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Krupová M, Leszczenko P, Sierka E, Hamplová SE, Klepetářová B, Pelc R, Andrushchenko V. Vibrational circular dichroism of adenosine crystals. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 319:124381. [PMID: 38838602 DOI: 10.1016/j.saa.2024.124381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 04/18/2024] [Accepted: 04/28/2024] [Indexed: 06/07/2024]
Abstract
Adenosine is one of the building blocks of nucleic acids and other biologically important molecules. Spectroscopic methods have been among the most utilized techniques to study adenosine and its derivatives. However, most of them deal with adenosine in solution. Here, we present the first vibrational circular dichroism (VCD) spectroscopic study of adenosine crystals in solid state. Highly regular arrangement of adenosine molecules in a crystal resulted in a strongly enhanced supramolecular VCD signal originating from long-range coupling of vibrations. The data suggested that adenosine crystals, in contrast to guanosine ones, do not imbibe atmospheric water. Relatively large dimensions of the adenosine crystals resulted in scattering and substantial orientational artifacts affecting the spectra. Several strategies for tackling the artifacts have been proposed and tested. Atypical features in IR absorption spectra of crystalline adenosine (e.g., extremely low absorption in mid-IR spectral range) were observed and attributed to refractive properties of adenosine crystals.
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Affiliation(s)
- Monika Krupová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 2, 16610 Prague, Czech Republic; Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, UiT The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Patrycja Leszczenko
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 2, 16610 Prague, Czech Republic; Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Kraków, Poland; Doctoral School of Exact and Natural Sciences, Jagiellonian University, Łojasiewicza 11, 30-348 Kraków, Poland
| | - Ewa Sierka
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 2, 16610 Prague, Czech Republic; Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Kraków, Poland
| | - Sára Emma Hamplová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 2, 16610 Prague, Czech Republic
| | - Blanka Klepetářová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 2, 16610 Prague, Czech Republic
| | - Radek Pelc
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 2, 16610 Prague, Czech Republic; Third Faculty of Medicine, Charles University, Ruská 87, 10000 Prague, Czech Republic
| | - Valery Andrushchenko
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 2, 16610 Prague, Czech Republic.
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Zubova EA, Strelnikov IA. Experimental detection of conformational transitions between forms of DNA: problems and prospects. Biophys Rev 2023; 15:1053-1078. [PMID: 37974981 PMCID: PMC10643659 DOI: 10.1007/s12551-023-01143-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Accepted: 09/06/2023] [Indexed: 11/19/2023] Open
Abstract
Under different conditions, the DNA double helix can take different geometric forms. Of the large number of its conformations, in addition to the "canonical" B form, the A, C, and Z forms are widely known, and the D, Hoogsteen, and X forms are less known. DNA locally takes the A, C, and Z forms in the cell, in complexes with proteins. We compare different methods for detecting non-canonical DNA conformations: X-ray, IR, and Raman spectroscopy, linear and circular dichroism in both the infrared and ultraviolet regions, as well as NMR (measurement of chemical shifts and their anisotropy, scalar and residual dipolar couplings and inter-proton distances from NOESY (nuclear Overhauser effect spectroscopy) data). We discuss the difficulties in applying these methods, the problems of theoretical interpretation of the experimental results, and the prospects for reliable identification of non-canonical DNA conformations.
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Affiliation(s)
- Elena A. Zubova
- N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 4 Kosygin St., Moscow, 119991 Russia
| | - Ivan A. Strelnikov
- N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 4 Kosygin St., Moscow, 119991 Russia
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Gulzar A, Noetzel J, Forbert H, Marx D. Elucidating the Self-cleavage Dynamics of Hairpin Ribozyme by Mode-decomposed Infrared Spectroscopy. J Phys Chem Lett 2023; 14:7940-7945. [PMID: 37646493 DOI: 10.1021/acs.jpclett.3c01724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
While catalytic reactions of biomolecular processes play an indispensable role in life, extracting the underlying molecular picture often remains challenging. Based on ab initio simulations of the self-cleavage reaction of hairpin ribozyme, mode-decomposed infrared spectra, and cosine similarity analysis to correlate the product with reactant IR spectra, we demonstrate a strategy to extract molecular details from characteristic spectral changes. Our results are in almost quantitative agreement with the experimental IR band library of nucleic acids and suggest that the spectral range of 800-1200 cm-1 is particularly valuable to monitor self-cleavage. Importantly, the cosine similarities also disclose that IR peaks subject to slight shifts due to self-cleavage might be unrelated, while strongly shifting resonances can correspond to the same structural dynamics. This framework of correlating complex IR spectra at the molecular level along biocatalytic reaction pathways is broadly applicable.
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Affiliation(s)
- Adnan Gulzar
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Jan Noetzel
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Harald Forbert
- Center for Solvation Science ZEMOS, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Dominik Marx
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany
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Xue Y, Wang Y, Wang S, Yan M, Huang J, Yang X. Label-Free and Regenerable Aptasensor for Real-Time Detection of Cadmium(II) by Dual Polarization Interferometry. Anal Chem 2020; 92:10007-10015. [PMID: 32618180 DOI: 10.1021/acs.analchem.0c01710] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Recently, numerous aptamer-based biosensors have been developed to detect heavy metal ions. Most of aptamer-based biosensors only can be used to get some quantitative information. The mechanism of the interaction between aptamer and metal ions, however, is rarely studied. In this work, a label-free and regenerable aptamer-based biosensor was constructed using dual polarization interferometry (DPI). This aptasensor was used to investigate the real-time interaction process between cadmium(II) and its aptamer. According to the information on mass, thickness, and density obtained by DPI, a Cd2+ concentration-dependent interaction mechanism and conformation of aptamer was proposed. At low Cd2+ concentration, Cd2+ mainly interacted with phosphate groups on aptamer, resulting in the stretched ssDNA and a few vertical hairpin structures. When adding the high concentration of Cd2+, Cd2+ primarily bound with bases of DNA by coordination interaction and the conformation of aptamer transferred to a tight and short hairpin structure. In addition, the association rate constant (ka), dissociation rate constant (kd) and disassociation constant (KD) between Cd2+ and its aptamer were calculated to be 96 M-1 S-1, 2.11 × 10-5 S-1, and 220 nM, respectively. The proposed aptasensor showed high sensitivity for Cd2+ detection with the detection limit of 0.61 μg/L, which was far below the 5.0 μg/L ranked by the U.S. Environmental Protection Agency. The biosensor also exhibited excellent regenerability and could be used for three cycles without obvious change in response signal. Therefore, the developed method could not only provide quantitative information, but also offered the information on conformation and kinetics for molecular interaction. This method can facilely extend to study the interaction of DNA with other ions, small molecules, or biomacromolecules.
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Affiliation(s)
- Yu Xue
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Changchun, Jilin 130022, China.,University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Yu Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Changchun, Jilin 130022, China.,University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Shuang Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Changchun, Jilin 130022, China.,University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Mengxia Yan
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Changchun, Jilin 130022, China.,University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Jianshe Huang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Changchun, Jilin 130022, China
| | - Xiurong Yang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Changchun, Jilin 130022, China.,University of Science and Technology of China, Hefei, Anhui 230026, China
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Vidal BDC, Ghiraldini FG, Mello MLS. Changes in liver cell DNA methylation status in diabetic mice affect its FT-IR characteristics. PLoS One 2014; 9:e102295. [PMID: 25019512 PMCID: PMC4096918 DOI: 10.1371/journal.pone.0102295] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Accepted: 06/16/2014] [Indexed: 12/21/2022] Open
Abstract
Background Lower levels of cytosine methylation have been found in the liver cell DNA from non-obese diabetic (NOD) mice under hyperglycemic conditions. Because the Fourier transform-infrared (FT-IR) profiles of dry DNA samples are differently affected by DNA base composition, single-stranded form and histone binding, it is expected that the methylation status in the DNA could also affect its FT-IR profile. Methodology/Principal Findings The DNA FT-IR signatures obtained from the liver cell nuclei of hyperglycemic and normoglycemic NOD mice of the same age were compared. Dried DNA samples were examined in an IR microspectroscope equipped with an all-reflecting objective (ARO) and adequate software. Conclusions/Significance Changes in DNA cytosine methylation levels induced by hyperglycemia in mouse liver cells produced changes in the respective DNA FT-IR profiles, revealing modifications to the vibrational intensities and frequencies of several chemical markers, including νas –CH3 stretching vibrations in the 5-methylcytosine methyl group. A smaller band area reflecting lower energy absorbed in the DNA was found in the hyperglycemic mice and assumed to be related to the lower levels of –CH3 groups. Other spectral differences were found at 1700–1500 cm−1 and in the fingerprint region, and a slight change in the DNA conformation at the lower DNA methylation levels was suggested for the hyperglycemic mice. The changes that affect cytosine methylation levels certainly affect the DNA-protein interactions and, consequently, gene expression in liver cells from the hyperglycemic NOD mice.
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Affiliation(s)
- Benedicto de Campos Vidal
- Department of Structural and Functional Biology, Institute of Biology, University of Campinas (Unicamp), Campinas, São Paulo, Brazil
| | - Flávia Gerelli Ghiraldini
- Department of Structural and Functional Biology, Institute of Biology, University of Campinas (Unicamp), Campinas, São Paulo, Brazil
| | - Maria Luiza S. Mello
- Department of Structural and Functional Biology, Institute of Biology, University of Campinas (Unicamp), Campinas, São Paulo, Brazil
- * E-mail:
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Brahms S, Brahms J, Pilet J. Infrared Studies on the Backbone Conformation of Nucleic Acids. Isr J Chem 2013. [DOI: 10.1002/ijch.197400015] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Kang F, Wang H, Gao Y, Long J, Wang Q. Ca2+ promoted the low transformation efficiency of plasmid DNA exposed to PAH contaminants. PLoS One 2013; 8:e58238. [PMID: 23484001 PMCID: PMC3590140 DOI: 10.1371/journal.pone.0058238] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2012] [Accepted: 02/01/2013] [Indexed: 11/18/2022] Open
Abstract
The effects of interactions between genetic materials and polycyclic aromatic hydrocarbons (PAHs) on gene expression in the extracellular environment remain to be elucidated and little information is currently available on the effect of ionic strength on the transformation of plasmid DNA exposed to PAHs. Phenanthrene and pyrene were used as representative PAHs to evaluate the transformation of plasmid DNA after PAH exposure and to determine the role of Ca2+ during the transformation. Plasmid DNA exposed to the test PAHs demonstrated low transformation efficiency. In the absence of PAHs, the transformation efficiency was 4.7 log units; however, the efficiency decreased to 3.72–3.14 log units with phenanthrene/pyrene exposures of 50 µg·L–1. The addition of Ca2+ enhanced the low transformation efficiency of DNA exposed to PAHs. Based on the co-sorption of Ca2+ and phenanthrene/pyrene by DNA, we employed Fourier-transform infrared spectroscopy (FTIR), X-ray photoelectron spectroscopy (XPS), and mass spectrometry (MS) to determine the mechanisms involved in PAH-induced DNA transformation. The observed low transformation efficiency of DNA exposed to either phenanthrene or pyrene can be attributed to a broken hydrogen bond in the double helix caused by planar PAHs. Added Ca2+ formed strong electrovalent bonds with “–POO––” groups in the DNA, weakening the interaction between PAHs and DNA based on weak molecular forces. This decreased the damage of PAHs to hydrogen bonds in double-stranded DNA by isolating DNA molecules from PAHs and consequently enhanced the transformation efficiency of DNA exposed to PAH contaminants. The findings provide insight into the effects of anthropogenic trace PAHs on DNA transfer in natural environments.
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Affiliation(s)
- Fuxing Kang
- Institute of Organic Contaminant Control and Soil Remediation, College of Resource and Environmental Sciences, Nanjing Agricultural University, Nanjing, People’s Republic of China
- Key Laboratory for Information System of Mountainous Areas and Protection of Ecological Environment of Guizhou Province, Guizhou Normal University, Guiyang, People’s Republic of China
| | - Hong Wang
- Institute of Organic Contaminant Control and Soil Remediation, College of Resource and Environmental Sciences, Nanjing Agricultural University, Nanjing, People’s Republic of China
| | - Yanzheng Gao
- Institute of Organic Contaminant Control and Soil Remediation, College of Resource and Environmental Sciences, Nanjing Agricultural University, Nanjing, People’s Republic of China
- * E-mail:
| | - Jian Long
- Key Laboratory for Information System of Mountainous Areas and Protection of Ecological Environment of Guizhou Province, Guizhou Normal University, Guiyang, People’s Republic of China
| | - Qian Wang
- School of Earth Science and Engineering, Nanjing University, Nanjing, People’s Republic of China
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Whelan DR, Bambery KR, Heraud P, Tobin MJ, Diem M, McNaughton D, Wood BR. Monitoring the reversible B to A-like transition of DNA in eukaryotic cells using Fourier transform infrared spectroscopy. Nucleic Acids Res 2011; 39:5439-48. [PMID: 21447564 PMCID: PMC3141270 DOI: 10.1093/nar/gkr175] [Citation(s) in RCA: 140] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The ability to detect DNA conformation in eukaryotic cells is of paramount importance in understanding how some cells retain functionality in response to environmental stress. It is anticipated that the B to A transition might play a role in resistance to DNA damage such as heat, desiccation and toxic damage. To this end, conformational detail about the molecular structure of DNA has been derived primarily from in vitro experiments on extracted or synthetic DNA. Here, we report that a B- to A-like DNA conformational change can occur in the nuclei of intact cells in response to dehydration. This transition is reversible upon rehydration in air-dried cells. By systematically monitoring the dehydration and rehydration of single and double-stranded DNA, RNA, extracted nuclei and three types of eukaryotic cells including chicken erythrocytes, mammalian lymphocytes and cancerous rodent fibroblasts using Fourier transform infrared (FTIR) spectroscopy, we unequivocally assign the important DNA conformation marker bands within these cells. We also demonstrate that by applying FTIR spectroscopy to hydrated samples, the DNA bands become sharper and more intense. This is anticipated to provide a methodology enabling differentiation of cancerous from non-cancerous cells based on the increased DNA content inherent to dysplastic and neoplastic tissue.
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Affiliation(s)
- Donna R Whelan
- Center for Biospectroscopy and School of Chemistry, Monash Immunology and Stem Cell Laboratories, Monash University, Clayton, Victoria, 3800 Australian Synchrotron, 800 Blackburn Road, Clayton, Victoria 3168, Australia
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9
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New marker of tumor cell death revealed by ATR-FTIR spectroscopy. Anal Bioanal Chem 2011; 399:2771-8. [DOI: 10.1007/s00216-011-4654-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2010] [Revised: 12/20/2010] [Accepted: 01/02/2011] [Indexed: 11/27/2022]
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10
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Rozenberg M, Shoham G. A reliable confirmation of the chemical structure of synthetic oligonucleotides: detection of active protons in DNA oligomers by low-temperature FT infrared spectroscopy. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2009; 71:1804-1809. [PMID: 18809351 DOI: 10.1016/j.saa.2008.06.042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2008] [Revised: 06/29/2008] [Accepted: 06/30/2008] [Indexed: 05/26/2023]
Abstract
Cooling the samples allowed us to characterize solid oligonucleotides such as dimers, trimers and pentamers of cytidine, for the first time, in the IR range of the out-of-plane bending molecular modes (1000-400 cm(-1)) at 20K. Especially interesting are the narrow IR bands of the out-of-plane bending nu(4) NH(2) proton mode, which are apparently invisible at room temperature. This unequivocally defined and well-resolved NH(2) bending band should provide important information on the exact chemical form and hydrogen bonding interactions of cytidine amine groups. As such, this unique IR spectroscopy is suggested as a practical analytical tool to validate and characterize synthetic DNA bases and oligonucleotides. Using an approach of this type it was found that desalted oligonucleotide samples of the same nominal composition, but which had been produced by three different manufacturers, differ significantly in their IR spectra. These data suggest that the presumably identical oligonucleotides are in fact different, at least with respect to the content and nature of their NH protons.
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Affiliation(s)
- M Rozenberg
- Department of Inorganic and Analytical Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel.
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12
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Holmes RR. CONFORMATIONAL ENERGY CALCULATIONS ON FIVE-MEMBERED RINGS IN PENTACOORDINATE PHOSPHORUS. PHOSPHORUS SULFUR 2007. [DOI: 10.1080/10426509508036944] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Robert R. Holmes
- a Contribution from the Department of Chemistry , University of Massachusetts , Amherst , Massachusetts , 01002
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14
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Liu M, Karjalainen EL, Barth A. Use of helper enzymes for ADP removal in infrared spectroscopic experiments: application to Ca2+-ATPase. Biophys J 2005; 88:3615-24. [PMID: 15731382 PMCID: PMC1305508 DOI: 10.1529/biophysj.104.055368] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2004] [Accepted: 02/08/2005] [Indexed: 11/18/2022] Open
Abstract
Adenylate kinase (AdK) and apyrase were employed as helper enzymes to remove ADP in infrared spectroscopic experiments that study the sarcoplasmic reticulum Ca(2+)-ATPase. The infrared absorbance changes of their enzymatic reactions were characterized and used to monitor enzyme activity. AdK transforms ADP to ATP and AMP, whereas apyrase consumes ATP and ADP to generate AMP and inorganic phosphate. The benefits of using them as helper enzymes are severalfold: i), both remove ADP generated after ATP hydrolysis by ATPase, which enables repeat of ATP-release experiments several times with the same sample without interference by ADP; ii), AdK helps maintain the presence of ATP for a longer time by regenerating 50% of the initial ATP; iii), apyrase generates free P(i), which can help stabilize the ADP-insensitive phosphoenzyme (E2P); and iv), apyrase can be used to monitor ADP dissociation from transient enzyme intermediates with relatively high affinity to ADP, as shown here for ADP dissociation from the ADP-sensitive phosphoenzyme intermediate (Ca(2)E1P). The respective infrared spectra indicate that ADP dissociation relaxes the closed conformation immediately after phosphorylation partially back toward the open conformation of Ca(2)E1 but does not trigger the transition to E2P. The helper enzyme approach can be extended to study other nucleotide-dependent proteins.
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Affiliation(s)
- Man Liu
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, S-106 91 Stockholm, Sweden
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15
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Zhang R, Ceulemans A, Nguyen * M. A theoretical study of uracil and its tautomers in their lowest-lying triplet state. Mol Phys 2005. [DOI: 10.1080/00268970412331333537] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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16
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Rozenberg M, Jung C, Shoham G. Low-temperature FTIR spectra and hydrogen bonds in polycrystalline adenosine and uridine. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2005; 61:733-741. [PMID: 15649808 DOI: 10.1016/j.saa.2004.05.024] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2004] [Accepted: 05/15/2004] [Indexed: 05/24/2023]
Abstract
FTIR spectra of polycrystalline samples of adenosine and uridine, pure and containing small (<10%) quantity of N(O)H or N(O)D groups, were measured in KBr pellets from 4000 to 400 cm(-1) at temperatures from 300 to 20 K. For the first time, the bands of narrow isotopically decoupled proton stretching vibration nu1 mode of NH- and OH- groups were found and assigned to ordered hydrogen bonds according to crystal structural data for both nucleosides. The FTIR adenosine spectra in the out-of-plane bending proton nu4 mode range (lower than 1000 cm(-1)) of N(O)H groups revealed at low temperature at least twice more bands, than in the nu1 range, which are influenced by isotopic exchange and (or) cooling. Almost all of them have their counterparts in the N(O)D substance spectrum with an isotopic frequency ratio of 1.30-1.40. These bands were assigned to the differently H-bound disordered NH and OH protons, which could not be seen with crystal structural methods. The energy and length of different H-bonds were estimated from peak positions of both mode bands (as the red shift of nu1 or blue shift of nu4 relatively free molecules) with well-established empirical correlations between spectral, thermodynamic and structural parameters of hydrogen bonds. The results were compared with independent experimental data.
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Affiliation(s)
- M Rozenberg
- Department of Inorganic and Analytical Chemistry, The Hebrew University of Jerusalem, Givat Ram, Jerusalem 91904, Israel.
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Rozenberg M, Jung C, Shoham G. Low temperature FTIR spectra and hydrogen bonds in polycrystalline cytidine. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2004; 60:2369-2375. [PMID: 15249027 DOI: 10.1016/j.saa.2003.12.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2003] [Accepted: 12/09/2003] [Indexed: 05/24/2023]
Abstract
FTIR spectra of polycrystalline samples of cytidine, pure and containing a small quantity of N(O)H or N(O)D groups (<20%), were measured in KBr pellets from 4000 to 400 cm(-1) at temperatures from 300 to 20K. For the first time the bands of the narrow isotopically decoupled proton stretching vibration mode (nu(1)) of OH- and NH- groups were found; their number corresponds to the number of H-bonds in crystal according to structural data. The FTIR spectra at low temperature in the out-of-plane bending nu(4) proton mode range (lower than 1000 cm(-1)) of N(O)H groups revealed narrow bands, which correspond to nu(1) bands together with several "extra" bands, which are influenced by the isotopic exchange and (or) cooling. All of them have their counterparts in the N(O)D-substance spectrum with an isotopic frequency ratio of 1.30-1.40. The "extra" bands are assigned to the H-bound OH and NH protons, which are disordered and cannot be seen with X-ray crystal structure analysis. The peak positions of both mode bands (expressed as the red shift of nu(1) or blue shift of nu(4) modes relatively free molecules) were used for the estimation of the energy of different H-bonds using previously established empirical correlations between spectral and thermodynamic parameters of hydrogen bonds. The correlation of the red shift and H-bond length is also confirmed for all five H-bonds of cytidine.
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Affiliation(s)
- M Rozenberg
- Department of Inorganic and Analytical Chemistry, The Hebrew University of Jerusalem, Jerusalem, Givat Ram, 91904, Israel.
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Pichler A, Rauch C, Flader W, Wellenzohn B, Liedl KR, Hallbrucker A, Mayer E. The conformer substates of nonoriented B-type DNA in double helical poly(dG-dC). J Biomol Struct Dyn 2003; 20:547-59. [PMID: 12529153 DOI: 10.1080/07391102.2003.10506871] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
A nonoriented hydrated film of poly(dG-dC) with ?20 water molecules per nucleotide (called B* by Loprete and Hartman (Biochem. 32, 4077-4082 (1993)) was studied by Fourier transform infrared (FT-IR) spectroscopy either as equilibrated sample between 290 and 270 K or, after quenching into the glassy state, as nonequilibrated film isothermally at 200 and 220 K. IR spectral changes on isothermal relaxation at 200 and 220 K, caused by interconversion of two conformer substates, are revealed by difference spectra. Comparison with difference curves obtained in the same manner from two classical B-DNA forms, namely the d(CGCGAATTCGCG)(2) dodecamer and polymeric NaDNA from salmon testes, revealed that the spectral changes on B(I)-to-B(II) interconversion in the classical B-DNA forms are very similar to those in the B*-form, and that the spectroscopic differences between the B(I) and B(II) features from classical B-DNA and those from the modified B*-form are minor. Nonexponential kinetics of the B(I)-->B(II) transition in the B*-form of poly(dG-dC) at 200 K showed that the structural relaxation time is about three times of that in the classical B-DNA forms (approximately equal to 30 versus approximately equal to 10 min at 200 K). The unexpected reversal of conformer substates interconversion (that is B(II)-->B(I) transition on cooling from 290 K and B(I)-->B(II) transition on isothermal relaxation at 200 K) observed for classical B-DNA occurs also in the modified B*-form. We therefore conclude that restructuring of hydration shells rules the low-temperature dynamics of the B*-form via its two conformer substates in the same manner reported for classical B-DNA by Pichler et al. (J. Phys. Chem. B 106, 3263-3274 (2002)).
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Affiliation(s)
- Arthur Pichler
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
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Rajani C, Kincaid JR, Petering DH. A systematic approach toward the analysis of drug-DNA interactions using Raman spectroscopy: the binding of metal-free bleomycins A(2) and B(2) to calf thymus DNA. Biopolymers 2001; 52:110-28. [PMID: 11169380 DOI: 10.1002/1097-0282(1999)52:3<110::aid-bip20>3.0.co;2-#] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Bleomycins A(2) and B(2) are the two active components in the antineoplastic drug Blenoxane. DNA is targeted by this drug in cancer cells and the mode of action of this drug involves DNA binding. Ambiguity exists as to the way in which bleomycin binds to DNA. Raman spectroscopy was used to examine both calf thymus DNA and a bleomycin/DNA complex at two temperatures. A curvefitting technique was applied to these spectra for a spectral region obscured by many overlapping bands associated with the nucleotide bases in order to derive information about frequencies, bandwidths, and intensities of the vibrational modes in this region. This allowed identification and analysis of bands associated with specific assigned nucleotide base residues. Upon binding of bleomycin, several significant changes in bandwidth, intensities, and frequencies relative to uncomplexed DNA were observed consistently at both higher (30 degrees C) and lower (19 degrees C) temperature. The data presented here support at least a partial intercalation mode of binding for bleomycin that is temperature dependent and more pronounced at the more physiologically relevant temperature of 30 degrees C.
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Affiliation(s)
- C Rajani
- Department of Chemistry, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA
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20
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Pohle W, Gauger D, Fritzsche H, Rattay B, Selle C, Binder H, Böhlig H. FTIR-spectroscopic characterization of phosphocholine-headgroup model compounds. J Mol Struct 2001. [DOI: 10.1016/s0022-2860(00)00830-9] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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21
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Nafisi S, Mohajerani N, Hadjiakhoondi A, Monajemi M, Garib F. Interaction of Tl+3 with mononucleotides: metal ion binding and sugar conformation. J Mol Struct 2001. [DOI: 10.1016/s0022-2860(00)00918-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2022]
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22
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How many uracil tautomers there are? Density functional studies of stability ordering of tautomers. Chem Phys 1999. [DOI: 10.1016/s0301-0104(99)00009-9] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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23
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Cepus V, Ulbrich C, Allin C, Troullier A, Gerwert K. Fourier transform infrared photolysis studies of caged compounds. Methods Enzymol 1998; 291:223-45. [PMID: 9661152 DOI: 10.1016/s0076-6879(98)91015-1] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Time-resolved FTIR difference spectroscopy is a powerful tool for investigating molecular reaction mechanisms of proteins. In order to detect, beyond the large background absorbance of the protein and the water, absorbance bands of protein groups that undergo reactions, difference spectra have to be performed between a ground state and an activated state of the sample. Because the absorbance changes are small, the reaction has to be started in situ, in the apparatus, and in thin protein films. The use of caged compounds offers an elegant approach to initiate protein reactions with a nanosecond UV laser flash. Here, time-resolved FTIR and FT-Raman photolysis studies of the commonly used caged compounds, caged Pi, caged ATP, caged GTP, and caged calcium are presented. The use of specific isotopic labels allows us to assign the IR bands to specific groups. Because metal ions play an important role in many biological systems, their influence on FTIR spectra of caged compounds is discussed. The results presented should provide a good basis for further FTIR studies on molecular reaction mechanisms of energy or signal transducing proteins. As an example of such investigations, the time-resolved FTIR studies on the GTPase reaction of H-ras p21 using caged GTP is presented.
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Affiliation(s)
- V Cepus
- Lehrstuhl für Biophysik, Fakultät Biologie, Bochum, Germany
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24
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Barth A, Mäntele W. ATP-Induced phosphorylation of the sarcoplasmic reticulum Ca2+ ATPase: molecular interpretation of infrared difference spectra. Biophys J 1998; 75:538-44. [PMID: 9649416 PMCID: PMC1299728 DOI: 10.1016/s0006-3495(98)77543-5] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Time-resolved infrared difference spectra of the ATP-induced phosphorylation of the sarcoplasmic reticulum Ca2+-ATPase have been recorded in H2O and 2H2O at pH 7.0 and 1 degrees C. The reaction was induced by ATP release from P3-1-(2-nitro)phenylethyladenosine 5'-triphosphate (caged ATP) and from [gamma-18O3]caged ATP. A band at 1546 cm-1, not observed with the deuterated enzyme, can be assigned to the amide II mode of the protein backbone and indicates that a conformational change associated with ATPase phosphorylation takes place after ATP binding. This is also indicated between 1700 and 1610 cm-1, where bandshifts of up to 10 cm-1 observed upon protein deuteration suggest that amide I modes of the protein backbone dominate the difference spectrum. From the band positions it is deduced that alpha-helical, beta-sheet, and probably beta-turn structures are affected in the phosphorylation reaction. Model spectra of acetyl phosphate, acetate, ATP, and ADP suggest the tentative assignment of some of the bands of the phosphorylation spectrum to the molecular groups of ATP and Asp351, which participate directly in the phosphate transfer reaction: a positive band at 1719 cm-1 to the C==O group of aspartyl phosphate, a negative band at 1239 cm-1 to the nuas(PO2-) modes of the bound ATP molecule, and a positive band at 1131 cm-1 to the nuas(PO32-) mode of the phosphoenzyme phosphate group, the latter assignment being supported by the band's sensitivity toward isotopic substitution in the gamma-phosphate of ATP. Band positions and shapes of these bands indicate that the alpha- and/or beta-phosphate(s) of the bound ATP molecule become partly dehydrated when ATP binds to the ATPase, that the phosphoenzyme phosphate group is unprotonated at pH 7.0, and that the C==O group of aspartyl phosphate does not interact with bulk water. The Ca2+ binding sites seem to be largely undisturbed by the phosphorylation reaction, and a functional role of the side chains of Asn, Gln, and Arg residues was not detected.
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Affiliation(s)
- A Barth
- Institut für Biophysik, Johann Wolfgang Goethe Universität, D-60590 Frankfurt am Main, Germany.
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25
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Fujiwara T, Kamoshida Y, Morita R, Yamashita M. Temporally-separated ultrafast-emission dynamics of neutral and cationic molecules in guanine and its derivative aqueous solutions. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 1997. [DOI: 10.1016/s1011-1344(97)00091-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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27
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Chhiba M, Vergoten G. The spasiba force field of model compounds related to lipids of biomembranes. J Mol Struct 1996. [DOI: 10.1016/s0022-2860(96)09243-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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28
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Guan Y, Thomas GJ. Vibrational analysis of nucleic acids. III. Conformation-dependent Raman markers of the phosphodiester backbone modeled by dimethyl phosphate. J Mol Struct 1996. [DOI: 10.1016/0022-2860(95)09059-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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29
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Barth A, Kreutz W, Mäntele W. Changes of protein structure, nucleotide microenvironment, and Ca(2+)-binding states in the catalytic cycle of sarcoplasmic reticulum Ca(2+)-ATPase: investigation of nucleotide binding, phosphorylation and phosphoenzyme conversion by FTIR difference spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA 1994; 1194:75-91. [PMID: 8075144 DOI: 10.1016/0005-2736(94)90205-4] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Changes of infrared absorbance of sarcoplasmic reticulum Ca(2+)-ATPase (EC 3.6.1.38) associated with partial reactions of its catalytic cycle were investigated in the region from 1800 to 950 cm-1 in H2O and 2H2O. Starting from Ca2E1, 3 reaction steps were induced in the infrared cuvette via photolytic release of ATP and ADP: (a) nucleotide binding, (b) formation of the ADP-sensitive phosphoenzyme (Ca2E1P) and (c) formation of the ADP-insensitive phosphoenzyme (E2P). All reaction steps caused distinct changes of the infrared spectrum which were characteristic for each reaction step but comparable for all steps in the number and magnitude of the changes. Most pronounced were absorbance changes in the amide I spectral region sensitive to protein secondary structure. However, they were small--less than 1% of the total protein absorbance--indicating that the reaction steps are associated with small and local conformational changes of the polypeptide backbone instead of a large conformational rearrangement. Especially, there is no outstanding conformational change associated with the phosphoenzyme conversion Ca2E1P-->E2P. ADP-binding induces conformational changes in the ATPase polypeptide backbone with alpha-helical structures and presumably beta-sheet or beta-turn structures involved. Phosphorylation is accompanied by the appearance of a keto group vibration that can tentatively be assigned to the phosphorylated residue Asp351. Phosphoenzyme conversion and Ca(2+)-release produce difference signals which can be explained by the release of Ca2+ from carboxylate groups and a change of hydrogen bonding or protonation state of carboxyl groups.
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Affiliation(s)
- A Barth
- Institut für Biophysik, Strahlenbiologie der Universität Freiburg, Freiburg, Germany
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31
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Grdadolnik J, Hadži D. Conformational effects of metal salt binding to the polar head of phosphatidylcholines investigated by FTIR spectroscopy. Chem Phys Lipids 1993. [DOI: 10.1016/0009-3084(93)90045-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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32
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Messinger A, Powell JW, Weidlich T, Genzel L. Far-infrared study of the vibrational modes of 5'-GMP gels and crystals of Na+ and K+. J Biomol Struct Dyn 1993; 10:841-52. [PMID: 8391267 DOI: 10.1080/07391102.1993.10508678] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Five Far-Infrared (50-600 cm-1) spectra are presented: the sodium and potassium salts of 5' Guanosine Monophosphate (GMP), each salt in both the gel and crystal conformations, and poly(rG). Measurements were performed at a sample temperature of 10 K under vacuum with a liquid He-cooled bolometer. The spectra were fit with Lorentzians and assignments are suggested. There are noteworthy differences in oscillator strengths and frequencies of the bands between all spectra. We report the tentative observation of a 100 cm-1 mode which is in the neighborhood of a mode observed by Raman spectroscopy in solution (1) and dried gels (2).
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Affiliation(s)
- A Messinger
- Department of Physics, University of California at San Diego, La Jolla 92093-0319
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33
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Taga K, Miyagai K, Hirabayashi N, Yoshida T, Okabayashi H. Vibrational spectra and normal coordinate analysis of barium dimethyl, diethyl and ethyl methyl phosphates. J Mol Struct 1991. [DOI: 10.1016/0022-2860(91)87001-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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34
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Ghomi M, Letellier R, Taillandier E. Determination of the nucleosidic structural parameters by means of DNA vibrational markers. J Mol Struct 1990. [DOI: 10.1016/0022-2860(90)85005-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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35
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Caubet A, Moreno V, Labarta A, Tejada X. Spectroscopic and thermogravimetric studies of Co(II)-nucleotides complexes. J Inorg Biochem 1990. [DOI: 10.1016/0162-0134(90)80025-s] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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36
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Pohle W, Bohl M, Flemming J, Böhlig H. Subsidiary hydrogen bonding of intercalated anthraquinonic anticancer drugs to DNA phosphate. Biophys Chem 1990; 35:213-26. [PMID: 2397273 DOI: 10.1016/0301-4622(90)80010-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Several anthraquinone derivatives are active against different kinds of human cancer. The cancerostatic activity has been mainly attributed to their ability to bind strongly to DNA by intercalation. Here, infrared spectroscopy was used to detect further, more specific DNA interactions with the prominent anticancer drugs daunomycin, adriamycin, aclacinomycin A and mitoxantrone as well as with the cytotoxic violamycin BI. The most striking result was a significant decrease in wave number of the band arising from antisymmetric stretching vibration of the PO2- groups of DNA upon complexation with adriamycin, aclacinomycin A, violamycin BI and mitoxantrone. This became evident after separation of the contributions from conformational changes of DNA to the influence on the wave number of that band. The drug-induced shift was interpreted in terms of the formation of a hydrogen bond between the intercalated drug molecules and the PO2- moiety of DNA via the following terminal hydroxyl groups: C14-OH for adriamycin, C4-OH for both aclacinomycin A and violamycin BI and, more tentatively, the external side-chain OH of mitoxantrone. Theoretical considerations, consisting of semi-empirical CNDO/2 calculations as well as normal coordinate analyses performed with molecular model fragments, provided results confirming and rationalising the experimental findings. The capacities of the anthracyclines for restriction of the conformational flexibility of DNA differ, presumably due to variations in the spatial dimensions of the sugar moieties of the drugs. The compatibility of the present results with data obtained from current geometrical models, especially those for the DNA-daunomycin and DNA-adriamycin complexes, is discussed in detail.
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Affiliation(s)
- W Pohle
- Central Institute of Microbiology and Experimental Therapy, Academy of Sciences of the G.D.R., Jena
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37
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38
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Ghomi M, Letellier R, Liquier J, Taillandier E. Interpretation of DNA vibrational spectra by normal coordinate analysis. THE INTERNATIONAL JOURNAL OF BIOCHEMISTRY 1990; 22:691-9. [PMID: 2205520 DOI: 10.1016/0020-711x(90)90003-l] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
1. In the following article we undertake a brief review of the most prominent DNA vibrational markers as observed experimentally by Raman and i.r. spectroscopies on polynucleotides and explain how a simplified valence force field can account for the evolution of the DNA vibrational spectra. 2. Our discussion made as a review of our previous investigations on the interpretation of DNA vibration modes, is based on some of the most characteristic and structure dependent DNA vibrational markers.
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Affiliation(s)
- M Ghomi
- Laboratoire de Spectroscopie Biomoléculaire, U.F.R. Biomédicale de Bobigny, Université Paris XIII, Bobigny, France
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39
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Mishra P. Interaction of guanine with oxygen and further evidence for its asymmetric double-well potential surfaces. J Mol Struct 1989. [DOI: 10.1016/0022-2860(89)80169-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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40
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Letellier R, Ghomi M, Taillandier E. Interpretation of DNA vibration modes: IV--A single-helical approach to assign the phosphate-backbone contribution to the vibrational spectra in A and B conformations. J Biomol Struct Dyn 1989; 6:755-68. [PMID: 2619939 DOI: 10.1080/07391102.1989.10507735] [Citation(s) in RCA: 33] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
A calculated approach based on the Higgs method for assigning the vibration modes of an infinite helicoidal polymeric chain has been performed on the basis of a reliable valence force field. The calculated results allowed the phosphate-backbone marker modes of the A and B forms, to be interpreted. In the dynamic models used, the bases have been omitted and no interchain interaction was considered. The calculation can also interprete quite satisfactorily the characteristic Raman peaks and infrared bands in the 1250-700 cm-1 spectral region arising from the sugar or sugar-phosphate association and reproduce their evolution upon the B----A DNA conformational transition. They clearly show that the phosphate-backbone modes in the above mentioned spectral region constitute the optical branches of the phonon dispersion curves with no detectable variation in the first Brillouin-zone.
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Affiliation(s)
- R Letellier
- Laboratoire de Spectroscopie Biomoléculaire U.F.R. Biomédicale de Bobigny, Université Paris XIII, France
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42
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Molecular vibrations and conformational analysis of methylphosphorodichloridate and ethylphosphorodichloridate. J Mol Struct 1988. [DOI: 10.1016/0022-2860(88)85007-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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43
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Sen A, Yang PW, Mantsch HH, Hui SW. Extended hydrogen-bonded structures of phosphatidylethanolamine. Chem Phys Lipids 1988; 47:109-16. [PMID: 3409437 DOI: 10.1016/0009-3084(88)90079-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The structure of phosphatidylethanolamine in pure dry hexane was studied. Viscosity measurements show that the hexane solution of PE has a very high viscosity, while freeze fracture electron microscopy revealed extensive fibre-like structures. These extended structures are disrupted by the addition of small amounts of water or organic solvents which are capable of hydrogen-bonding. The Fourier transform infrared spectra of the lipid solutions in dry and hydrated hexane show considerable differences in the phosphate and ethanolamine absorption bands, and demonstrate that the viscous fibre-like structures formed by phosphatidylethanolamine in dry hexane consist of extended intermolecular hydrogen-bonds, similar to those found in the solid lipid, with the ammonium group as the hydrogen-donor and the phosphate group as the hydrogen-acceptor. The high viscosity is not observed in hexane solution of phosphatidylcholine.
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Affiliation(s)
- A Sen
- Department of Biophysics, Roswell Park Memorial Institute, Buffalo, NY 14263
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44
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Thomas GJ, Wang AHJ. Laser Raman Spectroscopy of Nucleic Acids. NUCLEIC ACIDS AND MOLECULAR BIOLOGY 1988. [DOI: 10.1007/978-3-642-83384-7_1] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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45
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Casal HL, Mantsch HH, Paltauf F, Hauser H. Infrared and 31P-NMR studies of the effect of Li+ and Ca2+ on phosphatidylserines. BIOCHIMICA ET BIOPHYSICA ACTA 1987; 919:275-86. [PMID: 3593749 DOI: 10.1016/0005-2760(87)90267-0] [Citation(s) in RCA: 62] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Infrared and 31P-NMR spectra of solid samples of 1,2-dimyristoyl-sn-glycero-3-phospho-L-serine (DMPS), 1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine (POPS) and 1,2-dioleoyl-sn-glycero-3-phospho-L-serine (DOPS) have been recorded. Comparison of the spectra of the Na+ salts of these phospholipids with those of complexes formed with Li+ and Ca2+ ions allows the characterization of conformational changes induced by complexation with Li+ and Ca2+. Ca2+ forms tight, crystalline complexes with these phosphatidylserines (PS), irrespective of the degree of unsaturation in the hydrocarbon chains. In these PS-Ca2+ complexes the torsion angles of the two P-O ester bonds exhibit the antiplanar-antiplanar conformation which is significantly different from the standard gauche-gauche conformation commonly found in phosphodiesters. In contrast, complexation with Li+ does not induce this conformational change in the phosphodiester group. It is shown that the degree of unsaturation in the hydrocarbon chains, and related to it, the cross-sectional area of the phospholipid or the surface charge density, determine the affinity of the phosphatidylserine for the metal ion. In general, the affinity of phosphatidylserines for both Li+ and Ca2+ decreases with increasing unsaturation in the hydrocarbon chains or decreasing surface charge density; it is in the order DMPS greater than POPS greater than DOPS.
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46
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Pohle W, Flemming J. Interaction of the C14-OH group of adriamycin with DNA phosphate as spectroscopically evidenced. J Biomol Struct Dyn 1986; 4:243-50. [PMID: 3271442 DOI: 10.1080/07391102.1986.10506343] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Monitoring the band of the antisymmetric stretching vibration of the backbone PO-2 group in DNA-anthracycline complexes demonstrates an extraordinary wavenumber shift for the adriamycin complex compared to that of daunomycin. The structures of both anthracyclines, however, are very closely related and differ only by a surplus hydroxyl group of adriamycin in the C14 position. The wavenumber shift observed for the DNA-adriamycin complex is unequivocally attributed to an additional linkage of the C14-OH of adriamycin to the phosphate group of DNA. Thus, several of the hypothetical structural models for the DNA-adriamycin complex for which a hydrogen bond between the C14 hydroxyl of the drug and DNA phosphate was postulated (S. Neidle, Cancer Treatment Rep. 61, 928 (1977); G. J. Quigley et. al., Proc. Natl. Acad. Sci. USA 77, 7204 (1980)) get the first clear-cut experimental evidence.
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Affiliation(s)
- W Pohle
- Academy of Sciences of the GDR, Department of Biophysical Chemistry, Jena
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47
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Mikulski CM, Minutella R, De Franco N, Borges G, Karayannis NM. Adenosine adducts with first row transition metal perchlorates. Inorganica Chim Acta 1986. [DOI: 10.1016/s0020-1693(00)84309-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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48
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49
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Thermal reaction of aquaammineruthenium(III) complex with amino acid or imidazole derivative in the solid state. Polyhedron 1985. [DOI: 10.1016/s0277-5387(00)84081-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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50
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Scherer E, Tajmir-Riahi H, Theophanides T. Synthesis, structure and a fourier transform infrared study of Pt(II), Cu(II), and Mg(II) Complexes with xanthosine-5′-monophosphate. Inorganica Chim Acta 1984. [DOI: 10.1016/s0020-1693(00)80052-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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