1
|
Krošl I, Košćak M, Ribičić K, Žinić B, Majhen D, Božinović K, Piantanida I. Impact of the Histidine-Triazole and Tryptophan-Pyrene Exchange in the WHW Peptide: Cu(II) Binding, DNA/RNA Interactions and Bioactivity. Int J Mol Sci 2022; 23:ijms23137006. [PMID: 35806009 PMCID: PMC9266797 DOI: 10.3390/ijms23137006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 06/20/2022] [Accepted: 06/21/2022] [Indexed: 12/10/2022] Open
Abstract
In three novel peptidoids based on the tryptophan—histidine—tryptophan (WHW) peptide, the central histidine was replaced by Ala-(triazole), and two derivatives also had one tryptophan replaced with pyrene-alkyls of different lengths and flexibility. Pyrene analogues show strong fluorescence at 480–500 nm, attributed to intramolecular exciplex formation with tryptophan. All three peptidoids bind Cu2+ cation in water with strong affinity, with Trp- Ala-(triazole)-Trp binding comparably to the parent WHW, and the pyrene analogues even stronger, demonstrating that replacement of histidine with triazole in peptides does not hamper Cu2+ coordination. The studied peptidoids strongly bind to ds-DNA and ds-RNA, whereby their complexes with Cu2+ exhibit distinctively different interactions in comparison to metal-free analogues, particularly in the stabilization of ds-DNA against thermal denaturation. The pyrene peptidoids efficiently enter living cells with no apparent cytotoxic effect, whereby their red-shifted emission compared to the parent pyrene allows intracellular confocal microscopy imaging, showing accumulation in cytoplasmic organelles. However, irradiation with 350 nm light resulted in evident antiproliferative effect on cells treated with micromolar concentrations of the pyrene analogues, presumably attributed to pyrene-induced production of singlet oxygen and consecutive cellular damage.
Collapse
Affiliation(s)
- Ivona Krošl
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (I.K.); (M.K.); (K.R.); (B.Ž.)
| | - Marta Košćak
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (I.K.); (M.K.); (K.R.); (B.Ž.)
| | - Karla Ribičić
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (I.K.); (M.K.); (K.R.); (B.Ž.)
| | - Biserka Žinić
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (I.K.); (M.K.); (K.R.); (B.Ž.)
| | - Dragomira Majhen
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (D.M.); (K.B.)
| | - Ksenija Božinović
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (D.M.); (K.B.)
| | - Ivo Piantanida
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (I.K.); (M.K.); (K.R.); (B.Ž.)
- Correspondence: ; Tel.: +385-1-4571-326
| |
Collapse
|
2
|
Das S, Yau M, Noble J, De Pascalis L, Finn MG. Transport of Molecular Cargo by Interaction with Virus‐Like Particle RNA. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202111687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Soumen Das
- School of Chemistry and Biochemistry School of Biological Sciences Georgia Institute of Technology 901 Atlantic Dr. Atlanta GA 30306 USA
| | - Mei‐Kwan Yau
- School of Chemistry and Biochemistry School of Biological Sciences Georgia Institute of Technology 901 Atlantic Dr. Atlanta GA 30306 USA
| | - Jeffery Noble
- School of Chemistry and Biochemistry School of Biological Sciences Georgia Institute of Technology 901 Atlantic Dr. Atlanta GA 30306 USA
| | - Lucrezia De Pascalis
- School of Chemistry and Biochemistry School of Biological Sciences Georgia Institute of Technology 901 Atlantic Dr. Atlanta GA 30306 USA
| | - M. G. Finn
- School of Chemistry and Biochemistry School of Biological Sciences Georgia Institute of Technology 901 Atlantic Dr. Atlanta GA 30306 USA
| |
Collapse
|
3
|
Das S, Yau MK, Noble J, De Pascalis L, Finn MG. Transport of Molecular Cargo by Interaction with Virus-Like Particle RNA. Angew Chem Int Ed Engl 2022; 61:e202111687. [PMID: 34717043 PMCID: PMC9280655 DOI: 10.1002/anie.202111687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Indexed: 01/12/2023]
Abstract
Virus-like particles (VLPs) derived from Leviviridae virions contain substantial amounts of cellular and plasmid-derived RNA. This encapsidated polynucleotide serves as a reservoir for the efficient binding of the intercalating dye thiazole orange (TO). Polyethylene glycol (PEG) molecules and oligopeptides of varying length, end-functionalized with TO, were loaded into VLPs up to approximately 50 % of the mass of the capsid protein (hundreds to thousands of cargo molecules per particle, depending on size). The kinetics of TO-PEG binding included a significant entropic cost for the reptation of long chains through the capsid pores. Cargo molecules were released over periods of 20-120 hours following simple reversible first-order kinetics in most cases. These observations define a simple general method for the noncovalent packaging, and subsequent release, of functional molecules inside nucleoprotein nanocages in a manner independent of modifications to the capsid protein.
Collapse
Affiliation(s)
- Soumen Das
- School of Chemistry and Biochemistry, School of Biological Sciences, Georgia Institute of Technology, 901 Atlantic Dr., Atlanta, GA, 30306, USA
| | - Mei-Kwan Yau
- School of Chemistry and Biochemistry, School of Biological Sciences, Georgia Institute of Technology, 901 Atlantic Dr., Atlanta, GA, 30306, USA
| | - Jeffery Noble
- School of Chemistry and Biochemistry, School of Biological Sciences, Georgia Institute of Technology, 901 Atlantic Dr., Atlanta, GA, 30306, USA
| | - Lucrezia De Pascalis
- School of Chemistry and Biochemistry, School of Biological Sciences, Georgia Institute of Technology, 901 Atlantic Dr., Atlanta, GA, 30306, USA
| | - M G Finn
- School of Chemistry and Biochemistry, School of Biological Sciences, Georgia Institute of Technology, 901 Atlantic Dr., Atlanta, GA, 30306, USA
| |
Collapse
|
4
|
Lechner VM, Nappi M, Deneny PJ, Folliet S, Chu JCK, Gaunt MJ. Visible-Light-Mediated Modification and Manipulation of Biomacromolecules. Chem Rev 2021; 122:1752-1829. [PMID: 34546740 DOI: 10.1021/acs.chemrev.1c00357] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Chemically modified biomacromolecules-i.e., proteins, nucleic acids, glycans, and lipids-have become crucial tools in chemical biology. They are extensively used not only to elucidate cellular processes but also in industrial applications, particularly in the context of biopharmaceuticals. In order to enable maximum scope for optimization, it is pivotal to have a diverse array of biomacromolecule modification methods at one's disposal. Chemistry has driven many significant advances in this area, and especially recently, numerous novel visible-light-induced photochemical approaches have emerged. In these reactions, light serves as an external source of energy, enabling access to highly reactive intermediates under exceedingly mild conditions and with exquisite spatiotemporal control. While UV-induced transformations on biomacromolecules date back decades, visible light has the unmistakable advantage of being considerably more biocompatible, and a spectrum of visible-light-driven methods is now available, chiefly for proteins and nucleic acids. This review will discuss modifications of native functional groups (FGs), including functionalization, labeling, and cross-linking techniques as well as the utility of oxidative degradation mediated by photochemically generated reactive oxygen species. Furthermore, transformations at non-native, bioorthogonal FGs on biomacromolecules will be addressed, including photoclick chemistry and DNA-encoded library synthesis as well as methods that allow manipulation of the activity of a biomacromolecule.
Collapse
Affiliation(s)
- Vivian M Lechner
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Manuel Nappi
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Patrick J Deneny
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Sarah Folliet
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - John C K Chu
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Matthew J Gaunt
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| |
Collapse
|
5
|
Yumoto S, Kakimi S, Ishikawa A. Colocalization of Aluminum and Iron in Nuclei of Nerve Cells in Brains of Patients with Alzheimer's Disease. J Alzheimers Dis 2019; 65:1267-1281. [PMID: 30149443 PMCID: PMC6218123 DOI: 10.3233/jad-171108] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Increasing evidence indicates that metal-induced oxidative stress plays a pivotal role in the pathogenesis of Alzheimer's disease (AD). Recently, the presence of 8-hydroxydeoxyguanosine, a biomarker of oxidative DNA damage, was demonstrated in nuclear DNA (nDNA) in the AD brain. Iron (Fe) is a pro-oxidant metal capable of generating hydroxyl radicals that can oxidize DNA, and aluminum (Al) has been reported to facilitate Fe-mediated oxidation. In the present study, we examined the elements contained in the nuclei of nerve cells in AD brains using scanning electron microscopy coupled with energy-dispersive X-ray spectroscopy (SEM-EDS). Our results demonstrated that Al and Fe were colocalized in the nuclei of nerve cells in the AD brain. Within the nuclei, the highest levels of both Al and Fe were measured in the nucleolus. The SEM-EDS analysis also revealed the colocalization of Al and Fe in the heterochromatin and euchromatin in neuronal nuclei in the AD brain. Notably, the levels of Al and Fe in the nucleus of nerve cells in the AD brain were markedly higher than those in age-matched control brains. We hypothesize that the colocalization of Al and Fe in the nucleus of nerve cells might induce oxidative damage to nDNA and concurrently inhibit the repair of oxidatively damaged nDNA. An imbalance caused by the increase in DNA damage and the decrease in DNA repair activities might lead to the accumulation of unrepaired damaged DNA, eventually causing neurodegeneration and the development of AD.
Collapse
Affiliation(s)
- Sakae Yumoto
- Yumoto Institute of Neurology, Kawadacho, Shinjuku-ku, Tokyo, Japan
| | - Shigeo Kakimi
- Department of Functional Morphology, Nihon University School of Medicine, Ohyaguchiuemachi, Itabashi-ku, Tokyo, Japan
| | - Akira Ishikawa
- Department of Physics, College of Humanities and Sciences, Nihon University, Sakurajousui, Setagaya-ku, Tokyo, Japan
| |
Collapse
|
6
|
Šmidlehner T, Rožman A, Piantanida I. Advances in Cyanine - Amino Acid Conjugates and Peptides for Sensing of DNA, RNA and Protein Structures. Curr Protein Pept Sci 2019; 20:1040-1045. [PMID: 31092178 DOI: 10.2174/1389203720666190513084102] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Revised: 01/23/2019] [Accepted: 04/06/2019] [Indexed: 12/27/2022]
Abstract
Small molecule spectrophotometric probes for DNA/RNA and proteins are of the utmost importance for diagnostics in biochemical and biomedical research. Both, naturally occurring and synthetic probes, often include peptide sequence responsible for the selectivity toward the particular target; however, commercially available dyes are restricted to single point attachment to the peptide (having one reactive group). Here presented are our recent advances in the development of novel amino acidfluorophore probes, with the unique characteristic of free N- and C-terminus available for incorporation at any peptide backbone position. Intriguingly, already monomeric amino acid-fluorophores showed recognition among various DNA/RNA, whereby steric impact and contribution of halogens is systematically studied. Moreover, some dyes revealed intracellular mitochondria specificity. Further, several hetero-dimeric chromophore systems were prepared, demonstrating that synergistic effect can lead to simultaneous DNA, RNA and protein fluorimetric recognition, combined with enzyme inhibition. Also, homodimeric cyanines equipped with chlorine revealed intriguing DNA/RNA selectivity in respect to well-known parent TOTO and YOYO dyes.
Collapse
Affiliation(s)
- Tamara Šmidlehner
- Laboratory for Biomolecular Interactions and Spectroscopy, Division of Organic Chemistry and Biochemistry. Ruder Boskovic Institute, Zagreb, Croatia
| | - Andrea Rožman
- Pliva Croatia Ltd, Research and Development, Zagreb, Croatia
| | - Ivo Piantanida
- Laboratory for Biomolecular Interactions and Spectroscopy, Division of Organic Chemistry and Biochemistry. Ruder Boskovic Institute, Zagreb, Croatia
| |
Collapse
|
7
|
Berndl S, Dimitrov SD, Menacher F, Fiebig T, Wagenknecht HA. Thiazole Orange Dimers in DNA: Fluorescent Base Substitutions with Hybridization Readout. Chemistry 2016; 22:2386-95. [DOI: 10.1002/chem.201503849] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Indexed: 01/03/2023]
Affiliation(s)
- Sina Berndl
- Institute of Organic Chemistry; Karlsruhe Institute of Technology (KIT); Fritz-Haber-Weg 6 76131 Karlsruhe Germany
- Institute of Organic Chemistry; University of Regensburg; 93040 Regensburg Germany
| | - Stoichko D. Dimitrov
- Centre for Plastic Electronics; Department of Chemistry; Imperial College London; Exhibition Road London SW7 2AZ UK
| | - Florian Menacher
- Institute of Organic Chemistry; Karlsruhe Institute of Technology (KIT); Fritz-Haber-Weg 6 76131 Karlsruhe Germany
- Institute of Organic Chemistry; University of Regensburg; 93040 Regensburg Germany
| | - Torsten Fiebig
- Feinberg School of Medicine; Department of Otolaryngology; Northwestern University; 420 East Superior Street Chicago IL 60611 USA
| | - Hans-Achim Wagenknecht
- Institute of Organic Chemistry; Karlsruhe Institute of Technology (KIT); Fritz-Haber-Weg 6 76131 Karlsruhe Germany
- Institute of Organic Chemistry; University of Regensburg; 93040 Regensburg Germany
| |
Collapse
|
8
|
Tanaka M, Shigi N, Sumaoka J, Komiyama M. Thiazole orange-conjugated peptide nucleic acid for fluorescent detection of specific DNA sequences and site-selective photodamage. RSC Adv 2014. [DOI: 10.1039/c4ra13780a] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Conjugates of thiazole orange (TO) with a pseudo-complementary peptide nucleic acid (pcPNA) functioned as (i) fluorescent detector of specific DNA and (ii) site-selective photodamage inducer through generation of 1O2.
Collapse
Affiliation(s)
- Makiko Tanaka
- Life Science Center of Tsukuba Advanced Research Alliance
- University of Tsukuba
- Tsukuba, Japan
| | - Narumi Shigi
- Life Science Center of Tsukuba Advanced Research Alliance
- University of Tsukuba
- Tsukuba, Japan
| | - Jun Sumaoka
- Life Science Center of Tsukuba Advanced Research Alliance
- University of Tsukuba
- Tsukuba, Japan
| | - Makoto Komiyama
- Life Science Center of Tsukuba Advanced Research Alliance
- University of Tsukuba
- Tsukuba, Japan
| |
Collapse
|
9
|
Tonelli A, Tedeschi T, Germini A, Sforza S, Corradini R, Medici MC, Chezzi C, Marchelli R. Real time RNA transcription monitoring by Thiazole Orange (TO)-conjugated Peptide Nucleic Acid (PNA) probes: norovirus detection. MOLECULAR BIOSYSTEMS 2011; 7:1684-92. [PMID: 21399831 DOI: 10.1039/c0mb00353k] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Thiazole Orange (TO)-conjugated Peptide Nucleic Acid (PNA) probes have been reported as a valuable strategy for DNA analysis; however, no investigations targeting RNA molecules and no comparisons between different derivatization approaches have been reported so far. In this work, two TO-conjugated PNAs for genogroup II noroviruses (NoV GII) detection were designed and synthesized. Both the probes target the most conserved stretch of nucleotides identified in the open reading frame 1-2 (ORF1-ORF2) junction region and differ for the dye conjugation strategy: one PNA is end-labelled with the TO molecule tethered by a linker; the other probe bears the TO molecule directly linked to the PNA backbone, replacing a conventional nucleobase. The spectroscopic properties of the two PNA probes were studied and their applicability to NoVs detection, using an isothermal assay, was investigated. Both probes showed good specificity and high fluorescence enhancement upon hybridization, especially targeting RNA molecules. Moreover, the two probes were successfully employed for NoVs detection from stool specimens in an isothermal-based amplification assay targeting RNA 'amplicons'. The probes showed to be specific even in the presence of high concentrations of non-target RNA.
Collapse
Affiliation(s)
- Alessandro Tonelli
- Department of Organic and Industrial Chemistry, University of Parma, Vle GP Usberti 17/A, 43124 Parma, Italy
| | | | | | | | | | | | | | | |
Collapse
|
10
|
Kolevzon N, Yavin E. Site-Specific DNA Photocleavage and Photomodulation by Oligonucleotide Conjugates. Oligonucleotides 2010; 20:263-75. [DOI: 10.1089/oli.2010.0247] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Netanel Kolevzon
- The School of Pharmacy, The Institute for Drug Research, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Eylon Yavin
- The School of Pharmacy, The Institute for Drug Research, The Hebrew University of Jerusalem, Jerusalem, Israel
| |
Collapse
|
11
|
Biton A, Ezra A, Kasparkova J, Brabec V, Yavin E. DNA photocleavage by DNA and DNA-LNA amino acid-dye conjugates. Bioconjug Chem 2010; 21:616-21. [PMID: 20345124 DOI: 10.1021/bc900372h] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
DNA photocleavage by triplex forming oligonucleotides (TFO) has potential implications in both biotechnology and medicine. We have synthesized a series of homopurine DNA and DNA/LNA 14-mers to which an amino acid (glycine or l-tryptophan) and a cyanine dye are covalently linked. Two cyanine dyes were examined that include a quinolinium ring linked to a benzothiazolium ring through a monomethine (TO1) or trimethine (TO2) linker. The 14-mer sequence was chosen to target mdm2, a ubiquitin ligase (E3) that regulates p53 by promoting its ubiquitylation and proteosomal degradation. Such inhibition has been previously proposed as a therapeutic approach to target wild-type p53-expressing cancers. To examine whether our TFO conjugates photocleave the mdm2 target, we incubated the various conjugates with the mdm2 plasmid and irradiated the samples with visible light. We show that only the TFO with the complementary sequence and with an intervening l-tryptophan leads to the linearization of the plasmid after a short irradiation time (10 min) exciting the dye (lambda(max)(TO1) = 500 nm and lambda(max)(TO2) = 630 nm) with visible light. Furthermore, the photoreactivity is more pronounced for the LNA/DNA conjugate, an observation that is consistent with improved hybridization to the DNA target. Sequence specificity of the photoreaction is further corroborated on a synthetic 44-mer duplex containing the TFO site. Evidence for a ROS-dependent mechanism is also given and discussed.
Collapse
Affiliation(s)
- Adva Biton
- Department of Medicinal Chemistry, The Institute for Drug Research, The School of Pharmacy, The Hebrew University of Jerusalem, Hadassah Ein-Karem, Jerusalem 91120, Israel
| | | | | | | | | |
Collapse
|
12
|
Holzhauser C, Berndl S, Menacher F, Breunig M, Göpferich A, Wagenknecht HA. Synthesis and Optical Properties of Cyanine Dyes as Fluorescent DNA Base Substitutions for Live Cell Imaging. European J Org Chem 2010. [DOI: 10.1002/ejoc.200901423] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
|
13
|
Prunkl C, Berndl S, Wanninger-Weiß C, Barbaric J, Wagenknecht HA. Photoinduced short-range electron transfer in DNA with fluorescent DNA bases: lessons from ethidium and thiazole orange as charge donors. Phys Chem Chem Phys 2010; 12:32-43. [DOI: 10.1039/b914487k] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
|
14
|
Menacher F, Rubner M, Berndl S, Wagenknecht HA. Thiazole orange and Cy3: improvement of fluorescent DNA probes with use of short range electron transfer. J Org Chem 2008; 73:4263-6. [PMID: 18442293 DOI: 10.1021/jo8004793] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Thiazole orange was synthetically incorporated into oligonucleotides by using the corresponding phosphoramidite as the building block for automated DNA synthesis. Due to the covalent fixation of the TO dye as a DNA base surrogate, the TO-modified oligonucleotides do not exhibit a significant increase of fluorescence upon hybridization with the counterstrand. However, if 5-nitroindole (NI) is present as a second artificial DNA base (two base pairs away from the TO dye) a fluorescence increase upon DNA hybridization can be observed. That suggests that a short-range photoinduced electron transfer causes the fluorescence quenching in the single strand. The latter result represents a concept that can be transferred to the commercially available Cy3 label. It enables the Cy3 fluorophore to display the DNA hybridization by a fluorescence increase that is normally not observed with this dye.
Collapse
Affiliation(s)
- Florian Menacher
- University of Regensburg, Institute for Organic Chemistry, Universitätsstrasse 31, Regensburg, Germany
| | | | | | | |
Collapse
|
15
|
Hendry LB, Mahesh VB, Bransome ED, Ewing DE. Small molecule intercalation with double stranded DNA: implications for normal gene regulation and for predicting the biological efficacy and genotoxicity of drugs and other chemicals. Mutat Res 2007; 623:53-71. [PMID: 17449065 DOI: 10.1016/j.mrfmmm.2007.03.009] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2007] [Revised: 03/16/2007] [Accepted: 03/20/2007] [Indexed: 05/15/2023]
Abstract
The binding of small molecules to double stranded DNA including intercalation between base pairs has been a topic of research for over 40 years. For the most part, however, intercalation has been of marginal interest given the prevailing notion that binding of small molecules to protein receptors is largely responsible for governing biological function. This picture is now changing with the discovery of nuclear enzymes, e.g. topoisomerases that modulate intercalation of various compounds including certain antitumor drugs and genotoxins. While intercalators are classically flat, aromatic structures that can easily insert between base pairs, our laboratories reported in 1977 that a number of biologically active compounds with greater molecular thickness, e.g. steroid hormones, could fit stereospecifically between base pairs. The hypothesis was advanced that intercalation was a salient feature of the action of gene regulatory molecules. Two parallel lines of research were pursued: (1) development of technology to employ intercalation in the design of safe and effective chemicals, e.g. pharmaceuticals, nutraceuticals, agricultural chemicals; (2) exploration of intercalation in the mode of action of nuclear receptor proteins. Computer modeling demonstrated that degree of fit of certain small molecules into DNA intercalation sites correlated with degree of biological activity but not with strength of receptor binding. These findings led to computational tools including pharmacophores and search engines to design new drug candidates by predicting desirable and undesirable activities. The specific sequences in DNA into which ligands best intercalated were later found in the consensus sequences of genes activated by nuclear receptors implying intercalation was central to their mode of action. Recently, the orientation of ligands bound to nuclear receptors was found to match closely the spatial locations of ligands derived from intercalation into unwound gene sequences suggesting that nuclear receptors may be guiding ligands to DNA with remarkable precision. Based upon multiple lines of experimental evidence, we suggest that intercalation in double stranded DNA is a ubiquitous, natural process and a salient feature of the regulation of genes. If double stranded DNA is proven to be the ultimate target of genomic drug action, intercalation will emerge as a cornerstone of the future discovery of safe and effective pharmaceuticals.
Collapse
|
16
|
Abstract
The capability to relate phenotypic effects to damage associated with either the mitochondrial or nuclear genome is especially useful under a number of circumstances. Potential hazardous exposures can be evaluated for genotoxicity and related to diseases, particularly cancer. The correlation of DNA damage with adverse health effects is also important in evaluating the safety of various chemical agents and prospective therapeutics. Many techniques exist that afford the ability to identify and measure cellular DNA damage upon exposure to a suspected genotoxic agent; however, quite often these techniques are limited either by the advanced instrumentation and skill needed to perform the analyses or the amount of time needed and limited information obtained regarding the types of DNA damage generated. Recent advances in cellular-based methods have resulted in the timely and straightforward collection of reliable and specific data regarding levels of damage and the identity of the damage products. Antibodies developed for DNA damage lesions allow for the direct measurement of those lesions within a population of exposed cells, while the automation of the single-cell gel electrophoresis (comet) assay and the use of scoring software have led to rapid and standardized data collection. This essay describes the usefulness of these approaches, while providing a brief experimental overview of the techniques.
Collapse
Affiliation(s)
- Marc D Roy
- Polymers Division, Biomaterials Group, National Institute of Standards and Technology, Gaithersburg, MD, USA
| |
Collapse
|