scholarly journals Incorporation of a metal-mediated base pair into an ATP aptamer – using silver(I) ions to modulate aptamer function

2020 ◽  
Vol 16 ◽  
pp. 2870-2879
Author(s):  
Marius H Heddinga ◽  
Jens Müller
Keyword(s):  
Fluorescence Spectroscopy ◽  
Adenosine Triphosphate ◽  
Base Pair ◽  
Binding Assay ◽  
Binding Pocket ◽  
Pair Formation ◽  
Atp Binding ◽  
Base Pairs ◽  
First Time

For the first time, a metal-mediated base pair has been used to modulate the affinity of an aptamer towards its target. In particular, two artificial imidazole 2’-deoxyribonucleosides (Im) were incorporated into various positions of an established ATP-binding aptamer (ATP, adenosine triphosphate), resulting in the formation of three aptamer derivatives bearing Im:Im mispairs with a reduced ATP affinity. A fluorescence spectroscopy assay and a binding assay with immobilized ATP were used to evaluate the aptamer derivatives. Upon the addition of one Ag(I) ion per mispair, stabilizing Im–Ag(I)–Im base pairs were formed. As a result, the affinity of the aptamer derivative towards ATP is restored again. The silver(I)-mediated base-pair formation was particularly suitable to modulate the aptamer function when the Im:Im mispairs (and hence the resulting metal-mediated base pairs) were located close to the ATP-binding pocket of the aptamer. Being able to trigger the aptamer function opens new possibilities for applications of oligonucleotides.

scholarly journals The structure of metallo-DNA with consecutive thymine–HgII–thymine base pairs explains positive entropy for the metallo base pair formation

2013 ◽  
Vol 42 (6) ◽  
pp. 4094-4099 ◽  
Author(s):  
Hiroshi Yamaguchi ◽  
Jakub Šebera ◽  
Jiro Kondo ◽  
Shuji Oda ◽  
Tomoyuki Komuro ◽  
...  
Keyword(s):  
Base Pair ◽  
Pair Formation ◽  
Positive Entropy ◽  
Base Pairs

scholarly journals Where Quantum Biochemistry Meets Structural Bioinformatics: Excited Conformationally-Tautomeric States of the Classical A·T DNA Base Pair

2021 ◽  
Author(s):  
Ol’ha O. Brovarets’ ◽  
Kostiantyn S. Tsiupa ◽  
Dmytro M. Hovorun
Keyword(s):  
Base Pair ◽  
Biological Significance ◽  
Structural Bioinformatics ◽  
The Novel ◽  
Base Pairs ◽  
Dna Base ◽  
Dna Base Pair ◽  
First Time ◽  
Energy Hypersurface ◽  
Shed Light

This Chapter summarizes recent quantum-chemical (QM) investigations of the novel conformational and tautomeric states on the potential energy hypersurface of the classical A·T/A·U nucleobase pairs. For the first time, it was observed 28 local minima for each base pair excluding enantiomers - planar, non-planar base pairs and structures with wobble geometry. Considered excited conformationally-tautomeric states of the classical A·T DNA base pair have been revealed in the Nucleic Acid Database by structural bioinformatics. These data shed light on the biological significance of the unusual A·T/A·U nucleobase pairs for the functioning of the nucleic acids at the quantum level.

scholarly journals Crystal structure of unusual RNA duplex containing strontium ion binding motif

2014 ◽  
Vol 70 (a1) ◽  
pp. C1378-C1378
Author(s):  
Hiroki Kanazawa ◽  
Jiro Kondo
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Base Pair ◽  
Binding Pocket ◽  
Minor Groove ◽  
Diffusion Method ◽  
Ion Binding ◽  
Binding Motif ◽  
Base Pairs ◽  
Strontium Ion

Crystal structures of several functional non-coding RNAs, such as ribozymes, aptamers, ribosomes and tRNAs, have been reported so far. Unusual structural motifs and non-complementary base pairs are important for their functions. In the present study, we have determined a crystal structure of an unusual RNA duplex containing a strontium ion binding motif. A 19 mer RNA (5'-UUGUCGCUU[Br]CGAAAAAGUC-3') was chemical synthesized and purified by denaturing PAGE. Crystallizations were performed by the sitting-drop vapor diffusion method. The initial phase was solved by the SAD method. Atomic parameters were refined at a resolution of 3.0 Å. The 19 mer RNA forms an unusual antiparallel duplex. At both ends of the duplex, the Watson-Crick G=C and A-U and the Wobble GoU and AoC base pairs are formed. The Wobble C10oA14* pair is available only in acidic condition by protonation of N1 of A14* (* indicates residues of the opposite strand). Two hydrogen bonds, N1-H(A14*)...O2(C10) and N6-H(A14*)...N3(C10), are observed in the base pair. In the center of the duplex, two sheared G11oA13* and G11*oA13 base pairs are formed. The distance between two RNA chains becomes shorter by the GoA base pair and hydrogen bonds between the Watson-Crick edge of G11 and the phosphate group of A12*. Therefore, the central A12 residue cannot make a base pair, but it makes a stacking interaction with A12*. The A12 residue stacks also with A13 of the sheared GoA base pair. As a result, an A13-A12-A12*-A13* stacked column is formed at the minor groove of the duplex, and the G11 base of the sheared GoA base pair is inclined toward the minor groove. By taking such a unique structure, the RNA duplex has a Sr2+ ion binding pocket in the center. A hydrated Sr2+ ion binds to O6 and N7 of G11 and G11*. The Sr2+ ion is surrounded by four phosphate groups of two RNA chains. The Sr2+ ion is tightly captured by eight hydrogen bonds in total.

MercuryII-mediated base pairs in DNA: unexpected behavior in metal ion binding and duplex stability induced by 2′-deoxyuridine 5-substituents

2017 ◽  
Vol 15 (4) ◽  
pp. 870-883 ◽  
Author(s):  
Xiurong Guo ◽  
Sachin A. Ingale ◽  
Haozhe Yang ◽  
Yang He ◽  
Frank Seela
Keyword(s):  
Base Pair ◽  
Metal Ion ◽  
Pair Formation ◽  
Ion Binding ◽  
Side Chains ◽  
Mercury Ions ◽  
Metal Ion Binding ◽  
Base Pairs ◽  
Triple Bonds ◽  
Duplex Stability

DNA accepts small substituents at the 5-position of 2′-deoxyuridine residues within mercury ion mediated dU–HgII–dU base pairs, while triple bonds interact with mercury ions and those with space demanding aromatic side chains block metal ion mediated base pair formation.

Interactions of cytidine with N2-functionalized guanosines and cytidine – cytidine exchange involving a GC pair — NMR and fluorescence spectroscopic study

2010 ◽  
Vol 88 (6) ◽  
pp. 524-532 ◽  
Author(s):  
Sanela Martic ◽  
Gang Wu ◽  
Suning Wang
Keyword(s):  
Fluorescence Quenching ◽  
Fluorescence Spectroscopy ◽  
Spectroscopic Study ◽  
Base Pair ◽  
Visible Region ◽  
Pair Formation ◽  
Organic Media ◽  
Nmr Methods

Two N2-functionalized guanosines by diphenylaminobiphenyl and di(2-pyridyl)aminobiphenyl have been found to act as the effective probes for G–C interactions in organic media. Because of the highly emissive nature of the N2-functionalized guanosines in the visible region, the GC base pair formation event accompanied by distinct fluorescence quenching can be readily monitored by fluorescence spectroscopy. NMR and fluorescence results confirm that the N2-arylguanosines form H-bonded pairs with cytidine, selectively. An unusual exchange pathway between non-bound cytidine and bound cytidine, in the GC pair, has been identified and extensively studied by NMR methods.

Detection of the Glanzmann's Thrombasthenia Mutations in Arab and Iraqi-Jewish Patients by Polymerase Chain Reaction and Restriction Analysis of Blood or Urine Samples

1991 ◽  
Vol 66 (04) ◽  
pp. 500-504 ◽  
Author(s):  
H Peretz ◽  
U Seligsohn ◽  
E Zwang ◽  
B S Coller ◽  
P J Newman
Keyword(s):  
Polymerase Chain Reaction ◽  
Base Pair ◽  
Restriction Analysis ◽  
Urine Samples ◽  
Chain Reaction ◽  
Base Pairs ◽  
Glanzmann’S Thrombasthenia ◽  
Glanzmann's Thrombasthenia ◽  
Base Pair Deletion ◽  
Polymerase Chain

SummarySevere Glanzmann's thrombasthenia is relatively frequent in Iraqi-Jews and Arabs residing in Israel. We have recently described the mutations responsible for the disease in Iraqi-Jews – an 11 base pair deletion in exon 12 of the glycoprotein IIIa gene, and in Arabs – a 13 base pair deletion at the AG acceptor splice site of exon 4 on the glycoprotein IIb gene. In this communication we show that the Iraqi-Jewish mutation can be identified directly by polymerase chain reaction and gel electrophoresis. With specially designed oligonucleotide primers encompassing the mutation site, an 80 base pair segment amplified in healthy controls was clearly distinguished from the 69 base pair segment produced in patients. Patients from 11 unrelated Iraqi-Jewish families had the same mutation. The Arab mutation was identified by first amplifying a DNA segment consisting of 312 base pairs in controls and of 299 base pairs in patients, and then digestion by a restriction enzyme Stu-1, which recognizes a site that is absent in the mutant gene. In controls the 312 bp segment was digested into 235 and 77 bp fragments, while in patients there was no change in the size of the amplified 299 bp segment. The mutation was found in patients from 3 out of 5 unrelated Arab families. Both Iraqi-Jewish and Arab mutations were detectable in DNA extracted from blood and urine samples. The described simple methods of identifying the mutations should be useful for detection of the numerous potential carriers among the affected kindreds and for prenatal diagnosis using DNA extracted from chorionic villi samples.

scholarly journals Crizotinib acts as ABL1 inhibitor combining ATP-binding with allosteric inhibition and is active against native BCR-ABL1 and its resistance and compound mutants BCR-ABL1T315I and BCR-ABL1T315I-E255K

2021 ◽  
Author(s):  
Afsar Ali Mian ◽  
Isabella Haberbosch ◽  
Hazem Khamaisie ◽  
Abed Agbarya ◽  
Larissa Pietsch ◽  
...  
Keyword(s):  
Binding Site ◽  
Kinase Inhibitors ◽  
Therapeutic Potential ◽  
Lymphoblastic Leukemia ◽  
Philadelphia Chromosome ◽  
Binding Pocket ◽  
Atp Binding ◽  
Atp Binding Site ◽  
Lung Cancer Patients

AbstractResistance remains the major clinical challenge for the therapy of Philadelphia chromosome–positive (Ph+) leukemia. With the exception of ponatinib, all approved tyrosine kinase inhibitors (TKIs) are unable to inhibit the common “gatekeeper” mutation T315I. Here we investigated the therapeutic potential of crizotinib, a TKI approved for targeting ALK and ROS1 in non-small cell lung cancer patients, which inhibited also the ABL1 kinase in cell-free systems, for the treatment of advanced and therapy-resistant Ph+ leukemia. By inhibiting the BCR-ABL1 kinase, crizotinib efficiently suppressed growth of Ph+ cells without affecting growth of Ph− cells. It was also active in Ph+ patient-derived long-term cultures (PD-LTCs) independently of the responsiveness/resistance to other TKIs. The efficacy of crizotinib was confirmed in vivo in syngeneic mouse models of BCR-ABL1- or BCR-ABL1T315I-driven chronic myeloid leukemia–like disease and in BCR-ABL1-driven acute lymphoblastic leukemia (ALL). Although crizotinib binds to the ATP-binding site, it also allosterically affected the myristol binding pocket, the binding site of GNF2 and asciminib (former ABL001). Therefore, crizotinib has a seemingly unique double mechanism of action, on the ATP-binding site and on the myristoylation binding pocket. These findings strongly suggest the clinical evaluation of crizotinib for the treatment of advanced and therapy-resistant Ph+ leukemia.

scholarly journals A Molecular Modeling Approach to Identify Potential Antileishmanial Compounds Against the Cell Division Cycle (cdc)-2-Related Kinase 12 (CRK12) Receptor of Leishmania donovani

Biomolecules ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 458
Author(s):  
Emmanuel Broni ◽  
Samuel K. Kwofie ◽  
Seth O. Asiedu ◽  
Whelton A. Miller ◽  
Michael D. Wilson
Keyword(s):  
Natural Products ◽  
Cell Division ◽  
Leishmania Donovani ◽  
Therapeutic Potential ◽  
Neglected Tropical Diseases ◽  
Binding Pocket ◽  
Cell Division Cycle ◽  
World Health ◽  
Atp Binding ◽  
African Flora

The huge burden of leishmaniasis caused by the trypanosomatid protozoan parasite Leishmania is well known. This illness was included in the list of neglected tropical diseases targeted for elimination by the World Health Organization. However, the increasing evidence of resistance to existing antimonial drugs has made the eradication of the disease difficult to achieve, thus warranting the search for new drug targets. We report here studies that used computational methods to identify inhibitors of receptors from natural products. The cell division cycle-2-related kinase 12 (CRK12) receptor is a plausible drug target against Leishmania donovani. This study modelled the 3D molecular structure of the L. donovani CRK12 (LdCRK12) and screened for small molecules with potential inhibitory activity from African flora. An integrated library of 7722 African natural product-derived compounds and known inhibitors were screened against the LdCRK12 using AutoDock Vina after performing energy minimization with GROMACS 2018. Four natural products, namely sesamin (NANPDB1649), methyl ellagic acid (NANPDB1406), stylopine (NANPDB2581), and sennecicannabine (NANPDB6446) were found to be potential LdCRK12 inhibitory molecules. The molecular docking studies revealed two compounds NANPDB1406 and NANPDB2581 with binding affinities of −9.5 and −9.2 kcal/mol, respectively, against LdCRK12 which were higher than those of the known inhibitors and drugs, including GSK3186899, amphotericin B, miltefosine, and paromomycin. All the four compounds were predicted to have inhibitory constant (Ki) values ranging from 0.108 to 0.587 μM. NANPDB2581, NANPDB1649 and NANPDB1406 were also predicted as antileishmanial with Pa and Pi values of 0.415 and 0.043, 0.391 and 0.052, and 0.351 and 0.071, respectively. Molecular dynamics simulations coupled with molecular mechanics Poisson–Boltzmann surface area (MM/PBSA) computations reinforced their good binding mechanisms. Most compounds were observed to bind in the ATP binding pocket of the kinase domain. Lys488 was predicted as a key residue critical for ligand binding in the ATP binding pocket of the LdCRK12. The molecules were pharmacologically profiled as druglike with inconsequential toxicity. The identified molecules have scaffolds that could form the backbone for fragment-based drug design of novel leishmanicides but warrant further studies to evaluate their therapeutic potential.

Development and evaluation of an immunoenzymometric assay for the chicken progesterone receptor

1991 ◽  
Vol 129 (2) ◽  
pp. 189-196 ◽  
Author(s):  
M. K. Bläuer ◽  
P. J. Tuohimaa ◽  
P. J. Vilja
Keyword(s):  
Monoclonal Antibodies ◽  
Small Intestine ◽  
Horseradish Peroxidase ◽  
Progesterone Receptor ◽  
Ligand Binding ◽  
Binding Assay ◽  
Ligand Binding Assay ◽  
Coefficients Of Variation ◽  
First Time ◽  
Determination Range

ABSTRACT A specific and sensitive immunoenzymometric assay (IEMA) was developed for measuring the quantity of chicken progesterone receptor (PR) in tissue cytosol. The assay uses two monoclonal antibodies to the PR. One is used to capture the PR. The second (labelled with biotin) reacts first with the captured receptor and subsequently with avidin-labelled horseradish peroxidase to provide an enzymatic end-point. The method has a determination range from 0·3 to 60 pmol/l. Intra- and interassay coefficients of variation were 3·7% and 9·0% respectively. The assay can be performed with equal results as a rapid (3 h) or an overnight procedure. The IEMA is convenient, especially for signal measurement and the calculation of results. No ultracentrifugation of samples is needed, since the IEMA can be performed on low-speed cytosol samples. Assay results correlated well (r = 0·927) with those obtained by the conventional ligand-binding assay used in our laboratory. Similar results were obtained with the IEMA and the ligand-binding assay after exposure of cytosol samples to increased temperatures: at 20 °C the PR remained stable for the 4-h period examined, whereas at 37 °C almost complete degradation of the PR was observed in 30 min. Being more than 100 times as sensitive as the ligand-binding assay, the IEMA enabled the quantification of PR for the first time in such tissues as the bursa and small intestine even of immature animals. Journal of Endocrinology (1991) 129, 189–196

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