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Adámik M, Soldánová Z, Drotárová M, Brečková K, Petr M, Helma R, Jenner LP, Vorlíčková M, Sýkorová E, Brázdová M. Human ARMC6 binds in vitro to both cancer genes and telomeric RNA, favoring G-quadruplex structure recognition. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2024; 1867:195050. [PMID: 39029558 DOI: 10.1016/j.bbagrm.2024.195050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 06/25/2024] [Accepted: 07/13/2024] [Indexed: 07/21/2024]
Abstract
Armadillo repeat-containing proteins (ARMCs) are a large family found throughout eukaryotes, which play prominent roles in cell adhesion, signaling and cytoskeletal regulation. The ARMC6 protein is highly conserved in primates, including humans, but to date does not have a clear function beyond initial hints of a link to cancer and telomerase activity. We report here in vitro experiments showing ARMC6 binding to DNA promoter sequences from several cancer-related genes (e.g., EGFR, VEGF and c-MYC), and also to the telomeric RNA repeat (TERRA). ARMC6 binding activity appears to recognize G-quadruplex motifs, which are being increasingly implicated as structure-based protein binding sites in chromosome maintenance and repair. In vivo investigation of ARMC6 function revealed that when this protein is overexpressed in human cell lines, there is different expression of genes connected with oncogenic pathways and those implicated in downstream non-canonical telomerase pathways (e.g., VEGF, hTERT, c-MYC, ESM1, MMP3). ARMC6 is already known to interact with human shelterin protein TRF2 and telomerase. The protein binds G-quadruplex structures and does so preferentially to RNA over DNA. As such, this protein may be an example of how a non-canonical nucleic acid structural motif allows mediation between gene regulation and telomeric chromatin rearrangement pathways.
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Affiliation(s)
- Matej Adámik
- Institute of Biophysics, Academy of Sciences of the Czech Republic v.v.i., Královopolská 135, 612 00 Brno, Czech Republic
| | - Zuzana Soldánová
- Department of Molecular Pharmacy, Faculty of Pharmacy, Masaryk University, Palackého 1/3, 612 42 Brno, Czech Republic
| | - Magdaléna Drotárová
- Institute of Biophysics, Academy of Sciences of the Czech Republic v.v.i., Královopolská 135, 612 00 Brno, Czech Republic
| | - Katarína Brečková
- Department of Molecular Pharmacy, Faculty of Pharmacy, Masaryk University, Palackého 1/3, 612 42 Brno, Czech Republic
| | - Marek Petr
- Institute of Biophysics, Academy of Sciences of the Czech Republic v.v.i., Královopolská 135, 612 00 Brno, Czech Republic
| | - Robert Helma
- Institute of Biophysics, Academy of Sciences of the Czech Republic v.v.i., Královopolská 135, 612 00 Brno, Czech Republic
| | - Leon P Jenner
- Institute of Biophysics, Academy of Sciences of the Czech Republic v.v.i., Královopolská 135, 612 00 Brno, Czech Republic
| | - Michaela Vorlíčková
- Institute of Biophysics, Academy of Sciences of the Czech Republic v.v.i., Královopolská 135, 612 00 Brno, Czech Republic
| | - Eva Sýkorová
- Institute of Biophysics, Academy of Sciences of the Czech Republic v.v.i., Královopolská 135, 612 00 Brno, Czech Republic
| | - Marie Brázdová
- Institute of Biophysics, Academy of Sciences of the Czech Republic v.v.i., Královopolská 135, 612 00 Brno, Czech Republic; Department of Molecular Pharmacy, Faculty of Pharmacy, Masaryk University, Palackého 1/3, 612 42 Brno, Czech Republic.
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2
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Błaszczyk L, Ryczek M, Das B, Mateja-Pluta M, Bejger M, Śliwiak J, Nakatani K, Kiliszek A. Antisense RNA C9orf72 hexanucleotide repeat associated with amyotrophic lateral sclerosis and frontotemporal dementia forms a triplex-like structure and binds small synthetic ligand. Nucleic Acids Res 2024; 52:6707-6717. [PMID: 38738637 PMCID: PMC11194091 DOI: 10.1093/nar/gkae376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 04/05/2024] [Accepted: 04/26/2024] [Indexed: 05/14/2024] Open
Abstract
The abnormal expansion of GGGGCC/GGCCCC hexanucleotide repeats (HR) in C9orf72 is associated with amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Structural polymorphisms of HR result in the multifactorial pathomechanism of ALS/FTD. Consequently, many ongoing studies are focused at developing therapies targeting pathogenic HR RNA. One of them involves small molecules blocking sequestration of important proteins, preventing formation of toxic nuclear foci. However, rational design of potential therapeutics is hindered by limited number of structural studies of RNA-ligand complexes. We determined the crystal structure of antisense HR RNA in complex with ANP77 ligand (1.1 Å resolution) and in the free form (0.92 and 1.5 Å resolution). HR RNA folds into a triplex structure composed of four RNA chains. ANP77 interacted with two neighboring single-stranded cytosines to form pseudo-canonical base pairs by adopting sandwich-like conformation and adjusting the position of its naphthyridine units to the helical twist of the RNA. In the unliganded structure, the cytosines formed a peculiar triplex i-motif, assembled by trans C•C+ pair and a third cytosine located at the Hoogsteen edge of the C•C+ pair. These results extend our knowledge of the structural polymorphisms of HR and can be used for rational design of small molecules targeting disease-related RNAs.
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Affiliation(s)
- Leszek Błaszczyk
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704, Poland
| | - Marcin Ryczek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704, Poland
| | - Bimolendu Das
- Department of Regulatory Bioorganic Chemistry, SANKEN (The Institute of Scientific and Industrial Research), Osaka University, 8-1 Mihogaoka, Ibaraki 567-0047, Japan
| | - Martyna Mateja-Pluta
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704, Poland
| | - Magdalena Bejger
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704, Poland
| | - Joanna Śliwiak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704, Poland
| | - Kazuhiko Nakatani
- Department of Regulatory Bioorganic Chemistry, SANKEN (The Institute of Scientific and Industrial Research), Osaka University, 8-1 Mihogaoka, Ibaraki 567-0047, Japan
| | - Agnieszka Kiliszek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704, Poland
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3
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Saini S, Goel K, Ghosh S, Das A, Saraogi I. Effects of PNA Sequence and Target Site Selection on Function of a 4.5S Non-Coding RNA. Chembiochem 2024:e202400029. [PMID: 38595046 DOI: 10.1002/cbic.202400029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 04/09/2024] [Accepted: 04/09/2024] [Indexed: 04/11/2024]
Abstract
Peptide nucleic acid (PNA) based antisense strategy is a promising therapeutic approach to specifically inhibit target gene expression. However, unlike protein coding genes, identification of an ideal PNA binding site for non-coding RNA is not straightforward. Here, we compare the inhibitory activities of PNA molecules that bind a non-coding 4.5S RNA called SRP RNA, a key component of the bacterial signal recognition particle (SRP). A 9-mer PNA (PNA9) complementary to the tetraloop region of the RNA was more potent in inhibiting its interaction with the SRP protein, compared to an 8-mer PNA (PNA8) targeting a stem-loop. PNA9, which contained a homo-pyrimidine sequence could form a triplex with the complementary stretch of RNA in vitro as confirmed using a fluorescent derivative of PNA9 (F-PNA13). The RNA-PNA complex formation resulted in inhibition of SRP function with PNA9 and F-PNA13, but not PNA8 highlighting the importance of target site selection. Surprisingly, F-PNA13 which was more potent in inhibiting SRP function in vitro, showed weaker antibacterial activity compared to PNA9 likely due to poor cell penetration of the longer PNA. Our results underscore the importance of suitable target site selection and optimum PNA length to develop better antisense molecules against non-coding RNA.
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Affiliation(s)
- Snehlata Saini
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal Bhauri, Bhopal Bypass Road, Bhopal, 462066, Madhya Pradesh, India
| | - Khushboo Goel
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal Bhauri, Bhopal Bypass Road, Bhopal, 462066, Madhya Pradesh, India
| | - Sudipta Ghosh
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal Bhauri, Bhopal Bypass Road, Bhopal, 462066, Madhya Pradesh, India
| | - Anirban Das
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal Bhauri, Bhopal Bypass Road, Bhopal, 462066, Madhya Pradesh, India
| | - Ishu Saraogi
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal Bhauri, Bhopal Bypass Road, Bhopal, 462066, Madhya Pradesh, India
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal Bhauri, Bhopal Bypass Road, Bhopal, 462066, Madhya Pradesh, India
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4
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Shivakumar KM, Mahendran G, Brown JA. Locked Nucleic Acid Oligonucleotides Facilitate RNA•LNA-RNA Triple-Helix Formation and Reduce MALAT1 Levels. Int J Mol Sci 2024; 25:1630. [PMID: 38338910 PMCID: PMC10855403 DOI: 10.3390/ijms25031630] [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: 12/01/2023] [Revised: 01/25/2024] [Accepted: 01/25/2024] [Indexed: 02/12/2024] Open
Abstract
Metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) and multiple endocrine neoplasia-β (MENβ) are two long noncoding RNAs upregulated in multiple cancers, marking these RNAs as therapeutic targets. While traditional small-molecule and antisense-based approaches are effective, we report a locked nucleic acid (LNA)-based approach that targets the MALAT1 and MENβ triple helices, structures comprised of a U-rich internal stem-loop and an A-rich tract. Two LNA oligonucleotides resembling the A-rich tract (i.e., A9GCA4) were examined: an LNA (L15) and a phosphorothioate LNA (PS-L15). L15 binds tighter than PS-L15 to the MALAT1 and MENβ stem loops, although both L15 and PS-L15 enable RNA•LNA-RNA triple-helix formation. Based on UV thermal denaturation assays, both LNAs selectively stabilize the Hoogsteen interface by 5-13 °C more than the Watson-Crick interface. Furthermore, we show that L15 and PS-L15 displace the A-rich tract from the MALAT1 and MENβ stem loop and methyltransferase-like protein 16 (METTL16) from the METTL16-MALAT1 triple-helix complex. Human colorectal carcinoma (HCT116) cells transfected with LNAs have 2-fold less MALAT1 and MENβ. This LNA-based approach represents a potential therapeutic strategy for the dual targeting of MALAT1 and MENβ.
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Affiliation(s)
| | | | - Jessica A. Brown
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA; (K.M.S.); (G.M.)
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5
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Fazio NT, Mersch KN, Hao L, Lohman TM. E. coli RecB Nuclease Domain Regulates RecBCD Helicase Activity but not Single Stranded DNA Translocase Activity. J Mol Biol 2024; 436:168381. [PMID: 38081382 PMCID: PMC11131135 DOI: 10.1016/j.jmb.2023.168381] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 11/30/2023] [Accepted: 12/01/2023] [Indexed: 12/23/2023]
Abstract
Much is still unknown about the mechanisms by which helicases unwind duplex DNA. Whereas structure-based models describe DNA unwinding as occurring by the ATPase motors mechanically pulling the DNA duplex across a wedge domain in the helicase, biochemical data show that processive DNA unwinding by E. coli RecBCD helicase can occur in the absence of ssDNA translocation by the canonical RecB and RecD motors. Here we show that DNA unwinding is not a simple consequence of ssDNA translocation by the motors. Using stopped-flow fluorescence approaches, we show that a RecB nuclease domain deletion variant (RecBΔNucCD) unwinds dsDNA at significantly slower rates than RecBCD, while the ssDNA translocation rate is unaffected. This effect is primarily due to the absence of the nuclease domain since a nuclease-dead mutant (RecBD1080ACD), which retains the nuclease domain, showed no change in ssDNA translocation or dsDNA unwinding rates relative to RecBCD on short DNA substrates (≤60 base pairs). Hence, ssDNA translocation is not rate-limiting for DNA unwinding. RecBΔNucCD also initiates unwinding much slower than RecBCD from a blunt-ended DNA. RecBΔNucCD also unwinds DNA ∼two-fold slower than RecBCD on long DNA (∼20 kilo base pair) in single molecule optical tweezer experiments, although the rates for RecBD1080ACD unwinding are intermediate between RecBCD and RecBΔNucCD. Surprisingly, significant pauses in DNA unwinding occur even in the absence of chi (crossover hotspot instigator) sites. We hypothesize that the nuclease domain influences the rate of DNA base pair melting, possibly allosterically and that RecBΔNucCD may mimic a post-chi state of RecBCD.
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Affiliation(s)
- Nicole T Fazio
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, United States
| | - Kacey N Mersch
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, United States
| | - Linxuan Hao
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, United States
| | - Timothy M Lohman
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, United States.
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6
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Yelamanda Rao K, Jeelan Basha S, Monika K, Naidu Gajula N, Sivakumar I, Kumar S, Vadde R, Aramati BMR, Subramanyam R, Damu AG. Development of quinazolinone and vanillin acrylamide hybrids as multi-target directed ligands against Alzheimer's disease and mechanistic insights into their binding with acetylcholinesterase. J Biomol Struct Dyn 2023; 41:11148-11165. [PMID: 37098803 DOI: 10.1080/07391102.2023.2203255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 12/13/2022] [Indexed: 04/27/2023]
Abstract
In view of Multi-Target Directed Ligand (MTDL) approach in treating Alzheimer's Disease (AD), a series of novel quinazolinone and vanillin cyanoacetamide based acrylamide derivatives (9a-z) were designed, synthesized, and assessed for their activity against a panel of selected AD targets including acetylcholinesterase (AChE), butyrylcholinesterase (BChE), amyloid β protein (Aβ), and also 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging and neuroprotective activities. Five of the target analogs 9e, 9h, 9 l, 9t and 9z showed elevated AChE inhibitory activity with IC50 values of 1.058 ± 0.06, 1.362 ± 0.09, 1.434 ± 0.10, 1.015 ± 0.10, 1.035 ± 0.02 µM respectively, high inhibition selectivity against AChE over BChE and good DPPH radical scavenging activity. Enzyme kinetic studies of the potent hybrids in the series disclosed their mixed inhibition approach. Active analogs were found to be non-toxic on SK-N-SH cell lines and have excellent neuroprotective effects against H2O2-induced cell death. Strong modulating affinities on Aβ aggregation process were observed for most active compounds since; they irretrievably interrupted the morphology of Aβ42 fibrils, increased the aggregates and declined the Aβ-induced toxicity in neurons. From the fluorescence emission studies, the binding constants (K) were determined as 2.5 ± 0.021x103, 2.7 ± 0.015x103, 3.7 ± 0.020x103, 2.4 ± 0.013x104, and 5.0 ± 0.033x103 M-1 and binding free energies as -5.82 ± 0.033, -6.07 ± 0.042, -6.26 ± 0.015, -7.71 ± 0.024, and -6.29 ± 0.026 kcal M-1 for complexes of AChE-9e, 9h, 9 l, 9t and 9z, respectively. Moreover, the CD analysis inferred the limited modifications in the AChE secondary structure when it binds to 9e, 9h, 9 l, 9t and 9z. On the basis of docking studies against AChE, the most active congeners were well oriented in the enzyme's active site by interacting with both catalytic active site (CAS) and peripheral anionic site (PAS). In summary, these quinazolinone and vanillin acrylamide hybrid analogs can be used as promising molecular template to further explore their in vivo efficiency in the development of lead compound to treat AD.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Kandrakonda Yelamanda Rao
- Bioorganic Chemistry Research Laboratory, Department of Chemistry, Yogi Vemana University, Kadapa, Andhra Pradesh, India
| | - Shaik Jeelan Basha
- Bioorganic Chemistry Research Laboratory, Department of Chemistry, Yogi Vemana University, Kadapa, Andhra Pradesh, India
| | - Kallubai Monika
- Department of Biochemistry, Rayalaseema University, Kurnool, Andhra Pradesh, India
| | - Navya Naidu Gajula
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Irla Sivakumar
- Soft Condensed Matter, Raman Research Institute, Sadashivanagar, Bangalore, India
| | - Sandeep Kumar
- Soft Condensed Matter, Raman Research Institute, Sadashivanagar, Bangalore, India
- Department of Chemistry, Nitte Meenakshi Institute of Technology, Yelahanka, Bangalore, India
| | - Ramakrishna Vadde
- Department of Biotechnology and Bioinformatics, Yogi Vemana University, Kadapa, Andhra Pradesh, India
| | | | - Rajagopal Subramanyam
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Amooru Gangaiah Damu
- Bioorganic Chemistry Research Laboratory, Department of Chemistry, Yogi Vemana University, Kadapa, Andhra Pradesh, India
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Fazio N, Mersch KN, Hao L, Lohman TM. E. coli RecBCD Nuclease Domain Regulates Helicase Activity but not Single Stranded DNA Translocase Activity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.13.561901. [PMID: 37905078 PMCID: PMC10614803 DOI: 10.1101/2023.10.13.561901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Much is still unknown about the mechanisms by which helicases unwind duplex DNA. Whereas structure-based models describe DNA unwinding as a consequence of mechanically pulling the DNA duplex across a wedge domain in the helicase by the single stranded (ss)DNA translocase activity of the ATPase motors, biochemical data indicate that processive DNA unwinding by the E. coli RecBCD helicase can occur in the absence of ssDNA translocation of the canonical RecB and RecD motors. Here, we present evidence that dsDNA unwinding is not a simple consequence of ssDNA translocation by the RecBCD motors. Using stopped-flow fluorescence approaches, we show that a RecB nuclease domain deletion variant (RecB ΔNuc CD) unwinds dsDNA at significantly slower rates than RecBCD, while the rate of ssDNA translocation is unaffected. This effect is primarily due to the absence of the nuclease domain and not the absence of the nuclease activity, since a nuclease-dead mutant (RecB D1080A CD), which retains the nuclease domain, showed no significant change in rates of ssDNA translocation or dsDNA unwinding relative to RecBCD on short DNA substrates (≤ 60 base pairs). This indicates that ssDNA translocation is not rate-limiting for DNA unwinding. RecB ΔNuc CD also initiates unwinding much slower than RecBCD from a blunt-ended DNA, although it binds with higher affinity than RecBCD. RecB ΔNuc CD also unwinds DNA ∼two-fold slower than RecBCD on long DNA (∼20 kilo base pair) in single molecule optical tweezer experiments, although the rates for RecB D1080A CD unwinding are intermediate between RecBCD and RecB ΔNuc CD. Surprisingly, significant pauses occur even in the absence of chi (crossover hotspot instigator) sites. We hypothesize that the nuclease domain influences the rate of DNA base pair melting, rather than DNA translocation, possibly allosterically. Since the rate of DNA unwinding by RecBCD also slows after it recognizes a chi sequence, RecB ΔNuc CD may mimic a post- chi state of RecBCD.
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8
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Pontarelli A, Wilds CJ. C5-Propynyl modified 2'-fluoroarabinonucleic acids form stable duplexes with RNA that are RNase H competent. Org Biomol Chem 2023; 21:7437-7446. [PMID: 37667655 DOI: 10.1039/d3ob01297b] [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: 09/06/2023]
Abstract
The clinical success of the antisense approach for the treatment of genetic disorders is indisputably the result of chemical modifications along the oligonucleotide (ON) scaffold, which impart desirable properties including high RNA affinity, nuclease stability and improved drug delivery. While effective, many modifications are not capable of eliciting an RNase H response limiting their application in antisense systems. To contribute to the structural design and inventory of nucleoside analogues with favorable antisense properties, herein we describe the synthesis of C5-propynyl-2'-fluoroarabinonucleic acids (FANAP). Incorporation of individual and multiple uridine (FaraUP) and cytidine (FaraCP) inserts into ONs revealed, both stabilized duplexes formed with RNA. In contrast, these modifications demonstrated a negligible (FaraUP) or reduced (FaraCP) effect on DNA binding. Moreover, modified ONs containing these analogues supported E. coli RNase H cleavage of RNA with an altered cleavage pattern observed relative to controls. Moreover, a 2'-O-methoxyethyl (2'-O-MOE) gapmer with a FANAP core was able to elicit RNA cleavage at an increased rate compared to C5-propynyl-arabinonucleic acids (ANAP). Enzymatic hydrolysis of these gapmers was assessed with nuclease S1 digestion and revealed greater stability of ANAP compared to FANAP. These results suggest C5-propynyl ANA/FANA modifications demonstrate promising potential for the design of therapeutic ONs.
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Affiliation(s)
- Alexander Pontarelli
- Department of Chemistry and Biochemistry, Concordia University, 7141 Sherbrooke St. W., Montréal, Québec H4B 1R6, Canada.
| | - Christopher J Wilds
- Department of Chemistry and Biochemistry, Concordia University, 7141 Sherbrooke St. W., Montréal, Québec H4B 1R6, Canada.
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Yoon S, Ollie E, York DM, Piccirilli JA, Harris ME. Rapid Kinetics of Pistol Ribozyme: Insights into Limits to RNA Catalysis. Biochemistry 2023. [PMID: 37294744 DOI: 10.1021/acs.biochem.3c00160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Pistol ribozyme (Psr) is a distinct class of small endonucleolytic ribozymes, which are important experimental systems for defining fundamental principles of RNA catalysis and designing valuable tools in biotechnology. High-resolution structures of Psr, extensive structure-function studies, and computation support a mechanism involving one or more catalytic guanosine nucleobases acting as a general base and divalent metal ion-bound water acting as an acid to catalyze RNA 2'-O-transphosphorylation. Yet, for a wide range of pH and metal ion concentrations, the rate of Psr catalysis is too fast to measure manually and the reaction steps that limit catalysis are not well understood. Here, we use stopped-flow fluorescence spectroscopy to evaluate Psr temperature dependence, solvent H/D isotope effects, and divalent metal ion affinity and specificity unconstrained by limitations due to fast kinetics. The results show that Psr catalysis is characterized by small apparent activation enthalpy and entropy changes and minimal transition state H/D fractionation, suggesting that one or more pre-equilibrium steps rather than chemistry is rate limiting. Quantitative analyses of divalent ion dependence confirm that metal aquo ion pKa correlates with higher rates of catalysis independent of differences in ion binding affinity. However, ambiguity regarding the rate-limiting step and similar correlation with related attributes such as ionic radius and hydration free energy complicate a definitive mechanistic interpretation. These new data provide a framework for further interrogation of Psr transition state stabilization and show how thermal instability, metal ion insolubility at optimal pH, and pre-equilibrium steps such as ion binding and folding limit the catalytic power of Psr suggesting potential strategies for further optimization.
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Affiliation(s)
- Suhyun Yoon
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Edward Ollie
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Darrin M York
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - Joseph A Piccirilli
- Department of Chemistry and Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, United States
| | - Michael E Harris
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
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Trinh T, Thompson IAP, Clark F, Remington JM, Eisenstein M, Li J, Soh HT. A Photoresponsive Intramolecular Triplex Motif That Enables Rapid and Reversible Control of Aptamer Binding Activity. ACS NANO 2022; 16:14549-14557. [PMID: 36094303 DOI: 10.1021/acsnano.2c05010] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
DNA switches that can change conformation in response to certain wavelengths of light could enable rapid and noninvasive control of chemical processes for a wide range of applications. However, most current photoresponsive DNA switches are limited by either irreversible switching or reversible switching with impractically slow kinetics. Here, we report the design of an intramolecular triplex photoswitch (TPS) design based on single-stranded DNA that undergoes rapid and reversible photoswitching between folded and unfolded states through isomerization of internal azobenzene modifications. After optimizing the performance of our photoswitch design, we used molecular dynamics simulations to reveal how individual azobenzenes contribute to the stabilization or destabilization of the triplex depending on their photoisomerization state. By coupling our TPS to an existing aptamer, we can reversibly modulate its binding affinity with less than 15 s of UV light exposure. We further demonstrate reproducible shifting in affinity over multiple cycles of UV and blue light irradiation without substantial photobleaching.
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Affiliation(s)
- Tuan Trinh
- Department of Radiology, Stanford University, Stanford, California 94305, United States
| | - Ian Andrew Paul Thompson
- Department of Electrical Engineering, Stanford University, Stanford, California 94305, United States
| | - Finley Clark
- Department of Chemistry, The University of Vermont, Burlington, Vermont 05405, United States
| | - Jacob M Remington
- Department of Chemistry, The University of Vermont, Burlington, Vermont 05405, United States
| | - Michael Eisenstein
- Department of Radiology, Stanford University, Stanford, California 94305, United States
| | - Jianing Li
- Department of Chemistry, The University of Vermont, Burlington, Vermont 05405, United States
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
| | - Hyongsok Tom Soh
- Department of Radiology, Stanford University, Stanford, California 94305, United States
- Department of Electrical Engineering, Stanford University, Stanford, California 94305, United States
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11
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Géci I, Fatthalla MI, Heintz M, Jørgensen PT, Pedersen EB. Hoogsteen triplexes stabilized through ethynyl-linked pyrene-indole synthesized by high-temperature Sonogashira coupling. Org Biomol Chem 2022; 20:8873-8884. [PMID: 36102841 DOI: 10.1039/d2ob01466a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The low binding affinity of unmodified triplex-forming oligonucleotides (TFO) is the main drawback to their promising utilization in gene therapy. In the present study, we have synthesized DNA intercalator 5-(pyren-1-ylethynyl)indole Y, known as twisted intercalating nucleic acid (TINA), by a Cu-mediated Sonogashira palladium-catalyzed coupling reaction of 1-ethynylpyrene with 5-iodoindole at a high temperature under anaerobic conditions. Coupling with indole C-5 was far more preferable in obtaining stable TINA-indole than enamine site C-3, as neither hydration of the triple bond to ketones nor competitive Glaser-type homocoupling of acetylenes was observed. The insertion of the new TINA monomer Y as a bulge in the middle or at the 5'-end of the oligodeoxynucleotide sequence via a flexible butane-1,2-diol linker showed extraordinary binding potential, resulting in excellent thermal stabilization of Hoogsteen-type triplex- and duplex-deoxyribonucleic acid (DNA) structures which was detected by thermal denaturation studies and supported by circular dichroism (CD). Molecular dynamics AMBER* revealed the lowest energy conformation in which a pyrenyl residue of the TINA monomer Y stacks in the dsDNA part, while an indolyl unit intercalates between the nucleobases of the TFO pattern. Overall the torsionally rigid conjugated TINA system with a decent twisting of 15.1° around acetylene is confirmed here as a requirement for the best fit inside the intercalation site of the triplex, resulting in high TFO-dsDNA affinity.
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Affiliation(s)
- Imrich Géci
- Department of Medical and Clinical Biophysics, Faculty of Medicine, P. J. Šafárik University in Košice, Trieda SNP 1, 04011 Košice, Slovakia. .,Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230, Odense M, Denmark
| | - Maha I Fatthalla
- Department of Chemistry, Faculty of Science, Helwan University, 11795 Ain Helwan, Cairo, Egypt.,Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230, Odense M, Denmark.,Universite Paris-Sud, CNRS, Faculte de Pharmacie, 5 rue J.-B. Clement, Chatenay-Malabry, 92296 France
| | - Maike Heintz
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230, Odense M, Denmark
| | - Per T Jørgensen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230, Odense M, Denmark
| | - Erik B Pedersen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230, Odense M, Denmark
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12
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Yasuhara H, Yoshida T, Sasaki K, Obika S, Inoue T. Reduction of Off-Target Effects of Gapmer Antisense Oligonucleotides by Oligonucleotide Extension. Mol Diagn Ther 2022; 26:117-127. [PMID: 34994962 PMCID: PMC8766371 DOI: 10.1007/s40291-021-00573-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/05/2021] [Indexed: 12/03/2022]
Abstract
Aim Antisense oligonucleotide (ASO) has the potential to induce off-target effects by inadvertent binding of ASOs to unintended RNAs that have a sequence similar to the target RNA. In the present study, we focused on the association between oligonucleotide length and off-target effects. Oligonucleotide extension is assumed to have bilateral effects on hybridization-dependent changes in gene expression, i.e., one is the decrease of off-target effects based on the reduced number of off-target candidate genes with perfect matches, and the other is the increase of off-target effects based on the increased binding affinity between the ASO and the complementary RNAs that leads to better tolerability for mismatches. Methods To determine the effects of oligonucleotide extension of gapmer ASOs on off-target effects, an extensive microarray analysis was performed using human cells treated with a 14-mer gapmer ASO and the extended 18-mer derivatives with the same core 14-mer region. Results and Discussion Our data indicated that change in gene expression in the cells treated with 18-mer ASOs was significantly smaller than those with a 14-mer ASO, showing the decrease of off-target effects by oligonucleotide extension. Supplementary Information The online version contains supplementary material available at 10.1007/s40291-021-00573-z.
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Affiliation(s)
- Hidenori Yasuhara
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan
| | - Tokuyuki Yoshida
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan
- Division of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, Kawasaki, Kanagawa, Japan
| | - Kiyomi Sasaki
- Division of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, Kawasaki, Kanagawa, Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan.
| | - Takao Inoue
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan.
- Division of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, Kawasaki, Kanagawa, Japan.
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13
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Rusling DA. Triplex-forming properties and enzymatic incorporation of a base-modified nucleotide capable of duplex DNA recognition at neutral pH. Nucleic Acids Res 2021; 49:7256-7266. [PMID: 34233006 PMCID: PMC8287925 DOI: 10.1093/nar/gkab572] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 05/31/2021] [Accepted: 07/06/2021] [Indexed: 11/14/2022] Open
Abstract
The sequence-specific recognition of duplex DNA by unmodified parallel triplex-forming oligonucleotides is restricted to low pH conditions due to a necessity for cytosine protonation in the third strand. This has severely restricted their use as gene-targeting agents, as well as for the detection and/or functionalisation of synthetic or genomic DNA. Here I report that the nucleobase 6-amino-5-nitropyridin-2-one (Z) finally overcomes this constraint by acting as an uncharged mimic of protonated cytosine. Synthetic TFOs containing the nucleobase enabled stable and selective triplex formation at oligopurine-oligopyrimidine sequences containing multiple isolated or contiguous GC base pairs at neutral pH and above. Moreover, I demonstrate a universal strategy for the enzymatic assembly of Z-containing TFOs using its commercially available deoxyribonucleotide triphosphate. These findings seek to improve not only the recognition properties of TFOs but also the cost and/or expertise associated with their chemical syntheses.
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Affiliation(s)
- David A Rusling
- School of Biological Sciences, University of Southampton, Southampton, Hampshire SO17 1BJ, UK
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14
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The method utilized to purify the SARS-CoV-2 N protein can affect its molecular properties. Int J Biol Macromol 2021; 188:391-403. [PMID: 34371045 PMCID: PMC8343380 DOI: 10.1016/j.ijbiomac.2021.08.026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 08/02/2021] [Accepted: 08/03/2021] [Indexed: 12/30/2022]
Abstract
One of the main structural proteins of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the nucleocapsid protein (N). The basic function of this protein is to bind genomic RNA and to form a protective nucleocapsid in the mature virion. The intrinsic ability of the N protein to interact with nucleic acids makes its purification very challenging. Therefore, typically employed purification methods appear to be insufficient for removing nucleic acid contamination. In this study, we present a novel purification protocol that enables the N protein to be prepared without any bound nucleic acids. We also performed comparative structural analysis of the N protein contaminated with nucleic acids and free of contamination and showed significant differences in the structural and phase separation properties of the protein. These results indicate that nucleic-acid contamination may severely affect molecular properties of the purified N protein. In addition, the notable ability of the N protein to form condensates whose morphology and behaviour suggest more ordered forms resembling gel-like or solid structures is described.
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15
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Lohani N, Rajeswari MR. Antigene and Antiproliferative Effects of Triplex-Forming Oligonucleotide (TFO) Targeted on hmgb1 Gene in Human Hepatoma Cells. Anticancer Agents Med Chem 2021; 20:1943-1955. [PMID: 32560618 DOI: 10.2174/1871520620666200619170438] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 03/30/2020] [Accepted: 04/12/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND The high mobility group box 1 (hmgb1) is one of the frequently over-expressed genes whose aberrant expression is reported in a number of human cancers. Various strategies are underway to inhibit hmgb1 expression in cancer cells having considerable therapeutic value. OBJECTIVE The present work involves selective transcriptional inhibition of the hmgb1 gene using selective DNA triplex structure-based gene technology. Here, the promoter region of the hmgb1 gene at position (-183 to -165) from the transcription start site as a target was selected using bioinformatic tools. METHODS The DNA triplex formation by the DNA of the target gene and TFO was confirmed using UV absorption spectroscopy, Circular Dichroism, and Isothermal Calorimetry. RESULTS Treatment of HepG2 cell with specific Triplex-forming Oligonucleotide significantly downregulated HMGB1 expression level at mRNA and protein levels by 50%, while the classical anticancer drugs, actinomycin/ adriamycin as positive controls showed 65% and the combination of TFO and drug decreased by 70%. The anti-proliferative effects of TFO correlated well with the fact of accumulation of cells in the Go phase and apoptotic cell death. Further, the binding of anti-cancer drugs to hmgb1 is stronger in DNA triplex state as compared to hmgb1 alone, suggesting the combination therapy as a better option. CONCLUSION Therefore, the ability of hmgb1 targeted triplex-forming oligonucleotide in combination with triplex selective anticancer drug holds promise in the treatment of malignancies associated with hmgb1 overexpression. The result obtained may open up new vistas to provide a basis for the rational drug design and searching for high-affinity ligands with a high triplex selectivity.
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Affiliation(s)
- Neelam Lohani
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - Moganty R Rajeswari
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
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16
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RNA:DNA triple helices: from peculiar structures to pervasive chromatin regulators. Essays Biochem 2021; 65:731-740. [PMID: 33835128 DOI: 10.1042/ebc20200089] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 03/10/2021] [Accepted: 03/23/2021] [Indexed: 11/17/2022]
Abstract
The genomes of complex eukaryotes largely contain non-protein-coding DNA, which is pervasively transcribed into a plethora of non-coding RNAs (ncRNAs). The functional importance of many of these ncRNAs has been investigated in the last two decades, revealing their crucial and multifaceted roles in chromatin regulation. A common mode of action of ncRNAs is the recruitment of chromatin modifiers to specific regions in the genome. Whereas many ncRNA-protein interactions have been characterised in detail, binding of ncRNAs to their DNA target sites is much less understood. Recently developed RNA-centric methods have mapped the genome-wide distribution of ncRNAs, however, how ncRNAs achieve locus-specificity remains mainly unresolved. In terms of direct RNA-DNA interactions, two kinds of triple-stranded structures can be formed: R-loops consisting of an RNA:DNA hybrid and a looped out DNA strand, and RNA:DNA triple helices (triplexes), in which the RNA binds to the major groove of the DNA double helix by sequence-specific Hoogsteen base pairing. In this essay, we will review the current knowledge about RNA:DNA triplexes, summarising triplex formation rules, detection methods, and ncRNAs reported to engage in triplexes. While the functional characterisation of RNA:DNA triplexes is still anecdotal, recent advances in high-throughput and computational analyses indicate their widespread distribution in the genome. Thus, we are witnessing a paradigm shift in the appreciation of RNA:DNA triplexes, away from exotic structures towards a prominent mode of ncRNA-chromatin interactions.
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17
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Školáková P, Badri Z, Foldynová-Trantírková S, Ryneš J, Šponer J, Fojtová M, Fajkus J, Marek R, Vorlíčková M, Mergny JL, Trantírek L. Composite 5-methylations of cytosines modulate i-motif stability in a sequence-specific manner: Implications for DNA nanotechnology and epigenetic regulation of plant telomeric DNA. Biochim Biophys Acta Gen Subj 2020; 1864:129651. [DOI: 10.1016/j.bbagen.2020.129651] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 05/23/2020] [Accepted: 05/28/2020] [Indexed: 12/14/2022]
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18
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Bolz M, Thomas L, Scheffer U, Kalden E, Hartmann RK, Göbel MW. Redirection of miRNA-Argonaute Complexes to Specific Target Sites by Synthetic Adaptor Molecules. Chem Biodivers 2020; 17:e2000272. [PMID: 32428353 DOI: 10.1002/cbdv.202000272] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 05/19/2020] [Indexed: 12/28/2022]
Abstract
Dysregulation of miRNAs is connected with a multitude of diseases for which antagomirs and miRNA replacement are discussed as therapeutic options. Here, we suggest an alternative concept based on the redirection of RISCs to non-native target sites. Metabolically stable DNA-LNA mixmers are used to mediate the binding of RISCs to mRNAs without any direct base complementarity to the presented guide RNA strand. Physical redirection of a dye-labeled miRNA model and of specific miRNA-programmed RISC fractions present in HeLa extracts is demonstrated by pull-down experiments with biotinylated capture oligonucleotides.
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Affiliation(s)
- Mathias Bolz
- Institute of Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Max-von-Laue-Str. 7, DE-60438, Frankfurt, Germany
| | - Laura Thomas
- Institute of Pharmaceutical Chemistry, Philipps University Marburg, Marbacher Weg 6-10, DE-35032, Marburg, Germany
| | - Ute Scheffer
- Institute of Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Max-von-Laue-Str. 7, DE-60438, Frankfurt, Germany
| | - Elisabeth Kalden
- Institute of Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Max-von-Laue-Str. 7, DE-60438, Frankfurt, Germany
| | - Roland K Hartmann
- Institute of Pharmaceutical Chemistry, Philipps University Marburg, Marbacher Weg 6-10, DE-35032, Marburg, Germany
| | - Michael W Göbel
- Institute of Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Max-von-Laue-Str. 7, DE-60438, Frankfurt, Germany
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19
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Zellmann F, Göbel MW. A Trisbenzimidazole Phosphoramidite Building Block Enables High-Yielding Syntheses of RNA-Cleaving Oligonucleotide Conjugates. Molecules 2020; 25:molecules25081842. [PMID: 32316292 PMCID: PMC7221912 DOI: 10.3390/molecules25081842] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 04/13/2020] [Accepted: 04/14/2020] [Indexed: 12/03/2022] Open
Abstract
The RNA cleaving catalyst tris(2-aminobenzimidazole) when attached to the 5’ terminus of oligonucleotides cuts complementary RNA strands in a highly site-specific manner. Conjugation was previously achieved by the acylation of an amino linker by an active ester of the catalyst. However, this procedure was low yielding and not reliable. Here, a phosphoramidite building block is described that can be coupled to oligonucleotides by manual solid phase synthesis in total yields around 85%. Based on this chemistry, we have now studied the impact of LNA (locked nucleic acids) nucleotides on the rates and the site-specificities of RNA cleaving conjugates. The highest reaction rates and the most precise cuts can be expected when the catalyst is attached to a strong 5’ closing base pair and when the oligonucleotide contains several LNA units that are equally distributed in the strand. However, when placed in the 5’ position, LNA building blocks tend to diminish the specificity of RNA cleavage.
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20
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Školáková P, Renčiuk D, Palacký J, Krafčík D, Dvořáková Z, Kejnovská I, Bednářová K, Vorlíčková M. Systematic investigation of sequence requirements for DNA i-motif formation. Nucleic Acids Res 2019; 47:2177-2189. [PMID: 30715498 PMCID: PMC6412112 DOI: 10.1093/nar/gkz046] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 01/16/2019] [Accepted: 01/18/2019] [Indexed: 12/13/2022] Open
Abstract
The formation of intercalated motifs (iMs) - secondary DNA structures based on hemiprotonated C.C+ pairs in suitable cytosine-rich DNA sequences, is reflected by typical changes in CD and UV absorption spectra. By means of spectroscopic methods, electrophoresis, chemical modifications and other procedures, we characterized iM formation and stability in sequences with different cytosine block lengths interrupted by various numbers and types of nucleotides. Particular attention was paid to the formation of iMs at pH conditions close to neutral. We identified the optimal conditions and minimal requirements for iM formation in DNA sequences, and addressed gaps and inaccurate data interpretations in existing studies to specify principles of iM formation and modes of their folding.
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Affiliation(s)
- Petra Školáková
- Institute of Biophysics of the Czech Academy of Sciences, v.v.i., Královopolská 135, 612 65 Brno, Czech Republic
| | - Daniel Renčiuk
- Institute of Biophysics of the Czech Academy of Sciences, v.v.i., Královopolská 135, 612 65 Brno, Czech Republic
| | - Jan Palacký
- Institute of Biophysics of the Czech Academy of Sciences, v.v.i., Královopolská 135, 612 65 Brno, Czech Republic
| | - Daniel Krafčík
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 735/5, 625 00 Brno, Czech Republic
| | - Zuzana Dvořáková
- Institute of Biophysics of the Czech Academy of Sciences, v.v.i., Královopolská 135, 612 65 Brno, Czech Republic
| | - Iva Kejnovská
- Institute of Biophysics of the Czech Academy of Sciences, v.v.i., Královopolská 135, 612 65 Brno, Czech Republic
| | - Klára Bednářová
- Institute of Biophysics of the Czech Academy of Sciences, v.v.i., Královopolská 135, 612 65 Brno, Czech Republic
| | - Michaela Vorlíčková
- Institute of Biophysics of the Czech Academy of Sciences, v.v.i., Královopolská 135, 612 65 Brno, Czech Republic
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21
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Dvoráková Z, Renciuk D, Kejnovská I, Školáková P, Bednárová K, Sagi J, Vorlícková M. i-Motif of cytosine-rich human telomere DNA fragments containing natural base lesions. Nucleic Acids Res 2019; 46:1624-1634. [PMID: 29378012 PMCID: PMC5829569 DOI: 10.1093/nar/gky035] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 01/15/2018] [Indexed: 12/01/2022] Open
Abstract
i-Motif (iM) is a four stranded DNA structure formed by cytosine-rich sequences, which are often present in functionally important parts of the genome such as promoters of genes and telomeres. Using electronic circular dichroism and UV absorption spectroscopies and electrophoretic methods, we examined the effect of four naturally occurring DNA base lesions on the folding and stability of the iM formed by the human telomere DNA sequence (C3TAA)3C3T. The results demonstrate that the TAA loop lesions, the apurinic site and 8-oxoadenine substituting for adenine, and the 5-hydroxymethyluracil substituting for thymine only marginally disturb the formation of iM. The presence of uracil, which is formed by enzymatic or spontaneous deamination of cytosine, shifts iM formation towards substantially more acidic pH values and simultaneously distinctly reduces iM stability. This effect depends on the position of the damage sites in the sequence. The results have enabled us to formulate additional rules for iM formation.
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Affiliation(s)
- Zuzana Dvoráková
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Daniel Renciuk
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Iva Kejnovská
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Petra Školáková
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Klára Bednárová
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Janos Sagi
- Rimstone Laboratory, RLI, Carlsbad, CA 92010, USA
| | - Michaela Vorlícková
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
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22
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Charak S, Shandilya M, Mehrotra R. RNA targeting by an anthracycline drug: spectroscopic and in silico evaluation of epirubicin interaction with tRNA. J Biomol Struct Dyn 2019; 38:1761-1771. [PMID: 31084352 DOI: 10.1080/07391102.2019.1617786] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Anthracyclines are putative anticancer agents used to treat a wide range of cancers. Among these anthracyclines, epirubicin is derived from the doxorubicin by the subtle difference in the orientation of C4-hydroxyl group at sugar molecule. Epirubicin has great significance as it has propitious anticancer potential with lesser cardiotoxicity and faster elimination from the body. The present study is done to understand the molecular aspect of epirubicin binding to tRNA. We have used various spectroscopic techniques like Fourier transform infrared spectroscopy (FTIR), absorption spectroscopy and circular dichroism to illustrate the binding sites, the extent of binding and conformational changes associated with tRNA after interacting with epirubicin. From infrared studies, we infer that epirubicin interacts with guanine and uracil bases of tRNA. Results obtained from infrared and CD studies suggest that epirubicin complexation with tRNA does not result in any conformational change in tRNA structure. Binding constant (2.1 × 103 M-1) calculated from the absorbance data illustrates that epirubicin has a weak interaction with tRNA molecule. These spectroscopic results like the binding site of epirubicin and binding energy of epirubicin-tRNA complex were also verified by the molecular docking. Results of the present study provide information that aids in the development of efficient RNA targeted drugs from the existing drugs by certain chemical modification in their structure resulting in lesser side effects and better efficacy.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sonika Charak
- Physico Mechanical Metrology Division, CSIR-National Physical Laboratory, New Delhi, India
| | - Manish Shandilya
- Amity School of Applied Sciences, Amity University Haryana, Gurgaon, India
| | - Ranjana Mehrotra
- Physico Mechanical Metrology Division, CSIR-National Physical Laboratory, New Delhi, India
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23
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Erlenbach N, Grünewald C, Krstic B, Heckel A, Prisner TF. "End-to-end" stacking of small dsRNA. RNA (NEW YORK, N.Y.) 2019; 25:239-246. [PMID: 30404925 PMCID: PMC6348986 DOI: 10.1261/rna.068130.118] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 11/06/2018] [Indexed: 05/08/2023]
Abstract
PELDOR (pulsed electron-electron double resonance) is an established method to study intramolecular distances and can give evidence for conformational changes and flexibilities. However, it can also be used to study intermolecular interactions as for example oligerimization. Here, we used PELDOR to study the "end-to-end" stacking of small double-stranded (ds) RNAs. For this study, the dsRNA molecules were only singly labeled with the spin label TPA to avoid multispin effects and to measure only the intermolecular stacking interactions. It can be shown that small dsRNAs tend to assemble to rod-like structures due to π-π interactions between the base pairs at the end of the strands. On the one hand, these interactions can influence or complicate measurements aimed at the determining of the structure and dynamics of the dsRNA molecule itself. On the other hand, it can be interesting to study such intermolecular stacking interactions in more detail, as for example their dependence on ion concentration. We quantitatively determined the stacking probability as a function of the monovalent NaCl salt and the dsRNA concentration. From these data, the dissociation constant Kd was deduced and found to depend on the ratio between the NaCl salt and dsRNA concentrations. Additionally, the distances and distance distributions obtained predict a model for the stacking geometry of dsRNAs. Introducing a nucleotide overhangs at one end of the dsRNA molecule restricts the stacking to the other end, leading only to dimer formations. Introducing such an overhang at both ends of the dsRNA molecule fully suppresses stacking, as we demonstrate by PELDOR experiments quantitatively.
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Affiliation(s)
- Nicole Erlenbach
- Institute of Physical and Theoretical Chemistry, Center of Biomolecular Magnetic Resonance, Goethe University, D-60438 Frankfurt am Main, Germany
| | - Christian Grünewald
- Institute of Organic Chemistry and Chemical Biology, Goethe University, D-60438 Frankfurt am Main, Germany
| | - Bisera Krstic
- Institute of Physical and Theoretical Chemistry, Center of Biomolecular Magnetic Resonance, Goethe University, D-60438 Frankfurt am Main, Germany
| | - Alexander Heckel
- Institute of Organic Chemistry and Chemical Biology, Goethe University, D-60438 Frankfurt am Main, Germany
| | - Thomas F Prisner
- Institute of Physical and Theoretical Chemistry, Center of Biomolecular Magnetic Resonance, Goethe University, D-60438 Frankfurt am Main, Germany
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24
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Kejnovská I, Renčiuk D, Palacký J, Vorlíčková M. CD Study of the G-Quadruplex Conformation. Methods Mol Biol 2019; 2035:25-44. [PMID: 31444742 DOI: 10.1007/978-1-4939-9666-7_2] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Circular Dichroic (CD) spectroscopy is one of the most frequently used methods for guanine quadruplex studies and in general for studies of conformational properties of nucleic acids. The reason is its high sensitivity to even slight changes in mutual orientation of absorbing bases of DNA. CD can reveal formation of particular structural DNA arrangements and can be used to search for the conditions stabilizing the structures, to follow the transitions between various structural states, to explore kinetics of their appearance, to determine thermodynamic parameters, and also to detect formation of higher order structures. CD spectroscopy is an important complementary technique to NMR spectroscopy and X-ray diffraction in quadruplex studies due to its sensitivity, easy manipulation of studied samples, and relative inexpensiveness. In this part, we present the protocol for the use of CD spectroscopy in the study of guanine quadruplexes, together with practical advice and cautions about various, particularly interpretation, difficulties.
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Affiliation(s)
- Iva Kejnovská
- The Czech Academy of Sciences, Institute of Biophysics, Brno, Czech Republic
| | - Daniel Renčiuk
- The Czech Academy of Sciences, Institute of Biophysics, Brno, Czech Republic
| | - Jan Palacký
- The Czech Academy of Sciences, Institute of Biophysics, Brno, Czech Republic
| | - Michaela Vorlíčková
- The Czech Academy of Sciences, Institute of Biophysics, Brno, Czech Republic.
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25
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Kozuch S, Cultrara CN, Beck AE, Heller CJ, Shah S, Patel MR, Zilberberg J, Sabatino D. Enhanced Cancer Theranostics with Self-Assembled, Multilabeled siRNAs. ACS OMEGA 2018; 3:12975-12984. [PMID: 30411024 PMCID: PMC6217585 DOI: 10.1021/acsomega.8b01999] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Accepted: 09/26/2018] [Indexed: 05/12/2023]
Abstract
The integration of therapy and diagnostics, termed "theranostics", has recently gained widespread utility in the development of new and improved therapeutics that effectively diagnose and treat diseases, such as cancer. In this study, the covalent attachment of multiple fluorescent labels (i.e., fluorescein isothiocyanate (FITC)) to a wide range of siRNAs, including those adopting linear, V- and Y-shape nanostructures, was successfully accomplished by solid-phase bioconjugation for monitoring cell uptake, co-localization, and biological activity in cell culture. The FITC-labeled higher-order V- and Y-shape siRNAs maintained the requisite hybrid stabilities and A-type helical structures for invoking RNAi activity. The FITC-siRNA hybrids with sense-strand modifiers enabled efficient mRNA knockdown (∼50-90%), which also translated to increased cell death (∼20-95%) in a bone metastatic prostate cancer cell line, over a 72 h incubation period. Significantly, the Y-shaped siRNA containing three FITC probes enhanced fluorescent signaling relative to the siRNA constructs containing single and double fluorophores while retaining potent knockdown and cell death effects post-transfection. Taken together, this data highlights the theranostic utility of the multilabeled FITC-siRNA constructs for potential cancer gene therapy applications.
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Affiliation(s)
- Stephen
D. Kozuch
- Department
of Chemistry and Biochemistry, Seton Hall
University, South
Orange, New Jersey 07079, United States
| | - Christopher N. Cultrara
- Department
of Chemistry and Biochemistry, Seton Hall
University, South
Orange, New Jersey 07079, United States
| | - Adah E. Beck
- Department
of Chemistry and Biochemistry, Seton Hall
University, South
Orange, New Jersey 07079, United States
| | - Claudia J. Heller
- Department
of Chemistry and Biochemistry, Seton Hall
University, South
Orange, New Jersey 07079, United States
| | - Sunil Shah
- Department
of Chemistry and Biochemistry, Seton Hall
University, South
Orange, New Jersey 07079, United States
| | - Mayurbhai R. Patel
- Department
of Chemistry and Biochemistry, Seton Hall
University, South
Orange, New Jersey 07079, United States
- Nitto
Denko Avecia Inc, 8560
Reading Road, Cincinnati, Ohio 45215, United
States
| | - Jenny Zilberberg
- Department
of Biomedical Research, Hackensack University
Medical Center, Hackensack, New Jersey 07601, United States
| | - David Sabatino
- Department
of Chemistry and Biochemistry, Seton Hall
University, South
Orange, New Jersey 07079, United States
- E-mail: . Tel: +1-973-313-6359
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26
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Schmidt A, Altincekic N, Gustmann H, Wachtveitl J, Hengesbach M. The Protein Microenvironment Governs the Suitability of Labeling Sites for Single-Molecule Spectroscopy of RNP Complexes. ACS Chem Biol 2018; 13:2472-2483. [PMID: 30060648 DOI: 10.1021/acschembio.8b00348] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Single-molecule techniques allow unique insights into biological systems as they provide unrivaled access to structural dynamics and conformational heterogeneity. One major bottleneck for reliable single-molecule Förster resonance energy transfer (smFRET) analysis is the identification of suitable fluorophore labeling sites that neither impair the function of the biological system nor cause photophysical artifacts of the fluorophore. To address this issue, we identified the contribution of virtually all individual parameters that affect Förster resonance energy transfer between two fluorophores attached to a ribonucleoprotein complex consisting of the RNA-binding protein L7Ae and a cognate kink turn containing RNA. A non-natural amino acid was incorporated at various positions of the protein using an amber suppression system (pEVOL) to label the protein via copper(I)-catalyzed alkyne-azide cycloaddition. On the basis of simulations followed by functional, structural, and multiparameter fluorescence analysis of five different smFRET RNPs, new insights into the design of smFRET RNPs were obtained. From this, a correlation between the photophysical properties of fluorophores attached to the protein and the predictability of the corresponding smFRET construct was established. Additionally, we identify a straightforward experimental method for characterizing selected labeling sites. Overall, this protocol allows fast generation and assessment of functional RNPs for accurate single-molecule experiments.
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Affiliation(s)
- Andreas Schmidt
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, 60438 Frankfurt, Germany
| | - Nadide Altincekic
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, 60438 Frankfurt, Germany
| | - Henrik Gustmann
- Institute for Physical and Theoretical Chemistry, Goethe-University Frankfurt, 60438 Frankfurt, Germany
| | - Josef Wachtveitl
- Institute for Physical and Theoretical Chemistry, Goethe-University Frankfurt, 60438 Frankfurt, Germany
| | - Martin Hengesbach
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, 60438 Frankfurt, Germany
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27
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Basha SJ, Mohan P, Yeggoni DP, Babu ZR, Kumar PB, Rao AD, Subramanyam R, Damu AG. New Flavone-Cyanoacetamide Hybrids with a Combination of Cholinergic, Antioxidant, Modulation of β-Amyloid Aggregation, and Neuroprotection Properties as Innovative Multifunctional Therapeutic Candidates for Alzheimer’s Disease and Unraveling Their Mechanism of Action with Acetylcholinesterase. Mol Pharm 2018; 15:2206-2223. [DOI: 10.1021/acs.molpharmaceut.8b00041] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Shaik Jeelan Basha
- Department of Chemistry, Yogi Vemana University, Andhrapradesh, Kadapa 516003, India
| | - Penumala Mohan
- Department of Chemistry, Yogi Vemana University, Andhrapradesh, Kadapa 516003, India
| | - Daniel Pushparaju Yeggoni
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India
| | - Zinka Raveendra Babu
- Department of Chemistry, Yogi Vemana University, Andhrapradesh, Kadapa 516003, India
| | - Palaka Bhagath Kumar
- Centre for Bioinformatics, School of Life Sciences, Pondicherry Central University, Puducherry 605014, India
| | - Ampasala Dinakara Rao
- Centre for Bioinformatics, School of Life Sciences, Pondicherry Central University, Puducherry 605014, India
| | - Rajagopal Subramanyam
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India
| | - Amooru Gangaiah Damu
- Department of Chemistry, Yogi Vemana University, Andhrapradesh, Kadapa 516003, India
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28
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Tomko EJ, Lohman TM. Modulation of Escherichia coli UvrD Single-Stranded DNA Translocation by DNA Base Composition. Biophys J 2017; 113:1405-1415. [PMID: 28978435 DOI: 10.1016/j.bpj.2017.08.023] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 08/15/2017] [Accepted: 08/16/2017] [Indexed: 10/18/2022] Open
Abstract
Escherichia coli UvrD is an SF1A DNA helicase/translocase that functions in chromosomal DNA repair and replication of some plasmids. UvrD can also displace proteins such as RecA from DNA in its capacity as an anti-recombinase. Central to all of these activities is its ATP-driven 3'-5' single-stranded (ss) DNA translocation activity. Previous ensemble transient kinetic studies have estimated the average translocation rate of a UvrD monomer on ssDNA composed solely of deoxythymidylates. Here we show that the rate of UvrD monomer translocation along ssDNA is influenced by DNA base composition, with UvrD having the fastest rate along polypyrimidines although decreasing nearly twofold on ssDNA containing equal amounts of the four bases. Experiments with DNA containing abasic sites and polyethylene glycol spacers show that the ssDNA base also influences translocation processivity. These results indicate that changes in base composition and backbone insertions influence the translocation rates, with increased ssDNA base stacking correlated with decreased translocation rates, supporting the proposal that base-stacking interactions are involved in the translocation mechanism.
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Affiliation(s)
- Eric J Tomko
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri
| | - Timothy M Lohman
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri.
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29
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Dvořáková Z, Vorlíčková M, Renčiuk D. Spectroscopic insights into quadruplexes of five-repeat telomere DNA sequences upon G-block damage. Biochim Biophys Acta Gen Subj 2017; 1861:2750-2757. [DOI: 10.1016/j.bbagen.2017.07.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 06/16/2017] [Accepted: 07/24/2017] [Indexed: 11/26/2022]
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30
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Ault AP, Stark DI, Axson JL, Keeney JN, Maynard AD, Bergin IL, Philbert MA. Protein Corona-Induced Modification of Silver Nanoparticle Aggregation in Simulated Gastric Fluid. ENVIRONMENTAL SCIENCE. NANO 2016; 3:1510-1520. [PMID: 28357114 PMCID: PMC5366255 DOI: 10.1039/c6en00278a] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Due to their widespread incorporation into a range of biomedical and consumer products, the ingestion of silver nanoparticles (AgNPs) is of considerable concern to human health. However, the extent to which AgNPs will be modified within the gastric compartment of the gastrointestinal tract is still poorly understood. Studies have yet to fully evaluate the extent of physicochemical changes to AgNPs in the presence of biological macromolecules, such as pepsin, the most abundant protein in the stomach, or the influence of AgNPs on protein structure and activity. Herein, AgNPs of two different sizes and surface coatings (20 and 110 nm, citrate or polyvinylpyrrolidone) were added to simulated gastric fluid (SGF) with or without porcine pepsin at three pHs (2.0, 3.5, and 5.0), representing a range of values between preprandial (fasted) and postprandial (fed) conditions. Rapid increases in diameter were observed for all AgNPs, with a greater increase in diameter in the presence of pepsin, indicating that pepsin facilitated AgNPs aggregation. AgNPs interaction with pepsin only minimally reduced the protein's proteolytic functioning capability, with the greatest inhibitory effect caused by smaller (20 nm) particles of both coatings. No changes in pepsin secondary structural elements were observed for the different AgNPs, even at high particle concentrations. This research highlights the size-dependent kinetics of nanoparticle aggregation or dissolution from interaction with biological elements such as proteins in the gastrointestinal tract. Further, these results demonstrate that, in addition to mass, knowing the chemical form and aggregation state of nanoparticles is critical when evaluating toxicological effects from nanoparticle exposure in the body.
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Affiliation(s)
- Andrew P Ault
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, MI; Department of Chemistry, University of Michigan, Ann Arbor, MI
| | - Diana I Stark
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, MI
| | - Jessica L Axson
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, MI
| | - Justin N Keeney
- Department of Chemistry, University of Michigan, Ann Arbor, MI
| | - Andrew D Maynard
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, MI
| | - Ingrid L Bergin
- Unit for Laboratory Animal Medicine, School of Medicine, University of Michigan, Ann Arbor, MI
| | - Martin A Philbert
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, MI
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31
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G-quadruplex formation in the Oct4 promoter positively regulates Oct4 expression. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1860:175-183. [PMID: 27863263 DOI: 10.1016/j.bbagrm.2016.11.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 11/11/2016] [Accepted: 11/14/2016] [Indexed: 11/21/2022]
Abstract
The Oct4 gene codes for a transcription factor that plays a critical role in the maintenance of pluripotency in embryonic and cancer stem cells. Its expression thus has to be tightly regulated. We performed biophysical characterization of the promoter region using a combination of UV absorption, CD, and NMR spectroscopies, native PAGE and chemical probing, which was followed by functional studies involving luciferase reporter assays performed in osteosarcoma and human embryonic stem cell lines. We have shown that the evolutionarily conserved G-rich region close to the Oct4 transcription start site in the non-template strand forms a parallel G-quadruplex structure. We characterized its structure and stability upon point mutations in its primary structure. Functional studies then revealed that whereas the wild type quadruplex sequence ensures high reporter gene expression, the expression of mutated variants is significantly decreased proportionally to the destabilizing effect of the mutations on the quadruplex. A ligand, N-methyl mesoporphyrin IX that increases the stability of formed quadruplex rescued the reporter expression of single-mutated variants to the level of wild-type, but it has no effect on a mutated variant that cannot form quadruplex. These data indicate that the quadruplex acts as a strong, positive regulator of Oct4 expression and as such it might serve as a potential target for therapeutic intervention.
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32
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Patel MR, Kozuch SD, Cultrara CN, Yadav R, Huang S, Samuni U, Koren J, Chiosis G, Sabatino D. RNAi Screening of the Glucose-Regulated Chaperones in Cancer with Self-Assembled siRNA Nanostructures. NANO LETTERS 2016; 16:6099-6108. [PMID: 27669096 PMCID: PMC5378679 DOI: 10.1021/acs.nanolett.6b02274] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
The emerging field of RNA nanotechnology has been used to design well-programmed, self-assembled nanostructures for applications in chemistry, biology, and medicine. At the forefront of its utility in cancer is the unrestricted ability to self-assemble multiple siRNAs within a single nanostructure formulation for the RNAi screening of a wide range of oncogenes while potentiating the gene therapy of malignant tumors. In our RNAi nanotechnology approach, V- and Y-shape RNA templates were designed and constructed for the self-assembly of discrete, higher-ordered siRNA nanostructures targeting the oncogenic glucose regulated chaperones. The GRP78-targeting siRNAs self-assembled into genetically encoded spheres, triangles, squares, pentagons and hexagons of discrete sizes and shapes according to TEM imaging. Furthermore, gel electrophoresis, thermal denaturation, and CD spectroscopy validated the prerequisite siRNA hybrids for their RNAi application. In a 24 sample siRNA screen conducted within the AN3CA endometrial cancer cells known to overexpress oncogenic GRP78 activity, the self-assembled siRNAs targeting multiple sites of GRP78 expression demonstrated more potent and long-lasting anticancer activity relative to their linear controls. Extending the scope of our RNAi screening approach, the self-assembled siRNA hybrids (5 nM) targeting of GRP-75, 78, and 94 resulted in significant (50-95%) knockdown of the glucose regulated chaperones, which led to synergistic effects in tumor cell cycle arrest (50-80%) and death (50-60%) within endometrial (AN3CA), cervical (HeLa), and breast (MDA-MB-231) cancer cell lines. Interestingly, a nontumorigenic lung (MRC5) cell line displaying normal glucose regulated chaperone levels was found to tolerate siRNA treatment and demonstrated less toxicity (5-20%) relative to the cancer cells that were found to be addicted to glucose regulated chaperones. These remarkable self-assembled siRNA nanostructures may thus encompass a new class of potent siRNAs that may be useful in screening important oncogene targets while improving siRNA therapeutic efficacy and specificity in cancer.
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Affiliation(s)
- Mayurbhai R. Patel
- Program in Chemical Biology and Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
- Department of Chemistry and Biochemistry, Seton Hall University, South Orange, New Jersey 07079, United States
| | - Stephen D. Kozuch
- Department of Chemistry and Biochemistry, Seton Hall University, South Orange, New Jersey 07079, United States
| | - Christopher N. Cultrara
- Department of Chemistry and Biochemistry, Seton Hall University, South Orange, New Jersey 07079, United States
| | - Reeta Yadav
- Department of Chemistry and Biochemistry, Queens College, City University of New York, 65-30 Kissena Blvd., Flushing, New York 11367, United States
- Ph.D. Programs in Chemistry and Biochemistry, The Graduate Center of the City University of New York, New York City, New York 10016, United States
| | - Suiying Huang
- Department of Chemistry and Biochemistry, Queens College, City University of New York, 65-30 Kissena Blvd., Flushing, New York 11367, United States
- Ph.D. Programs in Chemistry and Biochemistry, The Graduate Center of the City University of New York, New York City, New York 10016, United States
| | - Uri Samuni
- Department of Chemistry and Biochemistry, Queens College, City University of New York, 65-30 Kissena Blvd., Flushing, New York 11367, United States
- Ph.D. Programs in Chemistry and Biochemistry, The Graduate Center of the City University of New York, New York City, New York 10016, United States
| | - John Koren
- Program in Chemical Biology and Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
| | - Gabriela Chiosis
- Program in Chemical Biology and Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
| | - David Sabatino
- Department of Chemistry and Biochemistry, Seton Hall University, South Orange, New Jersey 07079, United States
- Corresponding Author.
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33
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Adámik M, Kejnovská I, Bažantová P, Petr M, Renčiuk D, Vorlíčková M, Brázdová M. p53 binds human telomeric G-quadruplex in vitro. Biochimie 2016; 128-129:83-91. [PMID: 27422117 DOI: 10.1016/j.biochi.2016.07.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 07/11/2016] [Indexed: 01/08/2023]
Abstract
The tumor suppressor protein p53 is a key factor in genome stability and one of the most studied of DNA binding proteins. This is the first study on the interaction of wild-type p53 with guanine quadruplexes formed by the human telomere sequence. Using electromobility shift assay and ELISA, we show that p53 binding to telomeric G-quadruplexes increases with the number of telomeric repeats. Further, p53 strongly favors G-quadruplexes folded in potassium over those formed in sodium, thus indicating the telomeric G-quadruplex conformational selectivity of p53. The presence of the quadruplex-stabilizing ligand, N-methyl mesoporphyrin IX (NMM), increases p53 recognition of G-quadruplexes in potassium. Using deletion mutants and selective p53 core domain oxidation, both p53 DNA binding domains are shown to be crucial for telomeric G-quadruplex recognition.
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Affiliation(s)
- Matej Adámik
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Kralovopolska 135, CZ-612 65 Brno, Czech Republic
| | - Iva Kejnovská
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Kralovopolska 135, CZ-612 65 Brno, Czech Republic
| | - Pavla Bažantová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Kralovopolska 135, CZ-612 65 Brno, Czech Republic
| | - Marek Petr
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Kralovopolska 135, CZ-612 65 Brno, Czech Republic
| | - Daniel Renčiuk
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Kralovopolska 135, CZ-612 65 Brno, Czech Republic
| | - Michaela Vorlíčková
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Kralovopolska 135, CZ-612 65 Brno, Czech Republic
| | - Marie Brázdová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Kralovopolska 135, CZ-612 65 Brno, Czech Republic.
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34
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Hároníková L, Coufal J, Kejnovská I, Jagelská EB, Fojta M, Dvořáková P, Muller P, Vojtesek B, Brázda V. IFI16 Preferentially Binds to DNA with Quadruplex Structure and Enhances DNA Quadruplex Formation. PLoS One 2016; 11:e0157156. [PMID: 27280708 PMCID: PMC4900677 DOI: 10.1371/journal.pone.0157156] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 05/25/2016] [Indexed: 02/03/2023] Open
Abstract
Interferon-inducible protein 16 (IFI16) is a member of the HIN-200 protein family, containing two HIN domains and one PYRIN domain. IFI16 acts as a sensor of viral and bacterial DNA and is important for innate immune responses. IFI16 binds DNA and binding has been described to be DNA length-dependent, but a preference for supercoiled DNA has also been demonstrated. Here we report a specific preference of IFI16 for binding to quadruplex DNA compared to other DNA structures. IFI16 binds to quadruplex DNA with significantly higher affinity than to the same sequence in double stranded DNA. By circular dichroism (CD) spectroscopy we also demonstrated the ability of IFI16 to stabilize quadruplex structures with quadruplex-forming oligonucleotides derived from human telomere (HTEL) sequences and the MYC promotor. A novel H/D exchange mass spectrometry approach was developed to assess protein interactions with quadruplex DNA. Quadruplex DNA changed the IFI16 deuteration profile in parts of the PYRIN domain (aa 0–80) and in structurally identical parts of both HIN domains (aa 271–302 and aa 586–617) compared to single stranded or double stranded DNAs, supporting the preferential affinity of IFI16 for structured DNA. Our results reveal the importance of quadruplex DNA structure in IFI16 binding and improve our understanding of how IFI16 senses DNA. IFI16 selectivity for quadruplex structure provides a mechanistic framework for IFI16 in immunity and cellular processes including DNA damage responses and cell proliferation.
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Affiliation(s)
- Lucia Hároníková
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65, Brno, Czech Republic
- Department of Biochemistry, Faculty of Science, Masaryk University, Kotlarska 2, 61137, Brno, Czech Republic
| | - Jan Coufal
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65, Brno, Czech Republic
| | - Iva Kejnovská
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65, Brno, Czech Republic
| | - Eva B. Jagelská
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65, Brno, Czech Republic
| | - Miroslav Fojta
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65, Brno, Czech Republic
| | - Petra Dvořáková
- RECAMO, Masaryk Memorial Cancer Institute, Zluty kopec 7, 656 53, Brno, Czech Republic
| | - Petr Muller
- RECAMO, Masaryk Memorial Cancer Institute, Zluty kopec 7, 656 53, Brno, Czech Republic
| | - Borivoj Vojtesek
- RECAMO, Masaryk Memorial Cancer Institute, Zluty kopec 7, 656 53, Brno, Czech Republic
| | - Václav Brázda
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65, Brno, Czech Republic
- * E-mail:
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35
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Nguyen HN, Zhao L, Gray CW, Gray DM, Xia T. Nucleotides sequestered at different subsite loci within DNA-binding pockets of two OB-fold single-stranded DNA-binding proteins are unstacked to different extents. Biopolymers 2016; 99:484-96. [PMID: 23616216 DOI: 10.1002/bip.22204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Accepted: 01/03/2013] [Indexed: 11/07/2022]
Abstract
The gene 5 protein (g5p) encoded by the Ff strains of Escherichia coli bacteriophages is a dimeric single-stranded DNA-binding protein (SSB) that consists of two identical OB-fold (oligonucleotide/oligosaccharide-binding) motifs. Ultrafast time-resolved fluorescence measurements were carried out to investigate the effect of g5p binding on the conformation of 2-aminopurine (2AP) labels positioned between adenines or cytosines in the 16-nucleotide antiparallel tails of DNA hairpins. The measurements revealed significant changes in the conformational heterogeneity of the 2AP labels caused by g5p binding. The extent of the changes was dependent on sub-binding-site location, but generally resulted in base unstacking. When bound by g5p, the unstacked 2AP population increased from ∼ 22% to 59-67% in C-2AP-C segments and from 39% to 77% in an A-2AP-A segment. The OB-fold RPA70A domain of the human replication protein A also caused a significant amount of base unstacking at various locations within the DNA binding site as evidenced by steady-state fluorescence titration measurements using 2AP-labeled 5-mer DNAs. These solution studies support the concept that base unstacking at most of a protein's multiple sub-binding-site loci may be a feature that allows non-sequence specific OB-fold proteins to bind to single-stranded DNAs (ssDNAs) with minimal preference for particular sequences.
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Affiliation(s)
- Hieu N Nguyen
- Department of Molecular and Cell Biology, University of Texas at Dallas, Richardson, TX 75080, USA
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36
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Akhter MZ, Rajeswari MR. Triplex forming oligonucleotides targeted to hmga1 selectively inhibit its expression and induce apoptosis in human cervical cancer. J Biomol Struct Dyn 2016; 35:689-703. [PMID: 26923360 DOI: 10.1080/07391102.2016.1160257] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
High-mobility group A1 (HMGA1) is a non-histone chromosomal protein, which is known as 'architectural' transcription factor that facilitates the assembly of 'enhanceosome.' Because of its elevated expression in a number of human malignancies, with barely minimal levels in healthy adults, HMGA1 is considered as potential 'tumor marker.' Therefore, we looked at the inhibition of hmga1 using anti-gene strategy, as an attractive therapeutic approach. This was achieved by two triplex forming oligonucleotides (TFOs), TFO1 and TFO2 targeted to the promoter of hmga1 at positions, -284--304 and -2800--2826, respectively. The stability of two DNA triplexes was characterized using a variety of biophysical and thermodynamics techniques and was confirmed by gel retardation assay using γ-32P [ATP]. The efficacy of TFOs on HMGA1 expression was evaluated in HeLa cells using MTT assay, Flow cytometry, Western blot, and RT-PCR. Results revealed that DNA Triplex1 formed by TFO1 is more stable and stronger than the corresponding Triplex2. Although both TFOs downregulated hmga1 expression at mRNA and protein levels and caused apoptotic cell death in HeLa cell line, TFO1 demonstrated a greater effect at low concentration which corroborates well with the stability data. Thus, TFO-mediated inhibition of hmga1 expression can be a promising strategy for the development of novel anti-cancer therapeutics.
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Affiliation(s)
- Md Zahid Akhter
- a Department of Biochemistry , All India Institute of Medical Sciences , New Delhi - 110029 , India
| | - Moganty R Rajeswari
- a Department of Biochemistry , All India Institute of Medical Sciences , New Delhi - 110029 , India
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37
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Greive SJ, Fung HKH, Chechik M, Jenkins HT, Weitzel SE, Aguiar PM, Brentnall AS, Glousieau M, Gladyshev GV, Potts JR, Antson AA. DNA recognition for virus assembly through multiple sequence-independent interactions with a helix-turn-helix motif. Nucleic Acids Res 2015; 44:776-89. [PMID: 26673721 PMCID: PMC4737164 DOI: 10.1093/nar/gkv1467] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 11/30/2015] [Indexed: 11/14/2022] Open
Abstract
The helix-turn-helix (HTH) motif features frequently in protein DNA-binding assemblies. Viral pac site-targeting small terminase proteins possess an unusual architecture in which the HTH motifs are displayed in a ring, distinct from the classical HTH dimer. Here we investigate how such a circular array of HTH motifs enables specific recognition of the viral genome for initiation of DNA packaging during virus assembly. We found, by surface plasmon resonance and analytical ultracentrifugation, that individual HTH motifs of the Bacillus phage SF6 small terminase bind the packaging regions of SF6 and related SPP1 genome weakly, with little local sequence specificity. Nuclear magnetic resonance chemical shift perturbation studies with an arbitrary single-site substrate suggest that the HTH motif contacts DNA similarly to how certain HTH proteins contact DNA non-specifically. Our observations support a model where specificity is generated through conformational selection of an intrinsically bent DNA segment by a ring of HTHs which bind weakly but cooperatively. Such a system would enable viral gene regulation and control of the viral life cycle, with a minimal genome, conferring a major evolutionary advantage for SPP1-like viruses.
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Affiliation(s)
- Sandra J Greive
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK
| | - Herman K H Fung
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK Department of Biology, University of York, York YO10 5DD, UK
| | - Maria Chechik
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK
| | - Huw T Jenkins
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK
| | - Stephen E Weitzel
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403, USA
| | - Pedro M Aguiar
- Department of Chemistry, University of York, York YO10 5DD, UK
| | | | - Matthieu Glousieau
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK
| | - Grigory V Gladyshev
- Department of Biochemistry, School of Biology, Moscow State University, Moscow 119234, Russian Federation
| | | | - Alfred A Antson
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK
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Bhowmik D, Fiorillo G, Lombardi P, Suresh Kumar G. Recognition of human telomeric G-quadruplex DNA by berberine analogs: effect of substitution at the 9 and 13 positions of the isoquinoline moiety. J Mol Recognit 2015; 28:722-30. [DOI: 10.1002/jmr.2486] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Revised: 05/11/2015] [Accepted: 05/23/2015] [Indexed: 11/11/2022]
Affiliation(s)
- Debipreeta Bhowmik
- Biophysical Chemistry Laboratory; CSIR-Indian Institute of Chemical Biology; Kolkata 700 032 India
| | - Gaetano Fiorillo
- Naxospharma srl; Via G. Di Vittorio 70 20026 Novate Milanese MI Italy
| | - Paolo Lombardi
- Naxospharma srl; Via G. Di Vittorio 70 20026 Novate Milanese MI Italy
| | - G. Suresh Kumar
- Biophysical Chemistry Laboratory; CSIR-Indian Institute of Chemical Biology; Kolkata 700 032 India
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Akhter MZ, Luthra K, Rajeswari MR. Molecular aspects on adriamycin interaction with hmga1 regulatory region and its inhibitory effect on HMGA1 expression in human cervical cancer. J Biomol Struct Dyn 2015; 34:877-91. [PMID: 26084422 DOI: 10.1080/07391102.2015.1057617] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
High mobility group A1 (HMGA1), a non-histone chromosomal protein, is highly expressed in a wide range of human cancers including cervical, breast, and prostate cancers. Therefore, hmga1 gene is considered as an attractive potential target for anticancer drugs. We have chosen 27 bp DNA sequence from a regulatory region of hmga1 promoter and studied its interaction with adriamycin (ADM) and in vitro expression of HMGA1 in the presence of ADM in HeLa cell line. A variety of biophysical techniques were employed to understand the characteristics of [DNA-ADM] complex. Spectrophotometric titration data, DNA denaturation profiles, and quenching of fluorescence of ADM in the presence of DNA demonstrated a strong complexation between DNA and ADM with a high binding affinity (Ka) of 1.3 × 10(6) M(-1) and a stoichiometry of 1:3 (drug:nucleotide). The energetics of binding obtained from isothermal titration calorimetry and differential scanning calorimetry suggest the binding to be exothermic and enthalpy (∆H, -6.7 ± 2.4 kcal M(-1)) and entropy (TΔS, 18.5 ± 6.4 kcal M(-1)) driven (20°C), which is typical of intercalative mode of binding. Further, results on decreased expression (by ~70%) of HMGA1 both at mRNA and protein levels in association with the observed cell death (by ~75%) in HeLa cell line, clearly confirm that ADM does target hmga1; however, the effect of ADM on genes other than hmga1 either directly or via hmga1-mediated pathways cannot be ruled out in the observed cytotoxicity. Therefore, hmga1 in general and particularly the regulatory region is a promising target for therapeutic strategy in combating cancer.
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Affiliation(s)
- Md Zahid Akhter
- a Department of Biochemistry , All India Institute of Medical Sciences , New Delhi 110029 , India
| | - Kalpana Luthra
- a Department of Biochemistry , All India Institute of Medical Sciences , New Delhi 110029 , India
| | - Moganty R Rajeswari
- a Department of Biochemistry , All India Institute of Medical Sciences , New Delhi 110029 , India
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40
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Školáková P, Foldynová-Trantírková S, Bednářová K, Fiala R, Vorlíčková M, Trantírek L. Unique C. elegans telomeric overhang structures reveal the evolutionarily conserved properties of telomeric DNA. Nucleic Acids Res 2015; 43:4733-45. [PMID: 25855805 PMCID: PMC4482068 DOI: 10.1093/nar/gkv296] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2015] [Accepted: 03/25/2015] [Indexed: 11/16/2022] Open
Abstract
There are two basic mechanisms that are associated with the maintenance of the telomere length, which endows cancer cells with unlimited proliferative potential. One mechanism, referred to as alternative lengthening of telomeres (ALT), accounts for approximately 10–15% of all human cancers. Tumours engaged in the ALT pathway are characterised by the presence of the single stranded 5′-C-rich telomeric overhang (C-overhang). This recently identified hallmark of ALT cancers distinguishes them from healthy tissues and renders the C-overhang as a clear target for anticancer therapy. We analysed structures of the 5′-C-rich and 3′-G-rich telomeric overhangs from human and Caenorhabditis elegans, the recently established multicellular in vivo model of ALT tumours. We show that the telomeric DNA from C. elegans and humans forms fundamentally different secondary structures. The unique structural characteristics of C. elegans telomeric DNA that are distinct not only from those of humans but also from those of other multicellular eukaryotes allowed us to identify evolutionarily conserved properties of telomeric DNA. Differences in structural organisation of the telomeric DNA between the C. elegans and human impose limitations on the use of the C. elegans as an ALT tumour model.
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Affiliation(s)
- Petra Školáková
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Kralovopolska, 135, 612 65 Brno, Czech Republic
| | - Silvie Foldynová-Trantírková
- Central European Institute of Technology, Masaryk University, Kamenice 735/5, 625 00 Brno, Czech Republic Institute of Parasitology, Academy of Sciences of the Czech Republic, Branisovska, 31, 375 05 Ceske Budejovice, Czech Republic
| | - Klára Bednářová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Kralovopolska, 135, 612 65 Brno, Czech Republic Central European Institute of Technology, Masaryk University, Kamenice 735/5, 625 00 Brno, Czech Republic
| | - Radovan Fiala
- Central European Institute of Technology, Masaryk University, Kamenice 735/5, 625 00 Brno, Czech Republic
| | - Michaela Vorlíčková
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Kralovopolska, 135, 612 65 Brno, Czech Republic Central European Institute of Technology, Masaryk University, Kamenice 735/5, 625 00 Brno, Czech Republic
| | - Lukáš Trantírek
- Central European Institute of Technology, Masaryk University, Kamenice 735/5, 625 00 Brno, Czech Republic
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Di Meo F, Pedersen MN, Rubio-Magnieto J, Surin M, Linares M, Norman P. DNA Electronic Circular Dichroism on the Inter-Base Pair Scale: An Experimental-Theoretical Case Study of the AT Homo-Oligonucleotide. J Phys Chem Lett 2015; 6:355-359. [PMID: 26261947 DOI: 10.1021/jz502696t] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
A successful elucidation of the near-ultraviolet electronic circular dichroism spectrum of a short double-stranded DNA is reported. Time-dependent density functional theory methods are shown to accurately predict spectra and assign bands on the microscopic base-pair scale, a finding that opens the field for using circular dichroism spectroscopy as a sensitive nanoscale probe of DNA to reveal its complex interactions with the environment.
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Affiliation(s)
- Florent Di Meo
- †Department of Physics, Chemistry and Biology (IFM), Linköping University, SE-58183 Linköping, Sweden
| | - Morten N Pedersen
- †Department of Physics, Chemistry and Biology (IFM), Linköping University, SE-58183 Linköping, Sweden
- ‡Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Jenifer Rubio-Magnieto
- ||Laboratory for Chemistry of Novel Materials, Center for Innovation and Research in Materials and Polymers, University of Mons - UMONS, 20 Place du Parc, B-7000 Mons, Belgium
| | - Mathieu Surin
- ||Laboratory for Chemistry of Novel Materials, Center for Innovation and Research in Materials and Polymers, University of Mons - UMONS, 20 Place du Parc, B-7000 Mons, Belgium
| | - Mathieu Linares
- †Department of Physics, Chemistry and Biology (IFM), Linköping University, SE-58183 Linköping, Sweden
- ||Laboratory for Chemistry of Novel Materials, Center for Innovation and Research in Materials and Polymers, University of Mons - UMONS, 20 Place du Parc, B-7000 Mons, Belgium
| | - Patrick Norman
- †Department of Physics, Chemistry and Biology (IFM), Linköping University, SE-58183 Linköping, Sweden
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42
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Scarlett G, Siligardi G, Kneale GG. Circular Dichroism for the Analysis of Protein-DNA Interactions. Methods Mol Biol 2015; 1334:299-312. [PMID: 26404158 DOI: 10.1007/978-1-4939-2877-4_19] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The aim of this chapter is to provide information on the practical aspects of circular dichroism (CD) and synchrotron radiation circular dichroism (SRCD) in protein-nucleic acids interaction solution studies. The chapter will describe the guidelines appropriate to designing experiments and conducting correct data interpretation, the use of both benchtop and synchrotron CD approaches is discussed and the advantages of SRCD outlined. Further information and a good general review of the field a can be found in Gray (Circular Dichroism of protein-nucleic acid interactions. In: Fasman GD (ed) Circular dichroism and the conformational analysis of biomolecules. Plenum Press, New York. pp 469-500, 1996).
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Affiliation(s)
- Garry Scarlett
- Institute of Biomedical and Biomolecular Sciences, School of Biological Sciences, University of Portsmouth, King Henry 1st Building, Portsmouth, PO1 2DY, UK.
| | - Giuliano Siligardi
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, UK
| | - Geoffrey G Kneale
- Institute of Biomedical and Biomolecular Sciences, School of Biological Sciences, University of Portsmouth, King Henry 1st Building, Portsmouth, PO1 2DY, UK
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43
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α-Synuclein is prone to interaction with the GC-box-like sequence in vitro. Cell Mol Neurobiol 2014; 34:603-9. [PMID: 24659023 DOI: 10.1007/s10571-014-0046-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Accepted: 03/07/2014] [Indexed: 12/30/2022]
Abstract
α-Synuclein (α-syn) is a presynaptic protein that is widely implicated in the pathophysiology of Parkinson's disease, a neurodegenerative disorder characterized by a progressive loss of dopaminergic neurons and the formation of Lewy bodies. Evidence suggests that α-syn could be imported into the nucleus and subsequently disrupt normal neuronal function. The existence of α-syn in the nucleus provides the possibility of interaction with DNA leading to gene transcript regulation. Thus, CD spectra were used to determine the specific DNA sequence with which α-syn is most likely to interact. Our results indicated that α-syn was prone to preferentially interact with the GC-box-like sequence in vitro at a ratio of 2:1 or less (α-syn: the GC-box-like sequence).
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44
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Akhter MZ, Rajeswari MR. Interaction of doxorubicin with a regulatory element of hmga1 and its in vitro anti-cancer activity associated with decreased HMGA1 expression. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2014; 141:36-46. [DOI: 10.1016/j.jphotobiol.2014.08.026] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Revised: 08/20/2014] [Accepted: 08/23/2014] [Indexed: 11/26/2022]
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45
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Lexa M, Steflova P, Martinek T, Vorlickova M, Vyskot B, Kejnovsky E. Guanine quadruplexes are formed by specific regions of human transposable elements. BMC Genomics 2014; 15:1032. [PMID: 25431265 PMCID: PMC4407331 DOI: 10.1186/1471-2164-15-1032] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Accepted: 10/29/2014] [Indexed: 11/23/2022] Open
Abstract
Background Transposable elements form a significant proportion of eukaryotic genomes. Recently, Lexa et al. (Nucleic Acids Res 42:968-978, 2014) reported that plant long terminal repeat (LTR) retrotransposons often contain potential quadruplex sequences (PQSs) in their LTRs and experimentally confirmed their ability to adopt four-stranded DNA conformations. Results Here, we searched for PQSs in human retrotransposons and found that PQSs are specifically localized in the 3’-UTR of LINE-1 elements, in LTRs of HERV elements and are strongly accumulated in specific regions of SVA elements. Circular dichroism spectroscopy confirmed that most PQSs had adopted monomolecular or bimolecular guanine quadruplex structures. Evolutionarily young SVA elements contained more PQSs than older elements and their propensity to form quadruplex DNA was higher. Full-length L1 elements contained more PQSs than truncated elements; the highest proportion of PQSs was found inside transpositionally active L1 elements (PA2 and HS families). Conclusions Conservation of quadruplexes at specific positions of transposable elements implies their importance in their life cycle. The increasing quadruplex presence in evolutionarily young LINE-1 and SVA families makes these elements important contributors toward present genome-wide quadruplex distribution. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-1032) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | - Eduard Kejnovsky
- Department of Plant Developmental Genetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265 Brno, Czech Republic.
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Babinský M, Fiala R, Kejnovská I, Bednářová K, Marek R, Sagi J, Sklenář V, Vorlíčková M. Loss of loop adenines alters human telomere d[AG3(TTAG3)3] quadruplex folding. Nucleic Acids Res 2014; 42:14031-41. [PMID: 25428355 PMCID: PMC4267657 DOI: 10.1093/nar/gku1245] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Abasic (AP) lesions are the most frequent type of damages occurring in cellular DNA. Here we describe the conformational effects of AP sites substituted for 2′-deoxyadenosine in the first (ap7), second (ap13) or third (ap19) loop of the quadruplex formed in K+ by the human telomere DNA 5′-d[AG3(TTAG3)3]. CD spectra and electrophoresis reveal that the presence of AP sites does not hinder the formation of intramolecular quadruplexes. NMR spectra show that the structural heterogeneity is substantially reduced in ap7 and ap19 as compared to that in the wild-type. These two (ap7 and ap19) sequences are shown to adopt the hybrid-1 and hybrid-2 quadruplex topology, respectively, with AP site located in a propeller-like loop. All three studied sequences transform easily into parallel quadruplex in dehydrating ethanol solution. Thus, the AP site in any loop region facilitates the formation of the propeller loop. Substitution of all adenines by AP sites stabilizes the parallel quadruplex even in the absence of ethanol. Whereas guanines are the major determinants of quadruplex stability, the presence or absence of loop adenines substantially influences quadruplex folding. The naturally occurring adenine-lacking sites in the human telomere DNA can change the quadruplex topology in vivo with potentially vital biological consequences.
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Affiliation(s)
- Martin Babinský
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic
| | - Radovan Fiala
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic
| | - Iva Kejnovská
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, CZ-612 65 Brno, Czech Republic
| | - Klára Bednářová
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, CZ-612 65 Brno, Czech Republic
| | - Radek Marek
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic
| | - Janos Sagi
- Rimstone Laboratory, RLI, 29 Lancaster Way, Cheshire, CT 06410, USA
| | - Vladimír Sklenář
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic
| | - Michaela Vorlíčková
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, CZ-612 65 Brno, Czech Republic
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Sensor Design Based on Structure Adjustment in Loops of G-quadruplex. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2014. [DOI: 10.1016/s1872-2040(14)60772-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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48
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Curtis EA, Liu DR. A naturally occurring, noncanonical GTP aptamer made of simple tandem repeats. RNA Biol 2014; 11:682-92. [PMID: 24824832 PMCID: PMC4156500 DOI: 10.4161/rna.28798] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Recently, we used in vitro selection to identify a new class of naturally occurring GTP aptamer called the G motif. Here we report the discovery and characterization of a second class of naturally occurring GTP aptamer, the “CA motif.” The primary sequence of this aptamer is unusual in that it consists entirely of tandem repeats of CA-rich motifs as short as three nucleotides. Several active variants of the CA motif aptamer lack the ability to form consecutive Watson-Crick base pairs in any register, while others consist of repeats containing only cytidine and adenosine residues, indicating that noncanonical interactions play important roles in its structure. The circular dichroism spectrum of the CA motif aptamer is distinct from that of A-form RNA and other major classes of nucleic acid structures. Bioinformatic searches indicate that the CA motif is absent from most archaeal and bacterial genomes, but occurs in at least 70 percent of approximately 400 eukaryotic genomes examined. These searches also uncovered several phylogenetically conserved examples of the CA motif in rodent (mouse and rat) genomes. Together, these results reveal the existence of a second class of naturally occurring GTP aptamer whose sequence requirements, like that of the G motif, are not consistent with those of a canonical secondary structure. They also indicate a new and unexpected potential biochemical activity of certain naturally occurring tandem repeats.
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Affiliation(s)
- Edward A Curtis
- Department of Chemistry and Chemical Biology and Howard Hughes Medical Institute; Harvard University; Cambridge, MA USA
| | - David R Liu
- Department of Chemistry and Chemical Biology and Howard Hughes Medical Institute; Harvard University; Cambridge, MA USA
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Nielsen LM, Hoffmann SV, Nielsen SB. Electronic coupling between photo-excited stacked bases in DNA and RNA strands with emphasis on the bright states initially populated. Photochem Photobiol Sci 2014; 12:1273-85. [PMID: 23545881 DOI: 10.1039/c3pp25438k] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In biology the interplay between multiple light-absorbers gives rise to complex quantum effects such as superposition states that are of extreme importance for life, both for harvesting solar energy and likely protecting nucleic acids from radiation damage. Still the characteristics of these states and their quantum dynamics are a much debated issue. While the electronic properties of single bases are fairly well understood, the situation for strands is complicated by the fact that stacked bases electronically couple when photoexcited. These newly arising states are denoted as exciton states and are simply linear combinations of localised wavefunctions that involve N - 1 ground-state bases and one base in its excited state (cf. the Frenkel exciton model). There is disagreement over the number of bases, N, that coherently couple, i.e., the spatial extent of the exciton, and how electronic deexcitation back to the ground state occurs. The importance of dark charge-transfer states has been inferred both from time-resolved fluorescence and transient absorption experiments. These states were suggested to be responsible for long deexcitation times but it is unclear whether 'long' is tens of picoseconds or nanoseconds. In this review paper, we focus on the bright states initially populated and discuss their nature based on information obtained from systematic absorption and circular dichroism experiments on single strands of different lengths. Our results from the last five years are compared with those from other groups, and are discussed in the context of successive deexcitation schemes. Pieces to the puzzle have come from different experiments and theory but a complete description has yet to emerge. As such the story about DNA/RNA photophysical decay mechanisms resembles the tale about the blind men and the elephant where all see the beast in different, correct but incomplete ways.
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50
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Unraveling the Thermodynamics and Kinetics of RNA Assembly. Methods Enzymol 2014. [DOI: 10.1016/b978-0-12-801122-5.00017-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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