Crystal structures of deprotonated nucleobases from an expanded DNA alphabet

2016 ◽  
Vol 72 (12) ◽  
pp. 952-959 ◽  
Author(s):  
Mariko F. Matsuura ◽  
Hyo-Joong Kim ◽  
Daisuke Takahashi ◽  
Khalil A. Abboud ◽  
Steven A. Benner
Keyword(s):  
Crystal Structure ◽  
Information System ◽  
Hydrogen Bonding ◽  
Synthetic Biology ◽  
Genetic Information ◽  
Hydrogen Bonding Pattern ◽  
Artificial Dna ◽  
Donor Acceptor ◽  
Crystallization Conditions ◽  
New Form

Reported here is the crystal structure of a heterocycle that implements a donor–donor–acceptor hydrogen-bonding pattern, as found in theZcomponent [6-amino-5-nitropyridin-2(1H)-one] of an artificially expanded genetic information system (AEGIS). AEGIS is a new form of DNA from synthetic biology that has six replicable nucleotides, rather than the four found in natural DNA. Remarkably,Zcrystallizes from water as a 1:1 complex of its neutral and deprotonated forms, and forms a `skinny' pyrimidine–pyrimidine pair in this structure. The pair resembles the known intercalated cytosine pair. The formation of the same pair in two different salts, namely poly[[aqua(μ6-2-amino-6-oxo-3-nitro-1,6-dihydropyridin-1-ido)sodium]–6-amino-5-nitropyridin-2(1H)-one–water (1/1/1)], denoted Z-Sod, {[Na(C5H4N3O3)(H2O)]·C5H5N3O3·H2O}n, and ammonium 2-amino-6-oxo-3-nitro-1,6-dihydropyridin-1-ide–6-amino-5-nitropyridin-2(1H)-one–water (1/1/1), denoted Z-Am, NH4+·C5H4N3O3−·C5H5N3O3·H2O, under two different crystallization conditions suggests that the pair is especially stable. Implications of this structure for the use of this heterocycle in artificial DNA are discussed.

scholarly journals Artificially expanded genetic information system: a new base pair with an alternative hydrogen bonding pattern

2006 ◽  
Vol 34 (21) ◽  
pp. 6095-6101 ◽  
Author(s):  
Zunyi Yang ◽  
Daniel Hutter ◽  
Pinpin Sheng ◽  
A. Michael Sismour ◽  
Steven A. Benner
Keyword(s):  
Information System ◽  
Hydrogen Bonding ◽  
Base Pair ◽  
Genetic Information ◽  
Hydrogen Bonding Pattern ◽  
System A

Single-crystal investigation of L-tryptophan with Z′ = 16

2012 ◽  
Vol 68 (5) ◽  
pp. 549-557 ◽  
Author(s):  
Carl Henrik Görbitz ◽  
Karl Wilhelm Törnroos ◽  
Graeme M. Day
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonding ◽  
Asymmetric Unit ◽  
Hexagonal Symmetry ◽  
Unit Cell Parameters ◽  
Hexagonal Cell ◽  
Cell Parameters ◽  
Complex Disorder ◽  
Hydrogen Bonding Pattern ◽  
Aromatic Interactions

A complex, disorder-free structure in the space group P1 has been established for L-tryptophan, for which no crystal structure has previously been available. The 16 molecules in the asymmetric unit can be divided into two groups of eight; one where the side chains have gauche orientations and one with trans orientations. Molecules within each group have almost identical molecular geometries. The unit-cell parameters mimic a hexagonal cell, but deviations from 90° for the cell angles α = 84.421 (4) and β = 87.694 (4)° give a small tilt that rules out hexagonal symmetry. The hydrogen-bonding pattern resembles that found in the crystal structure of the racemic structure of DL-tryptophan, but a lower density combined with longer hydrogen bonds and inter-aromatic interactions show that the enantiomeric structure is less efficiently packed.

scholarly journals Crystal structure of 4,4′-(disulfanediyl)dibutanoic acid–4,4′-bipyridine (1/1)

2014 ◽  
Vol 70 (9) ◽  
pp. 157-160 ◽  
Author(s):  
Ana María Atria ◽  
Maria Teresa Garland ◽  
Ricardo Baggio
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Distinctive Feature ◽  
Title Compound ◽  
Molecular Shape ◽  
Hydrogen Bonding Pattern ◽  
Linear Chains ◽  
Packing Arrangement ◽  
The Way

4,4′-(Disulfanediyl)dibutanoic acid (dtba) and 4,4′-bipyridine (4,4′-bpy) crystallize in an 1:1 ratio, leading to the title co-crystal with composition C8H14O4S2·C10H8N2. A distinctive feature of the crystal structure is the geometry of the dtba moiety, which appears to be stretched [with a 9.98 (1) Å span between outermost carbons] and acts as an hydrogen-bonding connector, forming linear chains along [-211] with the 4,4′-bpy moiety by way of O—H...N hydrogen bonds and C—H...O interactions. The influence of the molecular shape on the hydrogen-bonding pattern is analysed by comparing the title compound and two other 4,4′-bpy co-crystals with closely related molecules of similar formulation but different geometry, showing the way in which this correlates with the packing arrangement.

scholarly journals Crystal structure of (4-chlorophenyl)[2-(10-hydroxyphenanthren-9-yl)phenanthro[9,10-b]furan-3-yl]methanone

2014 ◽  
Vol 70 (11) ◽  
pp. 355-358
Author(s):  
L. U. Sajitha ◽  
M. Sithambaresan ◽  
Jomon P. Jacob ◽  
M. R. Prathapachandra Kurup
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonding ◽  
Dihedral Angle ◽  
Three Dimensional ◽  
Dihedral Angles ◽  
Supramolecular Architecture ◽  
Intermolecular Hydrogen Bonding ◽  
Compound C ◽  
Hydrogen Bonding Interactions ◽  
Donor Acceptor

In the title compound, C37H21ClO3, the dihedral angle between the two phenanthrene moieties is 57.79 (5)°. The furan and one of the phenanthrene groups are fused in an almost coplanar arrangement [dihedral angle = 5.14 (8)°] and the furan unit makes dihedral angles of 70.27 (11) and 57.58 (8)° with the planes of the phenyl and the second phenanthrene group, respectively. In the crystal, neighbouring molecules are connectedviatwo intermolecular hydrogen-bonding interactions (O—H...O and C—H...O) towards the carbonyl O atom with donor–acceptor distances of 2.824 (2) and 3.277 (3) Å, creating an inversion dimer. A non-classical C—H...Cl interaction [3.564 (2) Å] and three C—H...π interactions, with C...π distances of 3.709 (3), 3.745 (2) and 3.628 (3) Å, connect the molecules, forming a three-dimensional supramolecular architecture in the solid state.

Square network based upon the molecular salt of the tetraprotonated photoproduct rtct-tetrakis(pyridin-4-yl)cyclobutane and the sulfate anion

2021 ◽  
Vol 77 (9) ◽  
Author(s):  
Carlos L. Santana ◽  
Eric W. Reinheimer ◽  
Ryan H. Groeneman
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Crystalline Solid ◽  
Water Molecules ◽  
Sulfate Anion ◽  
Hydrogen Bonding Pattern ◽  
Metastable Form ◽  
Ring Structures ◽  
Molecular Salt

The formation and crystal structure of a hydrated molecular salt that results in a square network is reported. The crystalline solid is based upon the tetraprotonated photoproduct rtct-tetrakis(pyridin-4-yl)cyclobutane (4H- rtct -TPCB)4+ along with two sulfate anions (SO4 2−) and eight waters of hydration, namely, 4,4′,4′′,4′′′-(cyclobutane-1,2,3,4-tetrayl)tetrapyridinium bis(sulfate) octahydrate, C24H24N4 4+·2SO4 2−·8H2O. The fully protonated photoproduct acts as a four-connecting node within the square network by engaging in four charge-assisted N+—H...O hydrogen bonds to the sulfate anion. The observed hydrogen-bonding pattern in this square network is akin to T-silica, which is a metastable form of SiO2. The included water molecules and sulfate anions engage in numerous O—H...O hydrogen bonds to form various hydrogen-bonded ring structures.

scholarly journals Redetermination of nickel(II) formate dihydrate

IUCrData ◽  
2018 ◽  
Vol 3 (3) ◽  
Author(s):  
Matthias Weil
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Structure Determination ◽  
Three Dimensional ◽  
The Other ◽  
Water Molecules ◽  
Hydrogen Bonding Pattern ◽  
Medium Strength

In comparison with the previous structure determination of poly[diaquadi-μ-formato-nickel(II)], [Ni(HCOO)2(H2O)2]n, based on Weissenberg film data [Krogmann & Mattes (1963).Z. Kristallogr.118, 291–302], the current redetermination from modern CCD data revealed the positions of the H atoms, thus making a detailed description of the hydrogen-bonding pattern possible. Both Ni2+cations in the crystal structure are located on inversion centres and are octahedrally coordinated. One Ni2+cation is bound to six O atoms of six formate anions whereas the other Ni2+cation is bound to four O atoms of water molecules and to two formate O atoms. In this way, the formate anions bridge the two types of Ni2+cations into a three-dimensional framework. O—H...O hydrogen bonds of medium strength between water molecules and formate O atoms consolidate the packing.

The surprising pairing of 2-aminoimidazo[1,2-a][1,3,5]triazin-4-one, a component of an expanded DNA alphabet

2019 ◽  
Vol 75 (1) ◽  
pp. 22-28 ◽  
Author(s):  
Roberto Laos ◽  
Christos Lampropoulos ◽  
Steven A. Benner
Keyword(s):  
Crystal Structure ◽  
Genetic Information ◽  
X Ray Diffraction ◽  
Acta Cryst ◽  
Taq Polymerase ◽  
X Ray ◽  
Dna And Rna ◽  
Donor Acceptor ◽  
Natural Living

Synthetic biologists demonstrate their command over natural biology by reproducing the behaviors of natural living systems on synthetic biomolecular platforms. For nucleic acids, this is being done stepwise, first by adding replicable nucleotides to DNA, and then removing its standard nucleotides. This challenge has been met in vitro with `six-letter' DNA and RNA, where the Watson–Crick pairing `concept' is recruited to increase the number of independently replicable nucleotides from four to six. The two nucleobases most successfully added so far are Z and P, which present a donor–donor–acceptor and an acceptor–acceptor–donor pattern, respectively. This pair of nucleobases are part of an `artificially expanded genetic information system' (AEGIS). The Z nucleobase has been already crystallized, characterized, and published in this journal [Matsuura et al. (2016). Acta Cryst. C72, 952–959]. More recently, variants of Taq polymerase have been crystallized with the pair P:Z trapped in the active site. Here we report the crystal structure of the nucleobase 2-aminoimidazo[1,2-a][1,3,5]triazin-4-one (trivially named P) as the monohydrate, C5H5N5O·H2O. The nucleobase P was crystallized from water and characterized by X-ray diffraction. Interestingly, the crystal structure shows two tautomers of P packed in a Watson–Crick fashion that cocrystallized in a 1:1 ratio.

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