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1.
Talanta ; 180: 396-402, 2018 Apr 01.
Article in English | MEDLINE | ID: mdl-29332829

ABSTRACT

From a three-dimensional (3D) metal-organic framework (MOF) of {[Cu(Cmdcp)(phen)(H2O)]2·9H2O}n (1, H3CmdcpBr = N-carboxymethyl-(3,5-dicarboxyl)pyridinium bromide, phen = phenanthroline), a sensitive and selective fluorescence sensor has been developed for the simultaneous detection of ebolavirus conserved RNA sequences and ebolavirus-encoded microRNA-like (miRNA-like) fragment. The results from molecular dynamics simulation confirmed that MOF 1 absorbs carboxyfluorescein (FAM)-tagged and 5(6)-carboxyrhodamine, triethylammonium salt (ROX)-tagged probe ss-DNA (probe DNA, P-DNA) by π…π stacking and hydrogen bonding, as well as additional electrostatic interactions to form a sensing platform of P-DNAs@1 with quenched FAM and ROX fluorescence. In the presence of targeted ebolavirus conserved RNA sequences or ebolavirus-encoded miRNA-like fragment, the fluorophore-labeled P-DNA hybridizes with the analyte to give a P-DNA@RNA duplex and released from MOF 1, triggering a fluorescence recovery. Simultaneous detection of two target RNAs has also been realized by single and synchronous fluorescence analysis. The formed sensing platform shows high sensitivity for ebolavirus conserved RNA sequences and ebolavirus-encoded miRNA-like fragment with detection limits at the picomolar level and high selectivity without cross-reaction between the two probes. MOF 1 thus shows the potential as an effective fluorescent sensing platform for the synchronous detection of two ebolavirus-related sequences, and offer improved diagnostic accuracy of Ebola virus disease.


Subject(s)
Copper/chemistry , Ebolavirus/chemistry , Hemorrhagic Fever, Ebola/virology , Metal-Organic Frameworks/chemistry , MicroRNAs/analysis , RNA, Viral/analysis , Base Sequence , Conserved Sequence , DNA Probes/chemistry , DNA Probes/genetics , Ebolavirus/genetics , Fluoresceins/chemistry , Fluorescent Dyes/chemistry , Humans , MicroRNAs/genetics , Molecular Dynamics Simulation , Nucleic Acid Hybridization , RNA, Viral/genetics , Spectrometry, Fluorescence/methods
2.
J Inorg Biochem ; 177: 138-142, 2017 12.
Article in English | MEDLINE | ID: mdl-28961476

ABSTRACT

We report herein five sensing platforms for the detection of five gastric cancer associated microRNAs (miRNAs). The sensing platforms are hybrids formed from a water-stable metal organic framework (MOF) {[Cu(dcbb)2(H2O)2]·10H2O}n (1, H2dcbbBr=1-(3,5-dicarboxybenzyl)-4,4'-bipyridinium bromide), respectively with five carboxyfluorescein (FAM) labeled probe single-stranded DNA (probe ss-DNA, denoted as P-DNA). Within the hybrid, MOF 1 tightly interacts with the P-DNA through electrostatic and/or π-stacking interactions and results in fluorescence quenching of FAM via a photo-induced electron transfer (PET) process. In the presence of the complementary target miRNAs miR-185, miR-20a, miR-92b, miR-25 and miR-210, which are expressed abnormally in the plasma of gastric carcinoma patients, P-DNA is released from the surface of MOF 1 ascribed to the stronger base pair matching, leading to the FAM fluorescence recovery. Each P-DNA@1 system is effective and reliable for the detection of its complementary target miRNA with the detection limits from 91 to 559pM, and is not interfered by other four miRNA sequences.


Subject(s)
DNA Probes/pharmacology , Metal-Organic Frameworks/pharmacology , MicroRNAs/analysis , Stomach Neoplasms/genetics , Base Sequence , Biosensing Techniques/methods , DNA Probes/chemistry , DNA Probes/genetics , Fluoresceins/chemistry , Fluoresceins/pharmacology , Humans , Limit of Detection , Metal-Organic Frameworks/chemistry , MicroRNAs/genetics , Nucleic Acid Hybridization , Stomach Neoplasms/diagnosis
3.
Anal Chim Acta ; 922: 55-63, 2016 May 30.
Article in English | MEDLINE | ID: mdl-27154832

ABSTRACT

Coordination reaction of a known three-dimensional (3D) polymer precursor {Na3[Na9(Cbdcp)6(H2O)18]}n (A, Cbdcp = N-(4-carboxybenzyl)-(3,5-dicarboxyl)pyridinium) with Zn(NO3)2·6H2O in H2O or H2O/DMF at 100 °C and in the presence of aspirin, 5-fluorouracil (5-FU) as modulators, trans-1,2-bis(4-pyridyl)ethylene (bpe) or 1,2-bis(4-pyridyl)ethane (bpea) as ancillary ligands afforded six novel Zn(II)-based metal-organic frameworks (MOFs), that is, {[Zn(Cbdcp)(H2O)3]·H2O}n (1, 1D zigzag chain), {[Zn(HCbdcp)2]·H2O}n (2, 2D sheet), {[Zn(Cbdcp)(bpe)1/2]·2H2O}n (3, 3D polymer), {[Zn(Cbdcp)(bpe)1/2]·2H2O}n (4, 2D network), {[Zn(Cbdcp)(bpea)1/2]·2H2O}n (5, 3D polymer) and {[Zn(Cbdcp)(bpea)1/2]·2H2O}n (6, 2D network). Among them, compound 2 contains aromatic rings, positively charged pyridinium, Zn(2+) cation centers and carboxylic acid groups lined up on the 2D sheet structure with a certain extended surface exposure. The unique structure of 2 facilitates effective association with carboxyfluorescein (FAM) labeled probe single stranded DNA (probe ss-DNA, delineates as P-DNA) to yield a P-DNA@2 system, and leads to fluorescence quenching of FAM via a photoinduced electron transfer process. The P-DNA@2 system is effective and reliable for the detection of human immunodeficiency virus 1 ds-DNA (HIV ds-DNA) sequences and capable of distinguishing complementary HIV ds-DNA from mismatched target sequences with the detection limit as low as 10 pM (S/N = 3).


Subject(s)
DNA, Viral/analysis , HIV-1/genetics , Zinc/chemistry , Coordination Complexes/chemistry , Powder Diffraction , Spectrum Analysis/methods , Thermogravimetry
4.
Dalton Trans ; 45(12): 5092-100, 2016 Mar 28.
Article in English | MEDLINE | ID: mdl-26883749

ABSTRACT

Polymorphic compounds {[Cu(dcbb)2(H2O)2]·10H2O}n (2, 1D chain), [Cu(dcbb)2]n (3, 2D layer) and their co-crystal {[Cu(dcbb)2(H2O)][Cu(dcbb)2]2}n (4) have been prepared from the coordination reaction of a 2D polymer [Na(dcbb)(H2O)]n (1, H2dcbbBr = 1-(3,5-dicarboxybenzyl)-4,4'-bipyridinium bromide) with Cu(NO3)2·3H2O at different temperatures in water. Compounds 2-4 have an identical metal-to-ligand stoichiometric ratio of 1 : 2, but absolutely differ in structure. Compound 3 features a 2D layer structure with aromatic rings, positively charged pyridinium and free carboxylates on its surface, promoting electrostatic, π-stacking and/or hydrogen-bonding interactions with the carboxyfluorescein (FAM) labeled probe single-stranded DNA (probe ss-DNA, delineates as P-DNA). The resultant P-DNA@3 system facilitated fluorescence quenching of FAM via a photoinduced electron transfer process. The P-DNA@3 system functions as an efficient fluorescent sensor selective for HIV double-stranded DNA (HIV ds-DNA) due to the formation of a rigid triplex structure with the recovery of FAM fluorescence. The system reported herein also distinguishes complementary HIV ds-DNA from mismatched target DNA sequences with the detection limit of 1.42 nM.


Subject(s)
DNA/chemistry , HIV/genetics , Coordination Complexes/chemical synthesis , Coordination Complexes/chemistry , Copper/chemistry , Crystallography, X-Ray , DNA/metabolism , Fluoresceins/chemistry , Hydrogen Bonding , Molecular Conformation , Polymers/chemistry , Spectrometry, Fluorescence
5.
Chem Commun (Camb) ; 52(1): 132-5, 2016 Jan 04.
Article in English | MEDLINE | ID: mdl-26502791

ABSTRACT

We herein report a water-stable 3D dysprosium-based metal-organic framework (MOF) that can non-covalently interact with probe ss-DNA. The formed system can serve as an effective fluorescence sensing platform for the detection of complementary Ebolavirus RNA sequences with the detection limit of 160 pM.


Subject(s)
Dysprosium/chemistry , Ebolavirus/isolation & purification , Fluorescent Dyes/chemistry , Hemorrhagic Fever, Ebola/diagnosis , Organometallic Compounds/chemistry , RNA, Viral/analysis , Base Sequence , Crystallography, X-Ray , DNA Probes/chemistry , DNA Probes/genetics , Ebolavirus/genetics , Hemorrhagic Fever, Ebola/virology , Humans , Limit of Detection , Models, Molecular , RNA, Viral/genetics , Spectrometry, Fluorescence/methods , Water/chemistry
6.
Anal Chem ; 87(24): 12206-14, 2015 Dec 15.
Article in English | MEDLINE | ID: mdl-26619043

ABSTRACT

We herein report a water-stable three-dimensional Cu-based metal-organic framework (MOF) 1 supported by a tritopic quaternized carboxylate and 4,4'-dipyridyl sulfide as an ancillary ligand. This MOF exhibits unique pore shapes with aromatic rings, positively charged pyridinium and unsaturated Cu(II) cation centers, free carboxylates, tessellating H2O, and coordinating SO4(2-) on the pore surface. Compound 1 can interact with two carboxyfluorescein (FAM)-labeled single-stranded DNA sequences (probe ss-DNA, delineated as P-DNA) through electrostatic, π-stacking, and/or hydrogen-bonding interactions to form two P-DNA@1 systems, and thus quench the fluorescence of FAM via a photoinduced electron-transfer process. These P-DNA@1 systems can be used as effective fluorescent sensors for human immunodeficiency virus 1 double-stranded DNA and Sudan virus RNA sequences, respectively, with detection limits of 196 and 73 pM, respectively.


Subject(s)
Biosensing Techniques , Copper/chemistry , DNA, Single-Stranded/analysis , DNA, Viral/analysis , Fluorescent Dyes/chemistry , Organometallic Compounds/chemistry , RNA, Viral/analysis , Crystallography, X-Ray , Ebolavirus/chemistry , HIV-1/chemistry , Models, Molecular , Molecular Structure , Organometallic Compounds/chemical synthesis
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