Porphyrins as spectroscopic sensors for conformational studies of DNA

2007 ◽  
Vol 79 (4) ◽  
pp. 801-809 ◽  
Author(s):  
Milan Balaz ◽  
Klaus Bitsch-Jensen ◽  
Angela Mammana ◽  
George A. Ellestad ◽  
Koji Nakanishi ◽  
...  

Molecular systems containing two or more interacting porphyrins show remarkable spectroscopic features that allow for a very sensitive detection of conformational changes on the microscale level by different methods, such as fluorescence and electronic circular dichroism (ECD). Covalent porphyrin-DNA assemblies can provide a CD profile (exciton couplet) within the porphyrin Soret band region which is very diagnostic for DNA conformational changes. Additionally, covalently linked porphyrins have been shown to function as DNA molecular caps and to stabilize the non-self-complementary non-Watson-Crick guanine-adenine DNA sequence via their strong π-π stacking.

2021 ◽  
Vol 22 (6) ◽  
pp. 2937
Author(s):  
Monika Halat ◽  
Magdalena Klimek-Chodacka ◽  
Jagoda Orleanska ◽  
Malgorzata Baranska ◽  
Rafal Baranski

The Streptococcus pyogenes Cas9 protein (SpCas9), a component of CRISPR-based immune system in microbes, has become commonly utilized for genome editing. This nuclease forms a ribonucleoprotein (RNP) complex with guide RNA (gRNA) which induces Cas9 structural changes and triggers its cleavage activity. Here, electronic circular dichroism (ECD) spectroscopy was used to confirm the RNP formation and to determine its individual components. The ECD spectra had characteristic features differentiating Cas9 and gRNA, the former showed a negative/positive profile with maxima located at 221, 209 and 196 nm, while the latter revealed positive/negative/positive/negative pattern with bands observed at 266, 242, 222 and 209 nm, respectively. For the first time, the experimental ECD spectrum of the gRNA:Cas9 RNP complex is presented. It exhibits a bisignate positive/negative ECD couplet with maxima at 273 and 235 nm, and it differs significantly from individual spectrum of each RNP components. Additionally, the Cas9 protein and RNP complex retained biological activity after ECD measurements and they were able to bind and cleave DNA in vitro. Hence, we conclude that ECD spectroscopy can be considered as a quick and non-destructive method of monitoring conformational changes of the Cas9 protein as a result of Cas9 and gRNA interaction, and identification of the gRNA:Cas9 RNP complex.


Molecules ◽  
2020 ◽  
Vol 25 (7) ◽  
pp. 1733 ◽  
Author(s):  
Ana Miljkovic ◽  
Sonia La Cognata ◽  
Greta Bergamaschi ◽  
Mauro Freccero ◽  
Antonio Poggi ◽  
...  

In this work, we report the synthesis of a new bis(tris(2-aminoethyl)amine) azacryptand L with triphenyl spacers. The binding properties of its dicopper complex for aromatic dicarboxylate anions (as TBA salts) were investigated, with the aim to obtain potential building blocks for supramolecular structures like rotaxanes and pseudo-rotaxanes. As expected, UV-Vis and emission studies of [Cu2L]4+ in water/acetonitrile mixture (pH = 7) showed a high affinity for biphenyl-4,4′-dicarboxylate (dfc2−), with a binding constant of 5.46 log units, due to the best match of the anion bite with the Cu(II)-Cu(II) distance in the cage’s cavity. Compared to other similar bistren cages, the difference of the affinity of [Cu2L]4+ for the tested anions was not so pronounced: conformational changes of L seem to promote a good interaction with both long (e.g., dfc2−) and short anions (e.g., terephthalate). The good affinity of [Cu2L]4+ for these dicarboxylates, together with hydrophobic interactions within the cage’s cavity, may promote the self-assembly of a stable 1:1 complex in water mixture. These results represent a good starting point for the application of these molecular systems as building units for the design of new supramolecular architectures based on non-covalent interactions, which could be of interest in all fields related to supramolecular devices.


2003 ◽  
Vol 07 (12) ◽  
pp. 787-794 ◽  
Author(s):  
Konstantin N. Solovyov ◽  
Serguei M. Arabei ◽  
Lev L. Gladkov ◽  
Vera K. Konstantinova ◽  
Alisa E. Turkova ◽  
...  

The quasi-line fluorescence and fluorescence excitation spectra of 2,3,12,13-tetrame-thyldibenzoporphine have been obtained at 77 K in n-octane and analyzed. The normal-coordinate analysis of this molecule has been performed, and the spectra have been interpreted in detail. In the Soret band region the fluorescence excitation quasi-line spectra clearly reveal two 0-0 components. The problem of the nature of the Soret band of free-base porphyrins is discussed.


Biochemistry ◽  
2000 ◽  
Vol 39 (12) ◽  
pp. 3377-3383 ◽  
Author(s):  
Sunanda Deb ◽  
Sumita Bandyopadhyay ◽  
Siddhartha Roy

2021 ◽  
Vol 24 (4) ◽  
pp. 126-135
Author(s):  
Muhammad Yusprianto ◽  
Titin Anita Zaharah ◽  
Imelda Hotmarisi Silalahi

The bandgap energy (Egap) of TiO2 material modified with metal-chlorophyll complex compounds (M = Cu2+, Fe3+) was observed. Chlorophyll (Chl) was isolated from cassava leaves, and its UV-Vis spectra showed absorption peaks in the Soret band region (410 nm) and in the Q band region (665 nm), which is the typical peak of chlorophyll. Copper(II)-chlorophyll complex was prepared from the reaction between chlorophyll and CuSO4.5H2O, while the iron(III)-chlorophyll was synthesized from chlorophyll and FeCl3.6H2O in methanol solvent under reflux at 65°C. The presence of copperand iron metals in the chlorophyll metal complexes was identified using Atomic Absorption Spectroscopy in methanol solution. The absorption of copper measured in Cu2+-Chl was 0.0488 (0.4805 mg/L), while the iron atom in Fe3+-Chl was 0.0050 (0.0195 mg/L). The UV-vis spectra demonstrate the hypsochromic shift of the Soret band to 405 nm (Cu2+-Chl) and 402 nm (Fe3+-Chl). The Infrared spectra of chlorophyll after being complexed with copper(II) shows the increase of vibrational absorption wavenumber of the C=N group from 1225.06 cm-1 to 1241.94 cm-1 indicates the coordination of the metal ion on the N atom in the pyrrole ring. The shift in the absorption band on the Fe3+-Chl spectrum was seen for the C=O ester group from 1720.49 cm-1 to 1721.10 cm-1 indicating the metal ion bonding in the C=O group of esters. The DR-UVis analysis of TiO2/metal-chlorophyll shows a bathochromic shift towards the visible light region. By using the Tauc plot method, it was observed that the Egap of TiO2 reduces from 3.08 eV to 2.89 eV and 2.93 eV in the compound of TiO2/Cu2+-Chl and TiO2/Fe3+-Chl, respectively.


Blood ◽  
2004 ◽  
Vol 104 (11) ◽  
pp. 124-124
Author(s):  
Samira B. Jeimy ◽  
Rachael A. Woram ◽  
Nola Fuller ◽  
Mary Anne Quinn-Allen ◽  
Gerard Nicolaes ◽  
...  

Abstract Activated coagulation factor V is a key non-enzymatic cofactor that is an essential component of the prothrombinase complex. In blood, much of the procoagulant factor V is stored in platelets, as a complex with the α-granule protein multimerin, for activation-induced release during clot formation. Presently, the molecular nature of multimerin - factor V binding has not been determined, although multimerin is known to interact with the light chain of factor V and Va. Using modified enzyme-linked immunoassays and recombinant factor V constructs, we previously found that discontinuous regions in the C2 domain of factor V were important for binding multimerin, and that these regions overlapped with areas in factor V important for its procoagulant function. Specifically, four (S2183T, W2063A/W2064A, K2060Q/K2061Q, K2060Q/K2061Q/W2063A/ W2064A) full-length, site-directed C2 mutants, and 12 (W2063A, W2064A (W2063, W2064)A, R2074A (R2072, R2074)A (K2101, K2103, K2104)A, L2116A (K2157, H2159, K2161)A, R2171A, R2174A, E2189A (R2187, E2189)A) B domain deleted, charge to alanine constructs had significantly reduced multimerin binding (p< 0.01), relative to the corresponding wild-type. In the present study, we evaluated multimerin-factor V binding with a new assay that used affinity purified, recombinant multimerin immobilized onto microtitre wells to test the binding of recombinant factor V constructs. Because results from the new binding assays were in agreement on the regions of the C2 domain important for multimerin binding, the new assay was used to examine the effect of thrombin on factor V-multimerin binding. Thrombin exposure led to significant dissociation of preformed multimerin-factor V complexes (p<0.01). In addition, thrombin cleaved factor Va had significantly reduced multimerin-binding in assays using antibodies against the factor Va heavy chain and light chain (p<0.01). Recently, our lab identified that platelets contain forms of factor V covalently linked to multimerin via cysteine 1085 in the factor V B-domain. After recombinant factor V was activated by thrombin, there was no detectable binding of the liberated B-domain to multimerin (p<0.001). Nonetheless, the B domain of factor V appeared to enhance factor V binding to multimerin, as factor V constructs synthesized without the B-domain had reduced multimerin binding even after conversion to factor Va, compared to wild-type factor V. Based on the overlap between multimerin-binding and procoagulant, PS binding regions in the C2 domain of factor V, we assessed the effect of multimerin on factor V procoagulant activity in one stage and two stage prothrombinase assays. However, multimerin did not neutralize factor V procoagulant activity when tested in molar excess. Our study indicates that multimerin binding of factor V is modulated by conformational changes in factor V upon activation, and that the factor V B-domain may function to enhance binding to multimerin. The dissociation of multimerin-factor V complexes by thrombin suggests multimerin might be important for delivering and localizing factor V onto platelets, prior to prothrombinase assembly.


2005 ◽  
Vol 70 (11) ◽  
pp. 1799-1810 ◽  
Author(s):  
Jakub Nový ◽  
Marie Urbanová ◽  
Karel Volka

The interactions of three different porphyrins, without axial ligands - 5,10,15,20-tetrakis(1-methylpyridinium-4-yl)porphyrin-Cu(II) tetrachloride (Cu(II)TMPyP), with axial ligands - 5,10,15,20-tetrakis(1-methylpyridinium-4-yl)porphyrin-Fe(III) pentachloride (Fe(III)TMPyP), and with bulky meso substituents - 5,10,15,20-tetrakis(N,N,N-trimethylanilinium-4-yl)-porphyrin tetrachloride (TMAP), with calf thymus DNA were studied by combination of vibrational circular dichroism (VCD) and electronic circular dichroism (ECD) spectroscopy, and by IR and UV-VIS absorption spectroscopy. It has been shown that Cu(II)TMPyP prefers the intercalative binding mode with DNA in the GC-rich regions and the intercalative sites are saturated at the c(DNA)/c(Cu(II)TMPyP) ratio ~3:1, where c(DNA) and c(Cu(II)TMPyP) are total molar concentrations of nucleic acid in base pairs and porphyrin, respectively. Fe(III)TMPyP does not intercalate between the GC base pairs but binds to DNA in the minor groove. At higher c(DNA)/c(TMAP) ratios, TMAP interacts with DNA in the minor groove, but at lower ratios in the major groove and by the external binding mode accompanied by self-stacking of porphyrins along the phosphate backbone. VCD spectroscopy reliably discriminates the binding modes and specifies the conformational changes of the DNA matrices. It has been also shown that VCD spectroscopy is an effective tool for the conformational studies of DNA-porphyrin complexes. New spectroscopic "markers" in VCD spectra have been found for the specific DNA-porphyrin interactions.


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