Studies on Tautomeric Forms of Guanine-Cytosine Base Pairs of Nucleic Acids and Their Interactions with Water Molecules

2008 ◽  
Vol 25 (6) ◽  
pp. 733-746 ◽  
Author(s):  
P. Deepa ◽  
P. Kolandaivel
Keyword(s):  
Nucleic Acids ◽  
Water Molecules ◽  
Base Pairs ◽  
Tautomeric Forms

Nucleic acids in two dimensions: layers of base pairs linked by carboxylate

2007 ◽  
Vol 31 (1) ◽  
pp. 21-24 ◽  
Author(s):  
Eva Corral ◽  
Huub Kooijman ◽  
Anthony L. Spek ◽  
Jan Reedijk
Keyword(s):  
Nucleic Acids ◽  
Two Dimensions ◽  
Base Pairs

Neutral 4-phenyl-1-[phenyl(pyridin-2-yl)methylidene]semicarbazide and its salt forms with inorganic anions

2019 ◽  
Vol 75 (1) ◽  
pp. 1-7
Author(s):  
Vinicius Oliveira Araujo ◽  
Bárbara Tirloni ◽  
Lívia Streit ◽  
Vânia Denise Schwade
Keyword(s):  
Solid State ◽  
Spectroscopic Characterization ◽  
Water Molecules ◽  
Keto Form ◽  
Chloride Dihydrate ◽  
Ir And Nmr Spectroscopy ◽  
Tautomeric Forms ◽  
Counter Ions ◽  
Salt Forms ◽  
Good Agreement

Semicarbazones can exist in two tautomeric forms. In the solid state, they are found in the keto form. This work presents the synthesis, structures and spectroscopic characterization (IR and NMR spectroscopy) of four such compounds, namely the neutral molecule 4-phenyl-1-[phenyl(pyridin-2-yl)methylidene]semicarbazide, C19H16N4O, (I), abbreviated as HBzPyS, and three different hydrated salts, namely the chloride dihydrate, C19H17N4O+·Cl−·2H2O, (II), the nitrate dihydrate, C19H17N4O+·NO3 −·2H2O, (III), and the thiocyanate 2.5-hydrate, C19H17N4O+·SCN−·2.5H2O, (IV), of 2-[phenyl({[(phenylcarbamoyl)amino]imino})methyl]pyridinium, abbreviated as [H2BzPyS]+·X −·nH2O, with X = Cl− and n = 2 for (II), X = NO3 − and n = 2 for (III), and X = SCN− and n = 2.5 for (IV), showing the influence of the anionic form in the intermolecular interactions. Water molecules and counter-ions (chloride or nitrate) are involved in the formation of a two-dimensional arrangement by the establishment of hydrogen bonds with the N—H groups of the cation, stabilizing the E isomers in the solid state. The neutral HBzPyS molecule crystallized as the E isomer due to the existence of weak π–π interactions between pairs of molecules. The calculated IR spectrum of the hydrated [H2BzPyS]+ cation is in good agreement with the experimental results.

scholarly journals Nucleic acids in mummified plant seeds: biochemistry and molecular genetics of pre-Columbian maize

1991 ◽  
Vol 58 (3) ◽  
pp. 193-201 ◽  
Author(s):  
Franco Rollo ◽  
Franco Maria Venanzi ◽  
Augusto Amici
Keyword(s):  
Nucleic Acids ◽  
Polyacrylamide Gel Electrophoresis ◽  
Dna Amplification ◽  
Degree Of Polymerization ◽  
Base Pairs ◽  
Plant Seeds ◽  
Maize Seeds ◽  
Maize Populations ◽  
Polymerase Chain ◽  
Seed Dna

SummaryNucleic acids fractions were isolated from pre-Columbian maize seeds and characterized using different approaches such as polyacrylamide gel electrophoresis, anti-DNA antibody binding, HPLC fractionation, molecular hybridization with cloned genes, and DNA amplification by the polymerase chain reaction. The nucleic acids were found to be very depolymerized (≤140 base pairs in length) and composed mainly of ribosomal RNA. Despite the very low amount and degree of polymerization of seed DNA, specific maize nuclear Mul, Mu4, Mu8 and, possibly, Mu5 element components could be detected, thanks to the use of amplification systems as short as 90 bp. The results suggest that evaluation of the relative proportions of Mu-type element components and, possibly, other maize genomic components in single mummified kernels, may offer a new key to the study of ancient maize populations.

Watson-Crick Base Pairs and Nucleic Acids Stability

2010 ◽  
Author(s):  
Luis A Marky ◽  
Hui-Ting Lee ◽  
Angel Garcia
Keyword(s):  
Nucleic Acids ◽  
Base Pairs

Bifunctional Photobinding of Psoralen to Single Stranded Nucleic Acids

1973 ◽  
Vol 28 (7-8) ◽  
pp. 370-375 ◽  
Author(s):  
S Marciani ◽  
M. Terbojevich ◽  
F Dall 'Acqua ◽  
G. Rodighiero
Keyword(s):  
Molecular Weight ◽  
Light Scattering ◽  
Nucleic Acids ◽  
Dilute Solutions ◽  
Base Pairs ◽  
Bacterial Dna ◽  
Disordered Structure ◽  
Concentrated Solution ◽  
Reduced Rate ◽  
Molecular Weight Of Dna

Abstract As psoralen and other furocoumarin derivatives, intercalated between two base pairs of native DNA, under irradiation at 365 nm form inter-strand cross-linkings as a consequence of bifunctional addition, the writers have investigated the ability of psoralen to give such bifunctional photo­ additions, too, with nucleic acids with disordered or partilly disordered structure (denatured DNA and r-RNA). On the basis of fluorimetric, light-scattering, viscosimetric measurements and of the renaturation ability of denatured bacterial DNA, certain results have been obtained. In addition to monofunctional photoadditions, psoralen can give bifunctional binding by irradiation at 365 nm both with denatured DNA and with r-RNA. However, when irradiation of denatured DNA in the presence of psoralen was performed in a concentrated solution (0.4%), the formation of bifunctional additions between two different strands was demonstrated by the increase (50%) of molecular weight of denatured DNA. However, when irradiation of denatured DNA was performed in more dilute solutions (0.1%), the bifunctional photoaddition of psoralen took place producing only bi­ functional additions in the same strand, very probably with the formation of loops, as has been shown by the absence of increase of molecular weight of DNA and by the more restricted structure assumed by the macromolecule, revealed by the light-scattering and viscosimetric measurements. The formation of these bifunctional additions was confirmed by the reduced rate of renaturation shown by denatured bacterial DNA after irradiation in the presence of psoralen. In the case of r-RNA, psoralen, when irradiated can form bifunctional additions only in the same strand.

Binding of metal ions and water molecules to nucleic acid bases: the influence of water molecule coordination to a metal ion on water–nucleic acid base hydrogen bonds

2019 ◽  
Vol 75 (3) ◽  
pp. 301-309
Author(s):  
Jelena M. Andrić ◽  
Ivana M. Stanković ◽  
Snežana D. Zarić
Keyword(s):  
Nucleic Acid ◽  
Hydrogen Bonds ◽  
Nucleic Acids ◽  
Metal Ions ◽  
Quantum Chemical Calculations ◽  
Quantum Chemical ◽  
Metal Ion ◽  
Water Molecules ◽  
Nucleic Acid Bases ◽  
Coordinated Water

The interactions of nucleic acid bases with non-coordinated and coordinated water molecules were studied by analyzing data in the Protein Data Bank (PDB) and by quantum chemical calculations. The analysis of the data in the crystal structures from the PDB indicates that hydrogen bonds involving oxygen or nitrogen atoms of nucleic acid bases and water molecules are shorter when water is bonded to a metal ion. These results are in agreement with the quantum chemical calculations on geometries and interaction energies of hydrogen bonds; the calculations on model systems show that hydrogen bonds of nucleic acid bases with water bonded to a metal ion are stronger than hydrogen bonds with non-coordinated water. These calculated values are similar to the strength of hydrogen bonds between nucleic acid bases. The results presented in this paper may be relevant to understand the role of water molecules and metal ions in the process of replication and stabilization of nucleic acids and also to understand the possible toxicity of metal ion interactions with nucleic acids.

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.

scholarly journals Crystal structure of the DNA sequence d(CGTGAATTCACG)2with DAPI

2017 ◽  
Vol 73 (9) ◽  
pp. 500-504 ◽  
Author(s):  
Hristina I. Sbirkova-Dimitrova ◽  
Boris Shivachev
Keyword(s):  
Crystal Structure ◽  
Crystal Packing ◽  
Minor Groove ◽  
Van Der Waals Interactions ◽  
Water Molecules ◽  
X Ray Diffraction ◽  
Base Pairs ◽  
X Ray ◽  
Dna Molecule ◽  
Dna Fragment

The structure of 4′,6-diamidine-2-phenylindole (DAPI) bound to the synthetic B-DNA oligonucleotide d(CGTGAATTCACG) has been solved in space groupP212121by single-crystal X-ray diffraction at a resolution of 2.2 Å. The structure is nearly isomorphous to that of the previously reported crystal structure of the oligonucleotide d(CGTGAATTCACG) alone. The adjustments in crystal packing between the native DNA molecule and the DNA–DAPI complex are described. DAPI lies in the narrow minor groove near the centre of the B-DNA fragment, positioned over the A–T base pairs. It is bound to the DNA by hydrogen-bonding and van der Waals interactions. Comparison of the two structures (with and without ligand) shows that DAPI inserts into the minor groove, displacing the ordered spine waters. Indeed, as DAPI is hydrophobic it confers this behaviour on the DNA and thus restricts the presence of water molecules.

Sign in / Sign up

Export Citation Format

Share Document