1
|
Babaylova ES, Ivanov AV, Malygin AA, Vorobjeva MA, Venyaminova AG, Polienko YF, Kirilyuk IA, Krumkacheva OA, Fedin MV, Karpova GG, Bagryanskaya EG. A versatile approach for site-directed spin labeling and structural EPR studies of RNAs. Org Biomol Chem 2015; 12:3129-36. [PMID: 24714823 DOI: 10.1039/c3ob42154f] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Site-directed spin labeling (SDSL) is widely applied for structural studies of biopolymers by electron paramagnetic resonance (EPR). However, SDSL of long RNA sequences still remains a challenging task. Here, we propose a novel SDSL approach potentially suitable for long natural RNAs, which is based on the attachment of a linker containing an aliphatic amino group to the target nucleotide residue followed by selective coupling of a spin label to this amino group. Such a linker can be attached to the desired RNA residue via a sequence-specific reaction with the derivatives of oligodeoxyribonucleotides. To verify this approach, we applied it to model RNA duplex with known structure and expected distance between corresponding residues. A new 2,5-bis(spirocyclohexane)-substituted spin label with advanced stability and relaxation properties has been used, and the distance distribution measured using Q-band (34 GHz) pulsed double electron-electron resonance corresponds well to the expected one. We have additionally validated the obtained results by studying a similar RNA duplex, where the linker with the aliphatic amino group was introduced via solid-phase synthesis. Although this novel SDSL approach does not provide an advantage in precision of molecular distance measurements, we believe that its applicability to long RNAs is a crucial benefit for future structural studies using pulse EPR.
Collapse
Affiliation(s)
- Elena S Babaylova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, pr. Lavrentjeva 8, Novosibirsk, 630090, Russia
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
2
|
Lambert G. Polyalkylcyanoacrylate Nanospheres and Nanocapsules for the Delivery of Antisense Oligonucleotides. J DISPER SCI TECHNOL 2007. [DOI: 10.1081/dis-120021800] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Gregory Lambert
- a Novagali SAS , Genopole Industries , 4 rue Pierre Fontaine, 91058 , Evry , France
| |
Collapse
|
3
|
Tumir LM, Piantanida I, Zinić M, Juranović Cindrić I, Meić Z, Kralj M, Tomić S. Synthesis of phenanthridinium-bis-nucleobase conjugates, interactions with poly U, nucleotides and in vitro antitumour activity of mono- and bis-nucleobase conjugates. Eur J Med Chem 2006; 41:1153-66. [PMID: 16793178 DOI: 10.1016/j.ejmech.2006.05.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 04/25/2006] [Accepted: 05/04/2006] [Indexed: 11/24/2022]
Abstract
Novel bis-nucleobase-phenanthridinium conjugates were synthesised and their aqueous solutions spectroscopically characterised. Bis-adenine conjugate revealed in aqueous solutions significantly more pronounced intramolecular aromatic stacking interactions than bis-uracil analogue. In contrast with previously reported poly A recognition by bis-uracil conjugate, recognition of complementary nucleotides and poly U was not observed due to the strong interference of bulk water with hydrogen bonding between nucleobases. The screening of anticancer activity on six human cell lines revealed that tethering of a nucleobase to phenanthridinium moiety diminished antiproliferative potential of phenanthridinium. However, among mono-nucleobase conjugates adenine derivative was found to be the most selective one (MiaPaCa-2, Hep-2).
Collapse
Affiliation(s)
- L-M Tumir
- Laboratory of Supramolecular and Nucleoside Chemistry, Division of Organic Chemistry and Biochemistry, Ruder Bosković Institute, Bijenicka 54, HR 10002 Zagreb, P.O.B. 180, Croatia
| | | | | | | | | | | | | |
Collapse
|
4
|
|
5
|
DNA and RNA Cleavage Mediated by Phenanthroline-Cuprous Oligonucleotides: From Properties to Applications. ARTIFICIAL NUCLEASES 2004. [DOI: 10.1007/978-3-642-18510-6_13] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
|
6
|
Schröder ARW, Riesner D. Detection and analysis of hairpin II, an essential metastable structural element in viroid replication intermediates. Nucleic Acids Res 2002; 30:3349-59. [PMID: 12140319 PMCID: PMC137078 DOI: 10.1093/nar/gkf454] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In (-)-stranded replication intermediates of the potato spindle tuber viroid (PSTVd) a thermodynamically metastable structure containing a specific hairpin structure (HP II) has been proposed to be essential for viroid replication. In the present work a method was devised allowing the direct detection of the HP II structure in vitro and in vivo using a biophysical approach. An RNA oligonucleotide was constructed which specifically binds to the HP II loop region in transient (-)-strand intermediates. Analysis of the resulting oligonucleotide/HP II complexes on temperature-gradient gels enabled us to follow the formation of HP II during in vitro transcription by T7 RNA polymerase. Moreover, we were able to demonstrate the formation of HP II during viroid replication in potato (Solanum tuberosum) cells.
Collapse
Affiliation(s)
- Astrid R W Schröder
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universtitätsstrasse 1, D-40225 Düsseldorf, Germany
| | | |
Collapse
|
7
|
Yang CF, Jackson PJ, Xi Z, Goldberg IH. Recognition of bulged DNA by a neocarzinostatin product via an induced fit mechanism. Bioorg Med Chem 2002; 10:1329-35. [PMID: 11886796 DOI: 10.1016/s0968-0896(01)00432-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The binding of the wedge-shaped isostructural analogue of the biradical species of the chromphore of antitumor antibiotic neocarzinostatin to sequence-specific bulged DNAs results in alterations in ellipticity of the DNAs. Circular dichroism (CD) spectroscopic results suggest that the drug specifically recognizes bulges of DNA via a combination of conformational selection and induced fit, not by binding to a preorganized site. Analysis of circular dichroism spectra indicates that the degree of induced fit observed is primarily a consequence of optimising van der Waals contacts with the walls of the bulge cavity. The effective recognition of the bulge site on duplex DNA appears to depend to a significant extent on the bent groove space being flexible enough to be able to adopt the geometrically optimal conformation compatible with the wedge-shaped drug molecule, rather than involving 'lock and key' recognition. The spectroscopic results indicate a change of DNA conformation, consistent with an allosteric binding model. Spectroscopic studies with various bulged DNAs also reveal that the binding strength directly correlates with the stability of the bulge structures.
Collapse
Affiliation(s)
- Catherine F Yang
- Department of Chemistry, Rowan University, Glassboro, NJ 08028, USA.
| | | | | | | |
Collapse
|
8
|
Dong F, Allawi HT, Anderson T, Neri BP, Lyamichev VI. Secondary structure prediction and structure-specific sequence analysis of single-stranded DNA. Nucleic Acids Res 2001; 29:3248-57. [PMID: 11470883 PMCID: PMC55824 DOI: 10.1093/nar/29.15.3248] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
DNA sequence analysis by oligonucleotide binding is often affected by interference with the secondary structure of the target DNA. Here we describe an approach that improves DNA secondary structure prediction by combining enzymatic probing of DNA by structure-specific 5'-nucleases with an energy minimization algorithm that utilizes the 5'-nuclease cleavage sites as constraints. The method can identify structural differences between two DNA molecules caused by minor sequence variations such as a single nucleotide mutation. It also demonstrates the existence of long-range interactions between DNA regions separated by >300 nt and the formation of multiple alternative structures by a 244 nt DNA molecule. The differences in the secondary structure of DNA molecules revealed by 5'-nuclease probing were used to design structure-specific probes for mutation discrimination that target the regions of structural, rather than sequence, differences. We also demonstrate the performance of structure-specific 'bridge' probes complementary to non-contiguous regions of the target molecule. The structure-specific probes do not require the high stringency binding conditions necessary for methods based on mismatch formation and permit mutation detection at temperatures from 4 to 37 degrees C. Structure-specific sequence analysis is applied for mutation detection in the Mycobacterium tuberculosis katG gene and for genotyping of the hepatitis C virus.
Collapse
Affiliation(s)
- F Dong
- Third Wave Technologies Inc., 502 South Rosa Road, Madison, WI 53719-1256, USA
| | | | | | | | | |
Collapse
|
9
|
Lambert G, Fattal E, Couvreur P. Nanoparticulate systems for the delivery of antisense oligonucleotides. Adv Drug Deliv Rev 2001; 47:99-112. [PMID: 11251248 DOI: 10.1016/s0169-409x(00)00116-2] [Citation(s) in RCA: 141] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Antisense oligonucleotides are molecules that are able to inhibit gene expression being therefore potentially active for the treatment of viral infections or cancer. However, because of their poor stability in biological medium and their weak intracellular penetration, colloidal drugs carriers such as nanoparticles were developed for the delivery of oligonucleotides (ODN). ODN associated to nanoparticles were shown to be protected against degradation and to penetrate more easily into different types of cells. As a consequence, nanoparticles were shown to improve the efficiency of ODNs for the inhibition of the proliferation of cells expressing the point mutated Ha-ras gene. In vivo, polyalkylcyanoacrylate (PACA) nanoparticles were able to efficiently distribute the ODNs to the liver whereas the alginate nanosponges could concentrate the ODNs in the lungs. Finally, ODN loaded to PACA nanoparticles were able to improve in mice, the treatment of RAS cells expressing the point mutated Ha-ras gene.
Collapse
Affiliation(s)
- G Lambert
- Laboratoire de Physico-Chimie, Pharmacotechnie et Biopharmacie, URA CNRS 8612, Faculté de Pharmacie, 5, Rue Jean-Baptiste Clément, 99296 Châtenay-Malabry, France
| | | | | |
Collapse
|
10
|
Abdel Megied AE, Ali OM, Kofoed T, Pedersen EB. Preparation of oligodeoxynucleotides containing 5-(N-methylpiperazinyl) and 5-benzyloxymethyl uracils. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2001; 20:1-9. [PMID: 11303555 DOI: 10.1081/ncn-100001434] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Deprotected compounds 1 and 9 were allowed to react with 4,4'-dimethoxytrityl chloride in pyridine to give 5'-O-DMT nucleosides 2 and 10. The 3'-phosphoramidites 4 and 11 were incorporated into oligodeoxynucleosides (ODNs). The hybridization properties of the modified ODNs with their complementary DNA strands were studied. Interesting results were obtained when 11 was inserted as a bulged nucleoside into TWAs, duplexes, and triplexes.
Collapse
Affiliation(s)
- A E Abdel Megied
- Department of Chemistry, Faculty of Science, Menoufia University, Shebien El-Koam, Egypt.
| | | | | | | |
Collapse
|
11
|
Bochot A, Couvreur P, Fattal E. Intravitreal administration of antisense oligonucleotides: potential of liposomal delivery. Prog Retin Eye Res 2000; 19:131-47. [PMID: 10674705 DOI: 10.1016/s1350-9462(99)00014-2] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Antisense oligonucleotides are short synthetic fragments of genes that are able to inhibit gene expression after being internalized by cells. They can therefore be used as antiviral compounds particularly, for the treatment of ocular viral infections (i.e. Herpes simplex virus or Cytomegalovirus, CMV). Antisense oligonucleotides are however poorly stable in biological fluids and their intracellular penetration is limited. Although oligonucleotides are now currently used in therapeutics for the treatment of CMV by intravitreal injection (Vitravene) their main drawbacks impose to repeat the number of administrations which can be very harmful and damaging. A system that is able to permit a protection of oligonucleotides against degradation and their slow delivery into the vitreous would be more favorable for improving patient compliance. The use of liposomes for intravitreal administration can be very promising since these lipid vesicles are able to protect oligonucleotides against degradation by nucleases and they allow to increase the retention time of many drugs in the vitreous. In this review, the potentialities of liposomes for the intravitreal delivery of oligonucleotides will be discussed.
Collapse
Affiliation(s)
- A Bochot
- Université Paris XI, Centre d'études Pharmaceutiques, UMR CNRS 8612, Châtenay-Malabry, France
| | | | | |
Collapse
|
12
|
El-Kafrawy SA, Zahran MA, Pedersen EB. MULTIPLE LID STABILIZATION OF THE DNA THREE-WAY JUNCTION. INSERTION OF N3-(1-PYRENYLMETHYL)THYMIDINE. HETEROCYCL COMMUN 1999. [DOI: 10.1515/hc.1999.5.6.539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
|
13
|
Khattab AF, Pedersen EB. Improved Targeting of the Flanks of a DNA Stem Using α-Oligodeoxynucleotides.-The Enhanced Effect of an Intercalator. ACTA ACUST UNITED AC 1998. [DOI: 10.1080/07328319808004323] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
14
|
Slama-Schwok A, Peronnet F, Hantz-Brachet E, Taillandier E, Teulade-Fichou MP, Vigneron JP, Best-Belpomme M, Lehn JM. A macrocyclic bis-acridine shifts the equilibrium from duplexes towards DNA hairpins. Nucleic Acids Res 1997; 25:2574-81. [PMID: 9185566 PMCID: PMC146785 DOI: 10.1093/nar/25.13.2574] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Nucleic acids can undergo dynamic conformational changes associated with the regulation of biological processes. A molecule presenting larger affinities for alternative structures relative to a duplex is expected to modify such conformational equilibria. We have previously reported that macrocyclic bis-acridine binds preferentially to single-stranded regions, especially DNA hairpins, due to steric effects. Here, we show, using gel electrophoresis, fluorescence and melting temperature experiments, that the macrocycle bis-acridine shifts an equilibrium from a duplex towards the corresponding hairpins. Competition experiments enlighten the higher affinity of the macrocycle for hairpins compared with double-stranded DNA. The macrocycle bis-acridine destabilizes a synthetic polynucleotide, by the formation of premelted areas. By extrapolation, the macrocycle bis-acridine should be able to disrupt, at least locally, genomic DNA duplexes and to stabilize unpaired areas, especially palindromic ones forming hairpins. Such macrocyclic compounds may have potential applications in the therapy of diseases involving hairpins.
Collapse
Affiliation(s)
- A Slama-Schwok
- Laboratoire de Spectroscopie Biomoléculaire, URA CNRS 1430, UFR de Santé, Médecine et Biologie Humaine, Université Paris XIII, Bobigny, France.
| | | | | | | | | | | | | | | |
Collapse
|
15
|
Lima WF, Brown-Driver V, Fox M, Hanecak R, Bruice TW. Combinatorial Screening and Rational Optimization for Hybridization to Folded Hepatitis C Virus RNA of Oligonucleotides with Biological Antisense Activity. J Biol Chem 1997. [DOI: 10.1074/jbc.272.1.626] [Citation(s) in RCA: 89] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
|
16
|
Abstract
Antisense oligonucleotides represent a novel class of potential drugs for highly selective blocking of genes. The basic concept of antisense strategy is simple: an antisense molecule recognizes a complementary mRNA (or DNA) by sequence-specific base pairing, and hence prevents translation (or transcription), resulting in a selective inhibition of protein synthesis. Because of these properties, antisense oligonucleotides have great potential as therapeutic agents in several human diseases, such as viral diseases, malignancies and dominant hereditary diseases. However, technical difficulties have slowed down their use as drugs: structural modifications are needed to increase the stability and potency of synthetic oligonucleotides, specific delivery systems are required to facilitate their entry into target cells, and more information is needed to their mechanism of action. Much of the current research on antisense oligonucleotides takes place at the interface of chemistry and biomedical sciences, a multidisciplinary field where finding a common language is sometimes difficult. The aim of this review is to present an overview of the antisense strategy in terms which should be understandable for chemists, biologists and physicians.
Collapse
Affiliation(s)
- H Lönnberg
- Department of Chemistry Turku University, Finland
| | | |
Collapse
|
17
|
Abdel-Rahman AAH, M. Ali O, B. Pedersen E. Insertion of 5-methyl-N4-(1-pyrenylmethyl)cytidine into DNA. Duplex, three-way junction and triplex stabilities. Tetrahedron 1996. [DOI: 10.1016/s0040-4020(96)00933-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
18
|
Woo J, Meyer RB, Gamper HB. G/C-modified oligodeoxynucleotides with selective complementarity: synthesis and hybridization properties. Nucleic Acids Res 1996; 24:2470-5. [PMID: 8692683 PMCID: PMC145964 DOI: 10.1093/nar/24.13.2470] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Modified oligodeoxyribonucleotides (ODNs) that have unique hybridization properties were designed and synthesized for the first time. These ODNs, called selective binding complementary ODNs (SBC ODNs), are unable to form stable hybrids with each other, yet are able to form stable, sequence specific hybrids with complementary unmodified strands of nucleic acid. To make SBC ODNs, deoxyguanosine (dG) and deoxycytidine (dC) were substituted with deoxyinosine (dI) and 3-(2'-deoxy-beta-D-ribofuranosyl)pyrrolo-[2,3-d]-pyrimidine-2-(3H)-one (dP), respectively. The hybridization properties of several otherwise identical complementary ODNs containing one or both of these nucleoside analogs were studied by both UV monitored thermal denaturation and non-denaturing PAGE. The data showed that while dI and dP did form base pairs with dC and dG, respectively, dI did not form a stable base pair with dP. A self-complementary ODN uniformly substituted with dI and dP acquired single-stranded character and was able to strand invade the end of a duplex DNA better than an unsubstituted ODN. This observation implies that SBC ODNs should effectively hybridize to hairpins present in single-stranded DNA or RNA.
Collapse
Affiliation(s)
- J Woo
- Epoch Pharmaceuticals, Inc., Bothell, WA 98021, USA
| | | | | |
Collapse
|
19
|
Orson FM, McShan WM, Kinsey BM. Sequence-specific binding and cleavage of duplex DNA by a radioiodinated, intercalator-linked, triplex-forming oligonucleotide. Nucl Med Biol 1996; 23:519-24. [PMID: 8832710 DOI: 10.1016/0969-8051(96)00034-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Applications of oligodeoxynucleotides to modulate gene expression have been the subject of much recent research. We have sought to develop a method to permanently inactivate a gene, or potentially kill cells containing abnormal genes. In this report, we show that a DNA intercalator conjugated to a triplex-forming oligonucleotide can be labeled with an Auger electron emitting radioisotope, can cleave its duplex DNA target, and can specifically bind the target sequence contained in a total of 10 kilobases of irrelevant DNA.
Collapse
Affiliation(s)
- F M Orson
- Veterans Affairs Medical Center Research Center on AIDS and HIV Infections, Houston, TX, USA
| | | | | |
Collapse
|
20
|
Afonina I, Kutyavin I, Lukhtanov E, Meyer RB, Gamper H. Sequence-specific arrest of primer extension on single-stranded DNA by an oligonucleotide-minor groove binder conjugate. Proc Natl Acad Sci U S A 1996; 93:3199-204. [PMID: 8622913 PMCID: PMC39582 DOI: 10.1073/pnas.93.8.3199] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
A minor groove binder (MGB) derivative (N-3-carbamoyl-1,2-dihydro-3H-pyrrolo[3,2-e]indole-7-carboxylate tripeptide; CDPI3) was covalently linked to the 5' or 3' end of several oligodeoxyribonucleotides (ODNs) totally complementary or possessing a single mismatch to M13mp19 single-stranded DNA. Absorption thermal denaturation and slot-blot hybridization studies showed that conjugation of CDPI3 to these ODNs increased both the specificity and the strength with which they hybridized. Primer extension of the same phage DNA by a modified form of phage T7 DNA polymerase (Sequenase) was physically blocked when a complementary 16-mer with a conjugated 5'-CDPI3 moiety was hybridized to a downstream site. Approximately 50% of the replicating complexes were arrested when the blocking ODN was equimolar to the phage DNA. Inhibition was unaffected by 3'-capping of the ODN with a hexanol group or by elimination of a preannealing step. Blockage was abolished when a single mismatch was introduced into the ODN or when the MGB was either removed or replaced by a 5'-acridine group. A 16-mer with a 3'-CDPI3 moiety failed to arrest primer extension, as did an unmodified 32-mer. We attribute the exceptional stability of hybrids formed by ODNs conjugated to a CDPI3 to the tethered tripeptide binding in the minor groove of the hybrid. When that group is linked to the 5' end of a hybridized ODN, it probably blocks DNA synthesis by inhibiting strand displacement. These ODNs conjugated to CDPI3 offer attractive features as diagnostic probes and antigene agents.
Collapse
Affiliation(s)
- I Afonina
- Epoch Pharmaceuticals, Bothell, WA 98201, USA
| | | | | | | | | |
Collapse
|
21
|
Sahasrabudhe PV, Gmeiner WH. The affinity of an oligodeoxynucleotide-peptide conjugate for an RNA hairpin loop depends on stereochemistry at the DNA-peptide junction. J Biomol Struct Dyn 1996; 13:585-91. [PMID: 8906879 DOI: 10.1080/07391102.1996.10508871] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Molecular models of an oligodeoxynucleotide-peptide conjugate complexed to an RNA hairpin loop were constructed to assess the effect of stereoisomerism at the point of attachment of the peptide to the oligodeoxynucleotide on the affinity of the conjugate for an RNA target. The peptide portion of the oligodeoxynucleotide-peptide conjugate, (L-lysine)8, was covalently attached to the N-allyl group of (D)- or (L)-aspartic alcohol that was incorporated into the interior of an antisense oligodeoxynucleotide. The stereocenter in the oligodeoxynucleotide interior originates from either (D)- or (L)-aspartic alcohol. The oligodeoxynucleotide portion of the oligodeoxynucleotide-peptide conjugate forms Watson-Crick base pairs with the single-stranded RNA that flanks the RNA hairpin loop. The positively charged peptide makes specific electrostatic contacts with the negatively charged phosphate backbone of the RNA hairpin loop when attached to the N-allyl of (D)-aspartic alcohol but does not have the proper orientation to make these electrostatic contacts when attached to the N-allyl of (L)-aspartic alcohol. This modelling study emphasizes the importance of stereocontrol at the point of branching in synthesizing oligodeoxynucleotide-peptide conjugates for binding of RNA hairpin loops.
Collapse
Affiliation(s)
- P V Sahasrabudhe
- Eppley Cancer Institute and Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha 68198-6805, USA
| | | |
Collapse
|
22
|
Abstract
The presence of folded regions in RNA competes with the binding of a complementary oligonucleotide, resulting in a weak antisense effect. Due to the key role played by a number of RNA structures in the natural regulation of gene expression it might be of interest to design antisense sequences able to selectively interact with such motifs in order to interfere with the biological processes they mediate. Different possibilities have been explored. A high affinity oligomer will disrupt the structure; if the target structure is solved one can take advantage of unpaired bases (bulges, loops) to minimize the thermodynamic cost of the binding. Alternatively, the folded structure can be accommodated within the complex via the formation of a local triple helix. Oligomers able to adapt to the RNA structure (aptamers) can be extracted by in vitro selection from randomly synthesized libraries comprising several billions of sequences.
Collapse
Affiliation(s)
- J J Toulmé
- INSERM U386, IFR Pathologies Infectieuses, Université Victor Segalen, Bordeaux II, France
| | | | | |
Collapse
|
23
|
Zenkova M, Ehresmann C, Caillet J, Springer M, Karpova G, Ehresmann B, Romby P. A novel approach to introduce site-directed specific cross-links within RNA-protein complexes. Application to the Escherichia coli threonyl-tRNA synthetase/translational operator complex. EUROPEAN JOURNAL OF BIOCHEMISTRY 1995; 231:726-35. [PMID: 7544283 DOI: 10.1111/j.1432-1033.1995.0726d.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
We describe a methodology which allows the introduction of a photoactivatable azido group at specific internal positions of any RNA in order to identify the neighboring elements of an interacting protein. The first step involves site-directed modification of the target RNA with an antisense oligodeoxyribonucleotide bearing, at its 3' or 5' phosphate, a 4-[-N-(2-chloroethyl)-N-methylamino]benzylmethylamino group. Position N7 of a guanine residue located in the close vicinity of the hybrid is the main target for alkylation. The antisense oligodeoxyribonucleotide is then removed by acidic pH treatment and a photoreactive reagent (2,4-dinitro-5-fluorophenylazide) is condensed to the modified nucleotide. This method was used to induce specific cross-links between Escherichia coli threonyl-tRNA synthetase and the leader region of threonyl-tRNA synthetase mRNA, which is involved in translational feedback regulation. Control experiments revealed that the modification affects neither the structure of the mRNA nor the interaction with the enzyme. More than 50% of the modified mRNA complexed with threonyl-tRNA synthetase can be cross-linked to the enzyme, depending on the nucleotide modified.
Collapse
Affiliation(s)
- M Zenkova
- Novosibirsk Institute of Bioorganic Chemistry, Siberian Division of Russian Academy of Sciences
| | | | | | | | | | | | | |
Collapse
|
24
|
|