c = 74.09 Å. The structure was solved by the multiple-wavelength anomalous dispersion method using a set of three-wavelength data of the isomorphous bromo derivative brUGGGGU and refined to 0.61-Å resolution. Each of the four strands in the asymmetric unit forms a parallel tetraplex with symmetry-related molecules. The tetraplex molecules stack on one another in opposite polarity (head-to-head or tail-to-tail) to form a pseudocontinuous column. All of the 5′-end uridines rotate around the backbone of G2, swing out, and form unique octaplexes with the neighboring G tetraplexes, whereas the 3′-end uridines are stacked-in and form uridine tetrads. All of the bases are anti, and the riboses are in the mixed C2′- and C3′-puckering mode. Strontium ions are observed in every other guanine tetrad plane, sitting on the fourfold axis and associated to the eight O6 atoms of neighboring guanine bases in a bipyramidal-antiprism geometry. The hydrogens are clearly observed in the structure.

The structure of r(UUCGCG) has a 5′-UU-overhang exhibiting Hoogsteen-like trans U•U base pairs

The crystal structure of the RNA fragment, 5′-r(UUCGCG)-3′, has been determined at 1.4 Å resolution by a combination of single isomorphous replacement and molecular search methods. The 3′-terminal CGCG portion of the hexamer engages in Watson–Crick hydrogen bonding while the S′-terminal UU-overhang forms novel Hoogsteen-like UU self-base pairs with the overhang of an adjacent duplex. The U·U pairs display a single conventional hydrogen bond between O4 (U1) and N3 (U8) and a CH–O hydrogen bond between C5-H (U1) and O4(U8), through the Hoogsteen face of the pyrimidine base U1. This unusual arrangement of one of the bases results in a trans U·U pair on antiparallel strands in contrast to the usual cis base pairs. The structure emphasizes the pronounced polymorphism of U·U pairs and has implications for folding of RNA molecules.

Crystal structure of an RNA purine-rich tetraplex containing adenine tetrads: Implications for specific binding in RNA tetraplexes

Purine-rich regions in DNA and RNA may contain both guanines and adenines, which have various biological functions. Here we report the crystal structure of an RNA purine-rich fragment containing both guanine and adenine at 1.4 A resolution. Adenines form an adenine tetrad in the N6-H em leader N7 conformation. Substitution of an adenine tetrad in the guanine tetraplex does not change the global conformation but introduces irregularity in both the hydrogen bonding interaction pattern in the groove and the metal ion binding pattern in the central cavity of the tetraplex. The irregularity in groove binding may be critical for specific binding in tetraplexes. The formation of G-U octads provides a mechanism for interaction in the groove. Ba(2+) ions prefer to bind guanine tetrads, and adenine tetrads can only be bound by Na(+) ions, illustrating the binding selectivity of metal ions for the tetraplex.

Lead Ion Binding and RNA Chain Hydrolysis in Phenylalanine tRNA

Crystalline complexes of yeast phenylalanine tRNA and Lead (II) ion were prepared by soaking pregrown orthorhombic crystals of tRNA in saturated lead chloride solutions. The locations of tightly bound lead ions on the tRNA were determined by difference Fourier methods. There are three major lead binding sites; two of these replace tightly bound magnesium ions in the native tRNA structure. Site I is located in the dihydrouridine loop of the molecule adjacent to phosphate P18 which is specifically cleaved by lead. This is evident from changes observed in the Pb-native difference electron density maps. A possible mechanism for lead ion hydrolysis of the polynucleotide chain is proposed.

The Crystal Structures of Metal Complexes of Nucleic Acids and Their Constituent

(1979). The Crystal Structures of Metal Complexes of Nucleic Acids and Their Constituent. CRC Critical Reviews in Biochemistry: Vol. 6, No. 3, pp. 245-336.

Crystallographic studies of drug-nucleic acid interactions: Proflavine intercalation between the non-complementary base-pairs of cytidilyl-3′,5′-adenosine

Abstract In order to get insights into the binding of dyes and mutagens with denatured and single-stranded nucleic acids and the possible implications in frameshift mutagenesis, a 1:1 complex between the non-self-complementary dinucleoside monophosphate cytidilyl-3′,5′-adenosine (CpA) and proflavine was crystallized. The crystals belong to the tetragonal space group P42212 with cell constants a = b = 19.38(1) A and c = 27.10(1) A . The asymmetric unit contains one CpA, one proflavine and nine water molecules by weight. The structure was determined using Patterson and direct methods and refined to an R-value of 11% using 2454 diffractometer intensities. The non-self-complementary dinucleoside monophosphate CpA forms a selfpaired parallel chain dimer with a proflavine molecule intercalated between the protonated cytosine-cytosine (C · C) pair and the neutral adenine-adenine (A · A) pair. The dimer complex exhibits a right-handed helical twist and an irregular girth. The neutral A · A pair is doubly hydrogen-bonded through the N(6) and N(7) sites (C(1′)C(1′) distance: 10.97(2) A) and the protonated C · C pair is triply hydrogen-bonded with a proton shared between the N(3) sites (C(1′)C(1′) distance: 9.59(2) A). To accommodate the intercalating dye, the sugars of successive nucleotide residues adopt the two fundamental conformations (5′ end: 3′-endo, 3′ end: 2′-endo), the backbone adopts torsion angle values that fluctuate within their preferred conformational domains: the PO bonds (ω, ω′) adopt the characteristic helical (gauche−-gauche−) conformation, the CO bonds (φ, φ′) are both in the trans domain and the C(4′)C(5′) bonds (ψ) are in the gauche+ region. The bases of both residues are disposed in the preferred anti domain with the glycosyl torsion angles (χ) correlated to the puckering mode of the sugar so that the cytidine residue is C(3′)-endo, low χ (12 dg), and the adenosine residue is C(2′)-endo, high χ (84 °). The intercalated proflavine stacks more extensively with the C · C pair than the A · A pair. Between 42-related CpA proflavine units there is a second proflavine which stacks well with both the A · A and the C · C pairs sandwiching it. Both proflavine molecules are positionally disordered. In each of its two disordered sites, the intercalated proflavine forms hydrogen-bonded interactions with only one sugar-phosphate backbone. A total of 26 water sites has been characterized of which only two are fully occupied. These hydration sites are involved in an intricate network of hydrogen bonds with both the dye and CpA and provide insights on the various modes of interactions between water molecules and between water molecules and nucleic acids. The structure of the proflavine-CpA complex shows that intercalation of planar drugs can occur between non-complementary base-pairs. This result can be relevant for understanding the strong binding of acridine dyes to denatured DNA, single-stranded RNA, and single-stranded polynucleotides. Also, the ability of proflayine to promote self-pairs of adenine and cytosine bases could provide a chemical basis for an alternative mechanism of frameshift mutagenesis.

Conformations of cyclic 3′,5′-nucleotides. Effect of the base on the syn-anti conformer distribution

Abstract The furanose and the phosphate rings of cyclic 3′,5′-nucleotides are locked in the 4T3 and chair conformations respectively. The only variable which shows major conformational flexibility in these molecules is the rotation about the glycosyl bond which describes the orientation of the base relative to the sugar-phosphate bicyclic system. The glycosyl torsion angle has been analyzed for cyclic nucleotides with different purine and pyrimidine bases by use of conformational energy calculations. The results indicate that all the pyrimidine bases, U, T and C show a very strong energetic preference for the anti range of conformations. The calculations predict that among cyclic 3′,5′-purine nucleotides cyclic GMP and cyclic IMP favor the syn conformation to the anti by 95:5 and 70:30 respectively, while cyclic AMP shows a preference for the anti conformation to syn by 70:30. Thus the purines show a greater probability for the syn conformation than the pyrimidines in cyclic 3′,5′-nucleotides.

An eight-stranded helical fragment in RNA crystal structure: Implications for tetraplex interaction

Multistranded helical structures in nucleic acids play various functions in biological processes. Here we report the crystal structure of a hexamer, rU(BrdG)r(AGGU),at 1.5 A resolution containing a structural complex of an alternating antiparallel eight-stranded helical fragment that is sandwiched in two tetraplexes. The octaplex is formed by groove binding interaction and base tetrad intercalation between two tetraplexes. Two different forms of octaplexes have been proposed, which display different properties in interaction with proteins and nucleic acids. Adenines form a base tetrad in the novel N6-H em leader N3 conformation and further interact with uridines to form an adenine-uridine octad in the reverse Hoogsteen pairing scheme. The conformational flexibility of adenine tetrad indicates that it can optimize its conformation in different interactions.