Base-pairing configurations between purines and pyrimidines in the solid state. 3. Crystal and molecular structure of two 2:1 hydrogen-bonded complexes, 1-methylthymine: 9-ethyl-2,6-diaminopurine and 1-methyl-5-iodouracil: 9-ethyl-2,6-diaminopurine

Bis(2,6-diamino-1H-purin-3-ium) di-μ-croconato-κ3O,O':O'';κ3O:O',O''-bis[tetraaqua(croconato-κ2O,O')neodymium(III)]

The structure of the ionic title compound, (C(5)H(7)N(6))(2)[Nd(2)(C(5)O(5))(4)(H(2)O)(8)], consists of anionic dimers built around an inversion centre and is made up of an Nd(III) cation, two croconate (croco) dianions and four water molecules (plus their inversion images), with two noncoordinated symmetry-related 2,6-diamino-1H-purin-3-ium (Hdap(+)) cations providing charge balance. Each Nd(III) atom is bound to nine O atoms from four water and three croco units. The coordination polyhedron has the form of a rather regular monocapped square antiprism. The croconate anions are regular and the Hdap(+) cation presents a unique, thus far unreported, protonation state. The abundance of hydrogen-bonding donors and acceptors gives rise to a complex packing scheme consisting of dimers interlinked along the three crystallographic directions and defining anionic `cages' where the unbound Hdap(+) cations lodge, linking to the mainframe via (N-H)(Hdap)···O(water/croco) and (O-H)(water)···N(Hdap) interactions.

High fidelity base pairing at the 3'-terminus

Binding target strands with single base selectivity at a terminal position is difficult with natural DNA or RNA hybridization probes. Nature uses a degenerate genetic code that is based on RNA:RNA codon:anticodon duplexes tolerating wobble base pairs at the terminus. The importance of short RNA strands in regulatory processes in the cell make it desirable to develop receptor-like approaches for high fidelity binding, even at the very 3'-terminus of a probe. Here, we report the three-dimensional structure of a DNA duplex with a 3'-terminal 2'-anthraquinoylamido-2'-deoxyuridine (Uaq) residue that was solved by NMR and restrained molecular dynamics. The Uaq residue binds the 5'-terminus of the target strand through a combination of pi-stacking, hydrogen bonding, and interactions in the minor groove. The acylated aminonucleoside is the best molecular cap for 3'-termini reported to date. The Uaq motif assists binding of DNA strands, but is particularly effective in enhancing the affinity for RNA target strands, with a DeltaT(m) in the UV melting point of up to +18.2 degrees C per residue. Increased base pairing selectivity is induced for all sequence motifs tested, even in cases where unmodified duplexes show no preference for the canonical base pair at all. A single mismatched nucleobase facing the 3'-terminus gives DeltaDeltaT(m) values as large as -23.9 degrees C (RNA) or -29.5 degrees C (DNA). The 5'-phosphoramidite of the Uaq cap reported here allows for routine incorporation during automated syntheses.

Interligand interactions controlling the mu-N7,N9-metal bonding of adenine (AdeH) to the N-benzyliminodiacetato(2-) copper(II) chelate and promoting the N9 versus N3 tautomeric proton transfer: molecular and crystal structure of [Cu2(NBzIDA)(2)(H2O)(2)(mu-N7,N9-Ade(N3)H)].(3)H2O

The reaction in water of the N-benzyliminodiacetate-copper(II) chelate ([Cu(NBzIDA)]) and the adenine:thymine base pair complex (AdeH:ThyH) with a Cu/NBzIDA/AdeH/ThyH molar ratio of 2:2:1:1 yields [Cu(2)(NBzIDA)(2)(H(2)O)(2)(mu-N7,N9-Ade(N3)H)].3H(2)O and free ThyH. The compound has been studied by thermal, spectral, and X-ray diffraction methods. In the asymmetric dinuclear complex units both Cu(II) atoms exhibit a square pyramidal coordination, where the four closest donors are supplied by NBzIDA in a mer-tridentate conformation and the N7 or N9 donors of AdeH, which is protonated at N3. The mu-N7,N9 bridge represents a new coordination mode for nonsubstituted AdeH, except for some adeninate(1-)-[methylmercury(II)] derivatives studied earlier. The dinuclear complex is stabilized by the Cu-N7 and Cu-N9 bonds and N6-H(exocyclic)...O(carboxyl) and N3-H(heterocyclic)...O(carboxyl) interligand interactions, respectively. The structure of the new compound differs from that of the mononuclear compound [Cu(NBzIDA)(Ade(N9)H)(H(2)O)].H(2)O, in which the unusual Cu-N3(AdeH) bond is stabilized by a N9-H...O(carboxyl) interligand interaction and where alternating benzyl-AdeH intermolecular pi,pi-stacking interactions produce infinite stacked chains. The possibility for ThyH to be involved in the molecular recognition between [Cu(NBzIDA)] and the AdeH:ThyH base pair is proposed.

Rebek imides and their adenine complexes: preferences for Hoogsteen binding in the solid state and in solution

Rebek imides (3), formed from Kemp's triacid, were developed in the mid-1980's as model receptors for adenine derivatives. We report here the first account of their hydrogen-bonding preferences upon binding 9-ethyladenine (1a) in the solid state. Structural analysis begins with simple imides 3a-e that form discrete dimers, while bis-imide 4 forms ribbon-like structures in the crystalline phase. The hydrogen-bonding interface within each of the representative assemblies features short intermolecular N(3)imide...O(8*)imide* distances (ca. 2.95 A), indicative of two-point hydrogen bonding. Imides 3f-h could be co-crystallized with 1a; single-crystal X-ray analysis of the resulting complexes reveals hydrogen-bonding geometries nearly identical to those observed in nucleobase complexes of adenine and pyrimidine derivatives. Imides 3f and 3g form 2:1 ternary assemblies with 1a; the complex of the former, (3f)2 x 1a, displays both Watson-Crick- and Hoogsteen-type hydrogen bonding, whereas the complex of the latter, (3g)2 x 1a, shows the Hoogsteen motif and imide hydrogen bonding to N(3) of the purine base (N(3)adenine...N(3'')imide = 3.07(1) A). Imide 3h forms a 1:1 complex with 1a (3h x 1a x CHCl3) and displays Hoogsteen binding exclusively. All of the 3 x 1a assemblies show C(adenine)...O(imide) distances (3.38-3.75 A) that are consistent with C-H...O hydrogen bonding. Base-pairing preferences for the Rebek imides are further explored in solution by 1H NMR one-dimensional NOE experiments and by computational means; in all cases the Hoogsteen motif is modestly favored relative to its Watson-Crick counterpart.

Stability and cooperativity of nucleic acid base triplets

Geometries and stabilities of various base triplets have been studied using ab initio quantum chemical methods. Their optimized geometries are determined using the STO-3G basis set, and those of Hoogsteen and reverse Hoogsteen base pairs are evaluated with the 4-31G basis set. Moreover, the preferred hydrogen bond patterns of the bases in triple helices are discussed. A cooperative effect for base pairing in triplets is presented, and it can be either positive or negative. Almost all base triplets that contain Watson-Crick G:C base pairs show a positive cooperativity. Conversely, the base triplets with Watson-Crick A:T base pairs mostly display a negative cooperativity. The interaction energies of base triplets are reported and the relative stabilities of base triplets are found as follows: A+.GC > C+.GC(H) > C+.GC(rH) > G.GC(H) > G.GC(rH) > A.GC > T.AT(rH) > U.AU(H) > U.AT(H) > A.AT > G.AT > T.AT(m) > G.TA(2) > G.TA(1) H and rH denote the Hoogsteen and reverse Hoogsteen positions of the third base that would lead to parallel and antiparallel orientations respectively of the third chain with respect to the Watson-Crick paired purine chain. 'm' denotes the middle pairing scheme, in which the third base hydrogen bonds to both bases of Watson-Crick pair.

Analysis of conformational parameters in nucleic acid fragments. II. Co-crystal complexes of nucleic acid bases

Studies have been made of conformational parameters in co-crystal complexes and compounds of nucleic acid bases in which there is the possibility of formation of hetero-base-pairs. Using published data extracted from the Cambridge structural database, a total of 37 base-pairs were found, of which 25 were hetero-pairs and 12 homo-pairs. These base-pairs were subject to analysis to reveal hydrogen bond parameters, propeller twist, buckle and C1'-C1' separation (or a similar parameter if C1' atoms were not present). Hetero-pairs were found to show larger twists than homo-pairs, the magnitude of twist being unrelated to hydrogen bond parameters or buckle value. The propeller twisting is less pronounced in these nucleic acid bases than in nucleosides, but still has a significant magnitude. Propeller twisting in hetero-pairs is found to be larger than in homo-pairs. Hetero-pairs appear to be formed preferentially in competitive situations.

Simulation of interactions between nucleic acid bases by refined atom-atom potential functions

Energy of interaction between nitrogen bases of nucleic acid has been calculated as a function of parameters determining the mutual position of two bases. Refined atom-atom potential functions are suggested. These functions contain terms proportional to the first (electrostatics), sixth (or tenth for the atoms forming a hydrogen bond) and twelfth (repulsion of all atoms) powers of interatomic distance. Calculations have shown that there are two groups of minima of the base interaction energy. The minima of the first group correspond to coplanar arrangement of the base pairs and hydrogen bond formation. The minima of the second group correspond to the position of bases one above the other in almost parallel planes. There are 28 energy minima corresponding to the formation of coplanar pairs with two (three for the G:C pair) almost linear N-H . . . O and (or) N-H . . . N hydrogen bonds. The position of nitrogen bases paired by two such H-bonds in any crystal of nucleic acid component in polynucleotide complexes and in tRNA is close to the position in one of these minima. Besides, for each pair there are energy minima corresponding to the formation of a single N-H . . . O or N-H . . . N and one C-H . . . O or C-H . . . N hydrogen bond. The form of potential surface in the vicinity of minima has been characterized. The results of calculations agree with the experimental data and with more rigorous calculations based on quantum-mechanical approach.