scholarly journals The nonenzymatic template-directed ligation of oligonucleotides

2006 ◽  
Vol 3 (3) ◽  
pp. 243-249 ◽  
Author(s):  
A. V. Lutay ◽  
E. L. Chernolovskaya ◽  
M. A. Zenkova ◽  
V. V. Vlassov
Keyword(s):  
Metal Ion ◽  
Divalent Cations ◽  
Bound Water ◽  
Transesterification Reaction ◽  
Water Molecules ◽  
Pka Values ◽  
Rna Molecules ◽  
High Reaction ◽  
Cyclic Phosphate ◽  
Cyclic Phosphates

Abstract. The nonenzymatic template-directed ligation of oligonucleotides containing 2', 3'-cyclic phosphate was investigated in the presence of divalent cations. Ligation of the oligonucleotides readily occurred in the presence of Mg2+, Mn2+, Co2+, Zn2+, Pb2+. Efficacy of the metal ion catalysts inversely correlated with pKa values of the metal-bound water molecules. The intermolecular transesterification reaction yielded at least 95metal ion. Relatively high reaction yields (up to 15fragmentation to oligonucleotides with 2',3'-cyclic phosphates, followed by reactions of those oligonucleotides could provide a source of new RNA molecules under prebiotic conditions.

scholarly journals The nonenzymatic template-directed ligation of oligonucleotides

2006 ◽  
Vol 3 (1) ◽  
pp. 1-21 ◽  
Author(s):  
A.V. Lutay ◽  
E. L. Chernolovskaya ◽  
M. A. Zenkova ◽  
V. V. Vlasso
Keyword(s):  
Metal Ion ◽  
Divalent Cations ◽  
Bound Water ◽  
Transesterification Reaction ◽  
Water Molecules ◽  
Pka Values ◽  
Rna Molecules ◽  
Phosphodiester Bonds ◽  
Cyclic Phosphate ◽  
Cyclic Phosphates

Abstract. The nonenzymatic template-directed ligation of oligonucleotides containing 2',3'-cyclic phosphate was investigated in the presence of divalent cations. Ligation of the oligonucleotides readily occurred in the presence of Mg2+, Mn2+, Co2+, Zn2+, Pb2+. Efficacy of the metal ion catalysts inversely correlated with pKa values of the metal-bound water molecules. The intermolecular transesterification reaction yielded at least 95% of 2',5'-phosphodiester bonds independently on the nature of the metal ion. Relatively high reaction yields (up to 15%) suggest, that RNA fragmentation to oligonucleotides with 2',3'-cyclic phosphates, followed by reactions of those oligonucleotides could provide a source of new RNA molecules under prebiotic conditions.

scholarly journals Mg2+ Sensing by an RNA Fragment: Role of Mg2+ Coordinated Water Molecules

2020 ◽  
Author(s):  
Antarip Halder ◽  
Sunil Kumar ◽  
Omar Valsson ◽  
Govardhan Reddy
Keyword(s):  
Metal Ions ◽  
Small Rna ◽  
Metal Ion ◽  
Spatial Organization ◽  
Specific Binding ◽  
Ion Selectivity ◽  
Water Molecules ◽  
Rna Molecules ◽  
Coordinated Water

AbstractRNA molecules selectively bind to specific metal ions to populate their functional active states making it important to understand their source of ion selectivity. In large RNA systems, metal ions interact with the RNA at multiple locations making it difficult to decipher the precise role of ions in folding. To overcome this complexity, we studied the role of different metal ions (Mg2+, Ca2+ and K+) in the folding of a small RNA hairpin motif (5′-ucCAAAga-3′) using unbiased all-atom molecular dynamics simulations. The advantage in studying this small system is that it requires specific binding of a single metal ion to fold to its native state. We find that even for this small RNA, the folding free energy surface (FES) is multidimensional as different metal ions present in the solution can simultaneously facilitate folding. The FES shows that specific binding of a metal ion is indispensable for its folding. We further show that in addition to the negatively charged phosphate groups, spatial organization of electronegative nucleobase atoms drive the site specific binding of the metal ion. Even though the binding site cannot discriminate between different metal ions, RNA folds efficiently only in Mg2+ solution. We show that the rigid network of Mg2+ coordinated water molecules facilitate the formation of important interactions in the transition state. The other metal ions such as K+ and Ca2+ cannot facilitate the formation of such interactions. These results allow us to hypothesize possible metal sensing mechanisms in large metallo-riboswitches and they also provide useful insights for the design of appropriate collective variables for studying large RNA molecules using enhanced sampling methods.

scholarly journals SANS quantification of bound water in water-soluble polymers across multiple concentration regimes

Soft Matter ◽  
2021 ◽  
Author(s):  
Helen Yao ◽  
Bradley D. Olsen
Keyword(s):  
Neutron Scattering ◽  
Small Angle ◽  
Small Angle Neutron Scattering ◽  
Bound Water ◽  
Water Soluble ◽  
Wide Concentration Range ◽  
Water Molecules ◽  
Water Soluble Polymers ◽  
Soluble Polymers

Small-angle neutron scattering is used to measure the number of bound water molecules associating with three polymers over a wide concentration range. Different fitting workflows are evaluated and recommended depending on the concentration regime.

Substrate specificity and affinity of a protein modulated by bound water molecules

Nature ◽  
1989 ◽  
Vol 340 (6232) ◽  
pp. 404-407 ◽  
Author(s):  
F. A. Quiocho ◽  
D. K. Wilson ◽  
N. K. Vyas
Keyword(s):  
Substrate Specificity ◽  
Bound Water ◽  
Water Molecules

Genetically Engineered Pores as Metal Ion Biosensors

1993 ◽  
Vol 330 ◽  
Author(s):  
John Kasianowicz ◽  
Barbara Walker ◽  
Musti Krishnasastry ◽  
Hagan Bayley
Keyword(s):  
Response Time ◽  
Lipid Bilayers ◽  
Metal Ion ◽  
Dynamic Range ◽  
Divalent Cations ◽  
High Sensitivity ◽  
Genetically Engineered ◽  
Great Promise ◽  
Lipid Bilayer Membranes ◽  
Time Dynamic

ABSTRACTWe are adapting proteins that form pores in lipid bilayers for use as components of biosensors. Specifically, we have produced genetically engineered variants of the α hemolysin (αHL) fromStaphylococcusaureus with properties that are sensitive to low concentrations of divalent cations. For example, the pore-forming activity of one mutant (αHL-H5: residues 130–134 inclusive replaced with histidine) is inhibited by Zn2+at concentrations as low as 1 μM, as judged by the reduction in its ability to lyse rabbit red blood cells and to increase the conductance of planar lipid bilayer membranes. When αHL-H5 is added to the aqueous phase bathing one side of a planar membrane, the subsequent addition of 100 μM Zn2+to either side blocks the pores that form. This result suggests that at least part of the mutated region lines the channel lumen. Ca2+and Mg2+do not block the channel and therefore the H5 mutation confers a degree of analyte specificity to the αHL pore. The results suggest that genetically engineered pores have great promise for the rapid and sensitive detection of metal cations and we discuss the merits and potential limitations for their use in this application. Specifically, we examine the issues of selectivity, sensitivity, response time, dynamic range and longevity. Some of these properties are interdependent. For example, the goals of high sensitivity and rapid response time can be in conflict.

scholarly journals Structure and hydrogen bonding of the hydrated selenite and selenate ions in aqueous solution

2014 ◽  
Vol 43 (17) ◽  
pp. 6315-6321 ◽  
Author(s):  
Lars Eklund ◽  
Ingmar Persson
Keyword(s):  
Aqueous Solution ◽  
Hydrogen Bonding ◽  
Free Electron ◽  
Electron Pair ◽  
Bound Water ◽  
Water Molecules ◽  
Hydration Sphere ◽  
Free Electron Pair

The selenite ion has an asymmetric hydration sphere with loosely electrostatically bound water molecules outside the free electron pair.

Properties of the mammalian and yeast metal-ion transporters DCT1 and Smf1p expressed in Xenopus laevis oocytes

2001 ◽  
Vol 204 (6) ◽  
pp. 1053-1061 ◽  
Author(s):  
A. Sacher ◽  
A. Cohen ◽  
N. Nelson
Keyword(s):  
Xenopus Laevis ◽  
Metal Ions ◽  
Metal Ion ◽  
Divalent Cations ◽  
Ion Uptake ◽  
Xenopus Laevis Oocytes ◽  
Ion Transporters ◽  
Divalent Metal Ions ◽  
Transport Pathway ◽  
Metal Ion Uptake

Transition metals are essential for many metabolic processes, and their homeostasis is crucial for life. Metal-ion transporters play a major role in maintaining the correct concentrations of the various metal ions in living cells. Little is known about the transport mechanism of metal ions by eukaryotic cells. Some insight has been gained from studies of the mammalian transporter DCT1 and the yeast transporter Smf1p by following the uptake of various metal ions and from electrophysiological experiments using Xenopus laevis oocytes injected with RNA copies (c-RNA) of the genes for these transporters. Both transporters catalyze the proton-dependent uptake of divalent cations accompanied by a ‘slippage’ phenomenon of different monovalent cations unique to each transporter. Here, we further characterize the transport activity of DCT1 and Smf1p, their substrate specificity and their transport properties. We observed that Zn(2+) is not transported through the membrane of Xenopus laevis oocytes by either transporter, even though it inhibits the transport of the other metal ions and enables protons to ‘slip’ through the DCT1 transporter. A special construct (Smf1p-s) was made to enhance Smf1p activity in oocytes to enable electrophysiological studies of Smf1p-s-expressing cells. 54Mn(2+) uptake by Smf1p-s was measured at various holding potentials. In the absence of Na(+) and at pH 5.5, metal-ion uptake was not affected by changes in negative holding potentials. Elevating the pH of the medium to 6.5 caused metal-ion uptake to be influenced by the holding potential: ion uptake increased when the potential was lowered. Na(+) inhibited metal-ion uptake in accordance with the elevation of the holding potential. A novel clutch mechanism of ion slippage that operates via continuously variable stoichiometry between the driving-force pathway (H(+)) and the transport pathway (divalent metal ions) is proposed. The possible physiological advantages of proton slippage through DCT1 and of Na(+) slippage through Smf1p are discussed.

Extrem asymmetrisch gebundene Wassermoleküle-Kristallstrukturen von Sr(OH)Cl · 4 H2O, Sr(OH)Br · 4 H2O und Ba(OH)I·4 H2O / Extremely Asymmetrically Bound Water Molecules-Crystal Structures of Sr(OH)Cl · 4 H2O, Sr(OH)Br · 4 H2O, and Ba(OH)I·4 H2O

1991 ◽  
Vol 46 (10) ◽  
pp. 1279-1286 ◽  
Author(s):  
Thomas Kellersohn ◽  
Konrad Beckenkamp ◽  
Heinz Dieter Lutz
Keyword(s):  
Crystal Structures ◽  
Bound Water ◽  
Structure Type ◽  
Water Molecules ◽  
Halide Ions ◽  
Weak Hydrogen Bond ◽  
Scanning Calorimetry ◽  
Unknown Structure ◽  
Stretching Vibrations ◽  
Strong Distortion

The crystal structures of isotypic Sr(OH)Cl ·4 H2O, Sr(OH)Br·4 H2O, and Ba(OH)I·4 H2O are reported. The title compounds crystallize in a hitherto unknown structure type, space group PĪ, Z = 2. The final R values obtained are 0.0261, 0.069, and 0.062, respectively. The coordination of the metal ions is monocapped square antiprismatic with 7 H2O, 1 OH- and 1 halide ion. The halide ions separate metal/water/hydroxide layers. Each of the four crystallographically different water molecules serves as donor for one very strong and one very weak hydrogen bond and, hence, is extremely asymmetrically bound. Owing to this strong distortion, the largest one known so far, the OH stretching vibrations of the H2O molecules are intramolecularly decoupled as shown from vibrational spectra. The enthalpies of dehydration obtained from differential scanning calorimetry are reported.

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