Nucleotide Recognition and Phosphate Linkage Hydrolysis at a Lipid Cubic Interface

2010 ◽  
Vol 132 (45) ◽  
pp. 16176-16184 ◽  
Author(s):  
Sergio Murgia ◽  
Sandrina Lampis ◽  
Paolo Zucca ◽  
Enrico Sanjust ◽  
Maura Monduzzi
Keyword(s):  
Phosphate Linkage ◽  
Nucleotide Recognition

The first 3′:5′-cyclic nucleotide–amino acid complex:L-His–cIMP

2012 ◽  
Vol 68 (8) ◽  
pp. o311-o316 ◽  
Author(s):  
Katarzyna Ślepokura
Keyword(s):  
Crystal Structure ◽  
Amino Acid ◽  
Cyclic Nucleotide ◽  
Phosphate Group ◽  
Specific Amino Acid ◽  
Π Stacking ◽  
Cyclic Phosphate ◽  
Nucleotide Recognition ◽  
Group Play ◽  
Phosphate Groups

In the crystal structure of the L-His–cIMP complex,i.e.L-histidinium inosine 3′:5′-cyclic phosphate [systematic name: 5-(2-amino-2-carboxyethyl)-1H-imidazol-3-ium 7-hydroxy-2-oxo-6-(6-oxo-6,9-dihydro-1H-purin-9-yl)-4a,6,7,7a-tetrahydro-4H-1,3,5,2λ5-furo[3,2-d][1,3,2λ5]dioxaphosphinin-2-olate], C6H10N3O2+·C10H10N4O7P−, the Hoogsteen edge of the hypoxanthine (Hyp) base of cIMP and the Hyp face are engaged in specific amino acid–nucleotide (His...cIMP) recognition,i.e.by abutting edge-to-edge and by π–π stacking, respectively. The Watson–Crick edge of Hyp and the cIMP phosphate group play a role in nonspecific His...cIMP contacts. The interactions between the cIMP anions (anti/C3′–endo/trans–gauche/chair conformers) are realized mainly between riboses and phosphate groups. The results for this L-His–cIMP complex, compared with those for the previously reported solvated L-His–IMP crystal structure, indicate a different nature of amino acid–nucleotide recognition and interactions upon the 3′:5′-cyclization of the nucleotide phosphate group.

scholarly journals DNA backbone interactions impact the sequence specificity of DNA sulfur-binding domains: revelations from structural analyses

2020 ◽  
Vol 48 (15) ◽  
pp. 8755-8766 ◽  
Author(s):  
Hao Yu ◽  
Jiayi Li ◽  
Guang Liu ◽  
Gong Zhao ◽  
Yuli Wang ◽  
...  
Keyword(s):  
Structural Analysis ◽  
Sulfur Atom ◽  
Dna Sequences ◽  
Restriction Enzymes ◽  
Sequence Specificity ◽  
Structural Determinants ◽  
Hydrogen Bonding Pattern ◽  
Type Iv ◽  
Phosphate Linkage ◽  
Positively Charged

Abstract The sulfur atom of phosphorothioated DNA (PT-DNA) is coordinated by a surface cavity in the conserved sulfur-binding domain (SBD) of type IV restriction enzymes. However, some SBDs cannot recognize the sulfur atom in some sequence contexts. To illustrate the structural determinants for sequence specificity, we resolved the structure of SBDSpr, from endonuclease SprMcrA, in complex with DNA of GPSGCC, GPSATC and GPSAAC contexts. Structural and computational analyses explained why it binds the above PT-DNAs with an affinity in a decreasing order. The structural analysis of SBDSpr–GPSGCC and SBDSco–GPSGCC, the latter only recognizes DNA of GPSGCC, revealed that a positively charged loop above the sulfur-coordination cavity electrostatically interacts with the neighboring DNA phosphate linkage. The structural analysis indicated that the DNA–protein hydrogen bonding pattern and weak non-bonded interaction played important roles in sequence specificity of SBD protein. Exchanges of the positively-charged amino acid residues with the negatively-charged residues in the loop would enable SBDSco to extend recognization for more PT-DNA sequences, implying that type IV endonucleases can be engineered to recognize PT-DNA in novel target sequences.

Control mechanisms in blood fluidity: role of adenosine triphosphate

1963 ◽  
Vol 18 (6) ◽  
pp. 1105-1110 ◽  
Author(s):  
L. O. Pilgeram ◽  
D. A. Loegering
Keyword(s):  
Energy Metabolism ◽  
Adenosine Triphosphate ◽  
High Energy ◽  
Control Mechanisms ◽  
High Energy Phosphate ◽  
Cellular Mechanisms ◽  
Blood Fluidity ◽  
Phosphate Linkage ◽  
Glass Surfaces

A possible role for cellular energy metabolism in the control of the blood clotting mechanism has been shown. High-energy phosphate was found to strongly inhibit the recalcification time of plasma prepared with siliconized or glass surfaces. The nucleotide, adenosine triphosphate, in crystalline form and chromatographically pure, will inhibit or completely prevent coagulation in vitro. Reactivity is based primarily on the high-energy phosphate linkage and secondarily upon the nucleoside, adenosine. The principal site of action for ATP is on an unidentified precursor of thromboplastin. Available evidence indicates an important role for energy metabolism in the cellular mechanisms which effect a control over thromboplastin generation and its possible thrombotic and arteriosclerotic sequelae. cellular control mechanisms; blood fluidity; thrombosis arteriosclerosis; aging Submitted on July 1, 1963

The Unusual Nucleotide Recognition Properties of the Resistance Enzyme ANT(4′): Inorganic Tri/Polyphosphate as a Substrate for Aminoglycoside Inactivation

2010 ◽  
Vol 16 (29) ◽  
pp. 8635-8640 ◽  
Author(s):  
Julia Revuelta ◽  
Francisco Corzana ◽  
Agatha Bastida ◽  
Juan Luis Asensio
Keyword(s):  
Nucleotide Recognition

Synthesis, physico-chemical and biological properties of DNA and RNA oligonucleotides containing short alkylamino internucleotide bond

2011 ◽  
Vol 76 (12) ◽  
pp. 1471-1486
Author(s):  
Milena Sobczak ◽  
Katarzyna Kubiak ◽  
Magdalena Janicka ◽  
Malgorzata Sierant ◽  
Barbara Mikolajczyk ◽  
...  
Keyword(s):  
Biological Properties ◽  
Protecting Group ◽  
Dna And Rna ◽  
Double Stranded Dna ◽  
Physico Chemical ◽  
Rna Oligomers ◽  
Phosphate Linkage ◽  
Sirna Molecule ◽  
Fetal Bovine ◽  
The Stability

The condensation of the 5′-O-DMT-3′-deoxy-3′-aminothymidine with 3′-O-TBDMS-thymidine- 5′-aldehyde, followed by reduction of the resultant imine derivative and removal of tert-butyldimethylsilyl (TBDMS) protecting group, provided a dimer (denoted as TNHT), which is a congener of dithymidine phosphate with the phosphate linkage 3′-O-P(O)(OH)-O-5′ replaced with an amino group (–NH–). After phosphitylation of the 3′-OH group, the dimer TNHT was introduced (by the standard phosphoramidite approach) into a central part of the nonadecathymidylate. This oligomer exhibited lower affinity to the complementary single and double stranded DNA complements as compared to unmodified T19 oligonucleotide. The cleavage of modified oligomer with the snake venom and calf spleen phosphodiesterases was completely suppressed at the site of modification. RNA oligomers containing the TNHT dimer were used for preparation of siRNA molecules directed towards mRNA of BACE1 (beta-site amyloid precursor protein cleaving enzyme). The presence of the TNHT units at the 3′-ends of the RNA strands of the siRNA molecule (the siRNA itself is an effective gene expression inhibitor for BACE1) preserved the gene silencing activity and improved the stability of the modified siRNA in 10% fetal bovine serum.

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