scholarly journals Structural variability of CG-rich DNA 18-mers accommodating double T–T mismatches

2020 ◽  
Vol 76 (12) ◽  
pp. 1233-1243
Author(s):  
Petr Kolenko ◽  
Jakub Svoboda ◽  
Jiří Černý ◽  
Tatsiana Charnavets ◽  
Bohdan Schneider
Keyword(s):  
Crystal Structures ◽  
Bacterial Species ◽  
Crystal Data ◽  
Temperature Dependent ◽  
Base Pairs ◽  
Biologically Relevant ◽  
Dynamic Temperature ◽  
Dna Crystals ◽  
Helical Geometry ◽  
Work Knowledge

Solution and crystal data are reported for DNA 18-mers with sequences related to those of bacterial noncoding single-stranded DNA segments called repetitive extragenic palindromes (REPs). Solution CD and melting data showed that the CG-rich, near-palindromic REPs from various bacterial species exhibit dynamic temperature-dependent and concentration-dependent equilibria, including architectures compatible with not only hairpins, which are expected to be biologically relevant, but also antiparallel duplexes and bimolecular tetraplexes. Three 18-mer oligonucleotides named Hpar-18 (PDB entry 6rou), Chom-18 (PDB entry 6ros) and its brominated variant Chom-18Br (PDB entry 6ror) crystallized as isomorphic right-handed A-like duplexes. The low-resolution crystal structures were solved with the help of experimental phases for Chom-18Br. The center of the duplexes is formed by two successive T–T noncanonical base pairs (mismatches). They do not deform the double-helical geometry. The presence of T–T mismatches prompted an analysis of the geometries of these and other noncanonical pairs in other DNA crystals in terms of their fit to the experimental electron densities (RSCC) and their geometric fit to the NtC (dinucleotide conformational) classes (https://dnatco.datmos.org/). Throughout this work, knowledge of the NtC classes was used to refine and validate the crystal structures, and to analyze the mismatches.

Crystal structures of the chromosomal proteins Sso7d/Sac7d bound to DNA containing T-G mismatched base-pairs

2000 ◽  
Vol 303 (3) ◽  
pp. 395-403 ◽  
Author(s):  
Shaoyu Su ◽  
Yi-Gui Gao ◽  
Howard Robinson ◽  
Yen-Chywan Liaw ◽  
Stephen P Edmondson ◽  
...  
Keyword(s):  
Crystal Structures ◽  
Base Pairs ◽  
Chromosomal Proteins

Strukturen der mehrkernigen nickelthiolato-komplexe [(μ-SMe)2(Ni(MeNHCS2))2] und cyclo-[(μ-SMe)2Ni]6 / Structures of Two Polynuclear Nickel-Thiolato-Complexes [(μ-SMe)2(Ni(MeNHCS2))2] and cyclo-[(μ-SMe)2Ni]6

1994 ◽  
Vol 49 (6) ◽  
pp. 770-772 ◽  
Author(s):  
Klaus Schulbert ◽  
Rainer Mattes
Keyword(s):  
Crystal Structures ◽  
Nickel Acetate ◽  
Monoclinic Space Group ◽  
Crystal Data ◽  
Orthorhombic Space Group ◽  
Space Group ◽  
Dithiocarbamic Acid ◽  
Coordination Spheres ◽  
Partial Degradation ◽  
Acid Esters

The reactions of N-substituted dithiocarbamic acid esters and nickel acetate yield, by partial degradation of the esters, the polynuclear nickel thiolato complexes cyclo-[(μ-SMe)2Ni]6, 1 and [(μ-SMe)2(Ni(MeNHCS2))2, 2. Their crystal structures have been determined. The Ni coordination spheres are comprised of four sulfur atoms in a planar arrangement. 1 is a second, highly symmetrical modification of the already known cyclic hexamer Ni6(SMe)12. In 2 two Ni(PhNHCS2) moieties are bridged to dimers by thiolato groups. Two of these dimers are connected to a tetramer by weak axial Ni-S interactions. Crystal data for 1: monoclinic, space group P21/n, a = 986.1(2), b = 1308.1(3), c = 1228.6(2) pm, β = 96.07(3)°, Z = 2, R = 0.072, Rw = 0.062, 3797 reflections. 2: orthorhombic, space group Pnma, a = 1790.0(4), b = 1806.7(4), c = 934.4(2) pm. Z = 4, R = 0.061, Rw = 0.051, 2079 reflections

Equilibrium studies of the reactions of palladium(ii) bis(imidazolin-2-imine) complexes with biologically relevant nucleophiles. The crystal structures of [(TLtBu)PdCl]ClO4 and [(BLiPr)PdCl2]

2011 ◽  
Vol 40 (24) ◽  
pp. 6515 ◽  
Author(s):  
Jovana Bogojeski ◽  
Ratomir Jelić ◽  
Dejan Petrović ◽  
Eberhardt Herdtweck ◽  
Peter G. Jones ◽  
...  
Keyword(s):  
Crystal Structures ◽  
Equilibrium Studies ◽  
Biologically Relevant

Three-centre C—H...O hydrogen bonds in the DNA minor groove: analysis of oligonucleotide crystal structures

1999 ◽  
Vol 55 (12) ◽  
pp. 2005-2012 ◽  
Author(s):  
Anirban Ghosh ◽  
Manju Bansal
Keyword(s):  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Base Pair ◽  
Minor Groove ◽  
Local Geometry ◽  
Data Sets ◽  
Base Pairs ◽  
Dna Minor Groove ◽  
Close Proximity ◽  
Using Data

AA·TT and GA·TC dinucleotide steps in B-DNA-type oligomeric crystal structures and in protein-bound DNA fragments (solved using data with resolution <2.6 Å) show very small variations in their local dinucleotide geometries. A detailed analysis of these crystal structures reveals that in AA·TT and GA·TC steps the electropositive C2—H2 group of adenine is in very close proximity to the keto O atoms of both the pyrimidine bases in the antiparallel strand of the duplex structure, suggesting the possibility of intra-base pair as well as cross-strand inter-base pair C—H...O hydrogen bonds in the DNA minor groove. The C2—H2...O2 hydrogen bonds in the A·T base pairs could be a natural consequence of Watson–Crick pairing. However, the cross-strand interactions between the bases at the 3′-end of the AA·TT and GA·TC steps obviously arise owing to specific local geometry of these steps, since a majority of the H2...O2 distances in both data sets are considerably shorter than their values in the uniform fibre model (3.3 Å) and many are even smaller than the sum of the van der Waals radii. The analysis suggests that in addition to already documented features such as the large propeller twist of A·T base pairs and the hydration of the minor groove, these C2—H2...O2 cross-strand interactions may also play a role in the narrowing of the minor groove in A-tract regions of DNA and help explain the high structural rigidity and stability observed for poly(dA)·poly(dT).

Lewis-Base Adducts of Group 1B Metal(I) Compounds. XXI The Crystal and Molecular Structures of the Unsolvated Forms of Dibromotris(triphenylphosphine)dicopper(I) and 'step' Tetrabromotetrakis(triphenyl-phosphine)tetracopper(I)

1985 ◽  
Vol 38 (8) ◽  
pp. 1243 ◽  
Author(s):  
JC Dyason ◽  
LM Engelhardt ◽  
C Pakawatchai ◽  
PC Healy ◽  
AH White
Keyword(s):  
Single Crystal ◽  
Crystal Structures ◽  
Molecular Structures ◽  
Lewis Base ◽  
Crystal Data ◽  
X Ray Diffraction ◽  
Triphenyl Phosphine ◽  
X Ray ◽  
Crystal And Molecular Structures

The crystal structures of the title compounds have been determined by single-crystal X-ray diffraction methods at 295 K. Crystal data for (PPh3)2CuBr2Cu(PPh3) (1) show that the crystals are iso-morphous with the previously studied chloro analogue, being monoclinic, P21/c, a 19.390(8), b 9.912(5), c 26.979(9) Ǻ, β 112,33(3)°; R 0.043 for No 3444. Cu( trigonal )- P;Br respectively are 2.191(3); 2.409(2), 2.364(2) Ǻ. Cu(tetrahedral)- P;Br respectively are 2.241(3), 2.249(3); 2.550(2), 2.571(2) Ǻ. Crystals of 'step' [PPh3CuBr]4 (2) are isomorphous with the solvated bromo and unsolvated iodo analogues, being monoclinic, C2/c, a 25.687(10), b 16.084(7), c 17.815(9) Ǻ, β 110.92(3)°; R 0.072 for No 3055. Cu( trigonal )- P;Br respectively are 2.206(5); 2.371(3), 2.427(2) Ǻ. Cu(tetrahedral)- P;Br are 2.207(4); 2.446(2), 2.676(3), 2.515(3) Ǻ.

scholarly journals Frequency and hydrogen bonding of nucleobase homopairs in small molecule crystals

2020 ◽  
Vol 48 (15) ◽  
pp. 8302-8319
Author(s):  
Małgorzata Katarzyna Cabaj ◽  
Paulina Maria Dominiak
Keyword(s):  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Small Molecule ◽  
Base Pair ◽  
Base Pairs ◽  
Standard Pattern ◽  
Planar Structures ◽  
Structural Database ◽  
Derivatives Of

Abstract We used the high resolution and accuracy of the Cambridge Structural Database (CSD) to provide detailed information regarding base pairing interactions of selected nucleobases. We searched for base pairs in which nucleobases interact with each other through two or more hydrogen bonds and form more or less planar structures. The investigated compounds were either free forms or derivatives of adenine, guanine, hypoxanthine, thymine, uracil and cytosine. We divided our findings into categories including types of pairs, protonation patterns and whether they are formed by free bases or substituted ones. We found base pair types that are exclusive to small molecule crystal structures, some that can be found only in RNA containing crystal structures and many that are native to both environments. With a few exceptions, nucleobase protonation generally followed a standard pattern governed by pKa values. The lengths of hydrogen bonds did not depend on whether the nucleobases forming a base pair were charged or not. The reasons why particular nucleobases formed base pairs in a certain way varied significantly.

scholarly journals Length Scale Plasticity: A Review from the Perspective of Dislocation Nucleation

2018 ◽  
Vol 56 (1) ◽  
pp. 21-61 ◽  
Author(s):  
Mahdi Bagheripoor ◽  
Robert Klassen
Keyword(s):  
Crystal Structures ◽  
Mechanical Behaviour ◽  
Dislocation Nucleation ◽  
Temperature Deformation ◽  
Dislocation Loops ◽  
Temperature Dependent ◽  
Size Dependent ◽  
Internal Sources ◽  
New Applications ◽  
Dependent Behaviour

Abstract Sub-micron and nano-size material systems and components are now regularly being fabricated for use in a wide variety of new applications. These systems exhibit mechanical properties that can be drastically different from their macroscopic counterparts and recently much work has focused on the size effects on the mechanical behaviour of materials. Although the size dependent behaviour has been observed in all of the crystal structures, the governing mechanisms have been found to be different. Different theories have been proposed to describe the size dependent behaviour of metallic samples and the governing mechanisms and it is well known that the surface plays an important role in the plasticity of small scales. Some of the theories indicate the importance of surface in nucleating dislocation and some other ones consider the surface importance as its effect on truncating dislocation loops and activation of internal sources. Moreover, recent studies have revealed that while dislocation based deformation in fcc metals is not very sensitive to temperature, deformation is strongly temperature dependent in bcc metals. The effect of orientation is more clear in the size scale behavior of hcp metals. This review covers recent literature that has focused on uniaxial compression of single crystals at the sub-micron and nanometer scale. The fundamental mechanisms governing the size dependent mechanical behaviour of different crystal structures are described. The effect of fabrication process and current experimental techniques for micro and nano-compression are studied as well.

scholarly journals Supramolecular Dimerization in a Polymer Melt from Small-Angle X-ray Scattering and Rheology: A Miscible Model System

Polymers ◽  
2020 ◽  
Vol 12 (4) ◽  
pp. 880
Author(s):  
Mariapaola Staropoli ◽  
Margarita Kruteva ◽  
Jürgen Allgaier ◽  
Andreas Wischnewski ◽  
Wim Pyckhout-Hintzen
Keyword(s):  
Hydrogen Bonding ◽  
Small Angle ◽  
Full Range ◽  
Polymer Melt ◽  
Self Healing ◽  
Temperature Dependent ◽  
Base Pairs ◽  
X Ray ◽  
X Ray Scattering ◽  
Ray Scattering

We present a structural and dynamic study on the simplest supramolecular hetero-association, recently investigated by the authors to prepare architectural homogeneous structures in the melt state, based on the bio-inspired hydrogen-bonding of thymine/diaminotriazine (thy–DAT) base-pairs. In the combination with an amorphous low Tg poly(butylene oxide) (PBO), no micellar structures are formed, which is expected for nonpolar polymers because of noncompatibility with the highly polar supramolecular groups. Instead, a clear polymer-like transient architecture is retrieved. This makes the heterocomplementary thy–DAT association an ideal candidate for further exploitation of the hydrogen-bonding ability in the bulk for self-healing purposes, damage management in rubbers or even the development of easily processable branched polymers with built-in plasticizer. In the present work, we investigate the temperature range from Tg + 20 °C to Tg + 150 °C of an oligomeric PBO using small-angle X-ray scattering (SAXS) and linear rheology on the pure thy and pure DAT monofunctionals and on an equimolar mixture of thy/DAT oligomers. The linear rheology performed at low temperature is found to correspond to fully closed-state dimeric configurations. At intermediate temperatures, SAXS probes the equilibrium between open and closed states of the thy–DAT mixtures. The temperature-dependent association constant in the full range between open and closed H-bonds and an enhancement of the monomeric friction coefficient due to the groups is obtained. The thy–DAT association in the melt is more stable than the DAT–DAT, whereas the thy–thy association seems to involve additional long-lived interactions.

scholarly journals Intrastrand backbone-nucleobase interactions stabilize unwound right-handed helical structures of heteroduplexes of L-aTNA/RNA and SNA/RNA

2020 ◽  
Vol 3 (1) ◽  
Author(s):  
Yukiko Kamiya ◽  
Tadashi Satoh ◽  
Atsuji Kodama ◽  
Tatsuya Suzuki ◽  
Keiji Murayama ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Nucleic Acids ◽  
Crystal Structures ◽  
Prebiotic Chemistry ◽  
Basic Research ◽  
Structural Features ◽  
Helical Structures ◽  
Base Pairs ◽  
Triplex Structure ◽  
Rna And Dna

Abstract Xeno nucleic acids, which are synthetic analogues of natural nucleic acids, have potential for use in nucleic acid drugs and as orthogonal genetic biopolymers and prebiotic precursors. Although few acyclic nucleic acids can stably bind to RNA and DNA, serinol nucleic acid (SNA) and L-threoninol nucleic acid (L-aTNA) stably bind to them. Here we disclose crystal structures of RNA hybridizing with SNA and with L-aTNA. The heteroduplexes show unwound right-handed helical structures. Unlike canonical A-type duplexes, the base pairs in the heteroduplexes align perpendicularly to the helical axes, and consequently helical pitches are large. The unwound helical structures originate from interactions between nucleobases and neighbouring backbones of L-aTNA and SNA through CH–O bonds. In addition, SNA and L-aTNA form a triplex structure via C:G*G parallel Hoogsteen interactions with RNA. The unique structural features of the RNA-recognizing mode of L-aTNA and SNA should prove useful in nanotechnology, biotechnology, and basic research into prebiotic chemistry.

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