151
|
Affiliation(s)
- Peter E. Nielsen
- Center for Biomolecular Recognition, Department of Medical Biochemistry & Genetics, Biochemical Laboratory B, The Panum Institute, Blegdamsvej 3c, 2200 Copenhagen N, Denmark
| |
Collapse
|
152
|
Frilander MJ, Steitz JA. Initial recognition of U12-dependent introns requires both U11/5' splice-site and U12/branchpoint interactions. Genes Dev 1999; 13:851-63. [PMID: 10197985 PMCID: PMC316595 DOI: 10.1101/gad.13.7.851] [Citation(s) in RCA: 90] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
We have investigated the formation of prespliceosomal complex A in HeLa nuclear extracts on a splicing substrate containing an AT-AC (U12-type) intron from the P120 gene. Using an RNase H protection assay and specific blocking oligonucleotides, we find that recognition of the 5' splice-site (5'ss) and branchpoint sequence (BPS) elements by U11 and U12 snRNPs, respectively, displays strong cooperativity, requiring both sites in the pre-mRNA substrate for efficient complex formation. Deletion analysis indicates that beside the 5'ss and BPS, no additional elements in the pre-mRNA are necessary for A-complex formation, although 5' exon sequences provide stimulation. Cross-linking studies with pre-mRNAs containing the 5'ss or BPS alone indicate that recognition of the BPS by the U12 snRNP is stimulated at least 20- to 30-fold by the binding of the U11 snRNP to the 5'ss in the same pre-mRNA molecule, whereas recognition of the 5'ss by U11 is stimulated approximately fivefold by the U12/BPS interaction. These results argue that intron recognition in the U12-dependent splicing pathway is carried out by a single U11/U12 di-snRNP complex, suggesting greater rigidity in the intron recognition process than in the major spliceosome.
Collapse
Affiliation(s)
- M J Frilander
- Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, Howard Hughes Medical Institute, New Haven, Connecticut 06536-0812 USA
| | | |
Collapse
|
153
|
Verheijen JC, van der Marel GA, van Boom JH, Bayly SF, Player MR, Torrence PF. 2,5-oligoadenylate-peptide nucleic acids (2-5A-PNAs) activate RNase L. Bioorg Med Chem 1999; 7:449-55. [PMID: 10220031 DOI: 10.1016/s0968-0896(98)00258-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
To potentiate the 2-5A (2',5'-oligoadenylate)-antisense and peptide nucleic acid (PNA) approaches to regulation of gene expression, composite molecules were generated containing both 2-5A and PNA moieties. 2-5A-PNA adducts were synthesized using solid-phase techniques. Highly cross-linked polystyrene beads were functionalized with glycine tethered through a p-hydroxymethylbenzoic acid linker and the PNA domain of the chimeric oligonucleotide analogue was added by sequential elongation of the amino terminus with the monomethoxytrityl protected N-(2-aminoethyl)-N-(adenin-1-ylacetyl)glycinate. Transition to the 2-5A domain was accomplished by coupling of the PNA chain to dimethoxytrityl protected N-(2-hydroxyethyl)-N-(adenin-1-ylacetyl)glycinate. Finally, (2-cyanoethyl)-N,N-diisopropyl-4-O-(4,4-dimethoxytrityl)butylphosphor amidite and the corresponding (2-cyanoethyl)-N,N-diisopropylphosphoramidite of 5-O-(4,4'-dimethoxytrityl)-3-O-(tert-butyldimethylsilyl)-N6-benzoyladeno sine were the synthons employed to add the 2 butanediol phosphate linkers and the four 2',5'-linked riboadenylates. The 5'-phosphate moiety was introduced with 2-[[2-(4,4'-dimethoxytrityloxy)ethyl]sulfonyl]ethyl-(2-cyanoethyl) -N,N-diisopropylphosphoramidite. Deprotection with methanolic NH3 and tetraethylammonium fluoride afforded the desired products, 2-SA-pnaA4, 2-5A-pnaA8 and 2-5A-pnaA12. When evaluated for their ability to cause the degradation of two different RNA substrates by the 2-5A-dependent RNase L, these new 2-5A-PNA conjugates were found to be potent RNase L activators. The union of 2-5A and PNA presents fresh opportunities to explore the biological and therapeutic implications of these unique approaches to antisense.
Collapse
Affiliation(s)
- J C Verheijen
- Leiden Institute of Chemistry, Gorlaeus Laboratories, The Netherlands
| | | | | | | | | | | |
Collapse
|
154
|
Affiliation(s)
- L Wordeman
- Department of Physiology and Biophysics, University of Washington School of Medicine, Seattle 98195, USA
| | | |
Collapse
|
155
|
Peptide nucleic acids. ACTA ACUST UNITED AC 1999. [DOI: 10.1016/s1874-5113(99)80009-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
|
156
|
|
157
|
Krotz AH, Larsen S, Buchardt O, Eriksson M, Nielsen PE. A 'retro-inverso' PNA: structural implications for DNA and RNA binding. Bioorg Med Chem 1998; 6:1983-92. [PMID: 9881091 DOI: 10.1016/s0968-0896(98)00152-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
'Retro-inverso' peptide nucleic acid (PNA) monomers of thymine (T*: N-(amidomethyl)-N-(N1-thyminyl-acetyl)-beta-alanyl) (and adenine) have been prepared and introduced in PNA oligomers. A homo 'retro-inverso' T*8 PNA was found not to hybridize to a complementary DNA or RNA oligonucleotide, whereas introduction of one retro-inverso thymine unit into the middle of a normal PNA 15-mer resulted in a c.a. 8 degrees C destabilization of the complex of this oligomer with a complementary DNA or RNA oligomer. In an effort to compensate for the structural nucleobase 'phase-shift' caused by the T* monomer by also introducing a beta-alanine monomer it is concluded that the effect of the T* backbone is -7 degrees C when hybridizing to DNA and -4.5 degrees C when hybridizing to RNA. Nonetheless, the T* unit shows good sequence discrimination comparable to that of normal PNA. Molecular dynamics simulations indicate an unfavourable conformation of the backbone amide carbonyl group resulting in reduced interaction with the aqueous medium and an 'electrostatic clash' with the carbonyl of the nucleobase linker. These results show that a simple inversion of an amide bond in the PNA backbone has a dramatic, and hardly predictable, effect on the DNA mimicking properties of the oligomer.
Collapse
Affiliation(s)
- A H Krotz
- Center for Biomolecular Recognition, H. C. Orsted Institute, University of Copenhagen, Denmark
| | | | | | | | | |
Collapse
|
158
|
|
159
|
Pooga M, Soomets U, Hällbrink M, Valkna A, Saar K, Rezaei K, Kahl U, Hao JX, Xu XJ, Wiesenfeld-Hallin Z, Hökfelt T, Bartfai T, Langel U. Cell penetrating PNA constructs regulate galanin receptor levels and modify pain transmission in vivo. Nat Biotechnol 1998; 16:857-61. [PMID: 9743120 DOI: 10.1038/nbt0998-857] [Citation(s) in RCA: 447] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Peptide nucleic acids (PNAs) form stable and tight complexes with complementary DNA and/or RNA and would be promising antisense reagents if their cellular delivery could be improved. We show that a 21-mer PNA, complementary to the human galanin receptor type 1 mRNA, coupled to the cellular transporter peptides, transportan or pAntennapedia(43-58), is efficiently taken up into Bowes cells where they block the expression of galanin receptors. In rat, the intrathecal administration of the peptide-PNA construct results in a decrease in galanin binding in the dorsal horn. The decrease in binding results in the inability of galanin to inhibit the C fibers stimulation-induced facilitation of the rat flexor reflex, demonstrating that peptide-PNA constructs act in vivo to suppress expression of functional galanin receptors.
Collapse
Affiliation(s)
- M Pooga
- Department of Neurochemistry and Neurotoxicology, Arrhenius Laboratories, Stockholm University, Sweden
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
160
|
Christensen L, Hansen HF, Koch T, Nielsen PE. Inhibition of PNA triplex formation by N4-benzoylated cytosine. Nucleic Acids Res 1998; 26:2735-9. [PMID: 9592162 PMCID: PMC147602 DOI: 10.1093/nar/26.11.2735] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The synthesis of N-((N4-(benzoyl)cytosine-1-yl)acetyl)- N -(2-Boc-aminoethyl)glycine (CBz) and the incorporation of this monomer into PNA oligomers are described. A single CBzresidue within a 10mer homopyrimidine PNA is capable of switching the preferred binding mode from a parallel to an antiparallel orientation when targeting a deoxyribonucleotide sequence at neutral pH. The resulting complex has a thermal stability equal to that of the corresponding PNA-DNA duplex, indicative of a strong destabilization of Hoogsteen strand PNA binding due to steric interference by the benzoyl moieties. Accordingly, incorporation of the CBz residue into linked PNAs (bis-PNAs) results in greatly reduced thermal stability of the formed PNA:DNA complexes. Thus, incorporation of the CBz monomer could eliminate the stability bias of triplex-forming sequences in PNA used in hybridization arrays and combinatorial library formats. Furthermore, it is shown that the benzoyl moiety does not severely interfere with Watson-Crick hydrogen bonding, thereby presenting an interesting route for novel cytosine modifications.
Collapse
Affiliation(s)
- L Christensen
- Center for Biomolecular Recognition, IMBG, Department of Biochemistry B, The Panum Institute, Blegdamsvej 3, 2200 Copenhagen N, Denmark
| | | | | | | |
Collapse
|
161
|
Le Tinévez R, Mishra RK, Toulmé JJ. Selective inhibition of cell-free translation by oligonucleotides targeted to a mRNA hairpin structure. Nucleic Acids Res 1998; 26:2273-8. [PMID: 9580674 PMCID: PMC147550 DOI: 10.1093/nar/26.10.2273] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Using an in vitro selection approach we have previously isolated oligodeoxy aptamers that can bind to a DNA hairpin structure without disrupting the double-stranded stem. We report here that these oligomers can bind to the RNA version of this hairpin, mostly through pairing with a designed 6 nt anchor. The part of the aptamer selected against the DNA hairpin did not increase stability of the RNA-aptamer complex. However, it contributed to the binding site for Escherichia coli RNase H, leading to very efficient cleavage of the target RNA. In addition, a 2'- O -methyloligoribonucleotide analogue of one selected sequence selectively blocked in vitro translation of luciferase in wheat germ extract by binding to the hairpin region inserted upstream of the initiation codon of the reporter gene. Therefore, non-complementary oligomers can exhibit antisense properties following hybridization with the target RNA. Our study also suggests that in vitro selection might provide a means to extend the repertoire of sequences that can be targetted by antisense oligonucleotides to structured RNA motifs of biological importance.
Collapse
Affiliation(s)
- R Le Tinévez
- INSERM U 386, IFR Pathologies Infectieuses, Université Victor Segalen, 146 rue Léo Saignat, 33076 Bordeaux cédex, France
| | | | | |
Collapse
|
162
|
Mologni L, leCoutre P, Nielsen PE, Gambacorti-Passerini C. Additive antisense effects of different PNAs on the in vitro translation of the PML/RARalpha gene. Nucleic Acids Res 1998; 26:1934-8. [PMID: 9518485 PMCID: PMC147505 DOI: 10.1093/nar/26.8.1934] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The potential use of peptide nucleic acid (PNA) as a sequence-specific inhibitor of RNA translation is investigated in this report. Three different regions of the PML/RARalpha oncogene, including two AUG potential start codons, were studied as targets of translation inhibition by antisense PNA in a cell-free system. A PNA targeted to the second AUG start codon, which was shown previously to be able to suppress in vitro translation from that site completely, was used alone or in combination with another PNA directed to the first AUG, and a third PNA within the 5'-untranslated region (5'-UTR) of mRNA. When used alone, no PNA was able to completely block the synthesis of the PML/RARalpha protein. The 5'-UTR PNA was the most potent translation inhibitor when used as single agent. However, a near complete (>/=90%) specific inhibition of the PML/RARalpha gene was obtained when the three PNAs were used in combination, thus obtaining an additive antisense effect.
Collapse
Affiliation(s)
- L Mologni
- Division of Experimental Oncology D, Istituto Nazionale Tumori, via Venezian 1, 20133 Milan, Italy
| | | | | | | |
Collapse
|
163
|
Gee JE, Robbins I, van der Laan AC, van Boom JH, Colombier C, Leng M, Raible AM, Nelson JS, Lebleu B. Assessment of high-affinity hybridization, RNase H cleavage, and covalent linkage in translation arrest by antisense oligonucleotides. ANTISENSE & NUCLEIC ACID DRUG DEVELOPMENT 1998; 8:103-11. [PMID: 9593048 DOI: 10.1089/oli.1.1998.8.103] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Antisense oligonucleotides (ONs) are designed to hybridize target mRNA in a sequence-specific manner and inhibit gene expression by preventing translation, either by activation of RNase H or steric blockage of the ribosome complex. Second-generation ONs, which possess greater binding affinity for target RNA relative to the isosequential phosphodiester (PO) ONs, have been developed and include, among others, peptide nucleic acids (PNA) and N3' P5' phosphoramidate oligonucleotides (npONs). In the present study, PNA and npON derivatives were targeted to the coding portion of the complementary mRNA of the N protein of the vesicular stomatitis virus (VSV) in order to evaluate their ability to arrest translation in an in vitro rabbit reticulocyte lysate system. High-affinity hybridization of ONs lacking RNase H activity was not sufficient to block translation in this test system. Only antisense ONs acting via an RNase H mechanism or by steric hindrance through covalent attachment (via transplatin modification) to the target mRNA were found to definitively arrest translation in this study.
Collapse
Affiliation(s)
- J E Gee
- Institut de Génétique Moléculaire de Montpellier, CNRS, France
| | | | | | | | | | | | | | | | | |
Collapse
|
164
|
Good L, Nielsen PE. Antisense inhibition of gene expression in bacteria by PNA targeted to mRNA. Nat Biotechnol 1998; 16:355-8. [PMID: 9555726 DOI: 10.1038/nbt0498-355] [Citation(s) in RCA: 175] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Peptide nucleic acid (PNA) is a DNA mimic with attractive properties for developing improved gene-targeted antisense agents. To test this potential of PNA in bacteria, PNAs were designed to target the start codon regions of the Escherichia coli beta-galactosidase and beta-lactamase genes. Dose-dependent and specific gene inhibition was observed in vitro using low nanomolar PNA concentrations and in vivo using low micromolar concentrations. Inhibition was more efficient for a permeable E. coli strain relative to wild-type K-12. The potency of the anti-beta-lactamase PNAs was abolished by a six base substitution, and inhibition could be re-established using a PNA with compensating base changes. Antisense inhibition of the beta-lactamase gene was sufficient to sensitize resistant cells to the antibiotic ampicillin. The results demonstrate gene- and sequence-specific antisense inhibition in E. coli and open possibilities for antisense antibacterial drugs and gene function analyses in bacteria.
Collapse
Affiliation(s)
- L Good
- Department of Biochemistry B, Panum Institute, University of Copenhagen, Denmark
| | | |
Collapse
|
165
|
van der Laan AC, Havenaar P, Oosting RS, Kuyl-Yeheskiely E, Uhlmann E, van Boom JH. Optimization of the binding properties of PNA-(5')-DNA chimerae. Bioorg Med Chem Lett 1998; 8:663-8. [PMID: 9871579 DOI: 10.1016/s0960-894x(98)00088-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The synthesis and evaluation of PNA-(5')-DNA chimerae containing either a 5'-amide (i.e. 1a), a 5'-phosphodiester (i.e. 1b) or 5'-phosphonate linkages (i.e. 1c,d) at the junction site are described. The 5'-linkages could be installed using either 5'-amino-5'-deoxythymidine phosphoramidite 2, O-[2-(2-aminoethyl)-(thymin-1-ylacetyl)amino]ethyl phosphoramidite 3, N-(2-aminoethyl)-N-(thymin-1-ylacetyl)aminomethyl phosphonate 4 or N-(2-aminoethyl)-N-(allyloxycarbonyl)aminomethyl phosphonate 5 as building blocks, respectively. It is shown that PNA-(5')-DNA of type 1a-c have a higher binding affinity with complementary RNA than native DNA, and that the antisense activity is mainly due to RNase H.
Collapse
Affiliation(s)
- A C van der Laan
- Leiden Institute of Chemistry, Gorlaeus Laboratories, The Netherlands
| | | | | | | | | | | |
Collapse
|
166
|
Good L, Nielsen PE. Inhibition of translation and bacterial growth by peptide nucleic acid targeted to ribosomal RNA. Proc Natl Acad Sci U S A 1998; 95:2073-6. [PMID: 9482840 PMCID: PMC19253 DOI: 10.1073/pnas.95.5.2073] [Citation(s) in RCA: 117] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Peptide nucleic acid (PNA) is a DNA mimic that has shown considerable promise as a lead compound for developing gene therapeutic drugs. We report that PNAs targeted to functional and accessible sites in ribosomal RNA can inhibit translation in an Escherichia coli cell-free transcription/translation system, with 50% reductions caused by nanomolar PNA concentrations. The effect in vitro is quantitatively similar to that of the known translation inhibitor and antibiotic tetracycline. Also, the targeted PNAs inhibited bacterial growth on agar plates and in liquid culture. A strain of E. coli (AS19) that is more permeable to antibiotics was approximately 10-fold more sensitive to the active PNAs, suggesting that the effect on growth indeed was caused by PNAs that entered cells. Inhibition was not observed when using control PNAs of similar composition but with an unrelated or mismatched sequence. The results demonstrate that ribosomal RNA is a possible target for sequence-designed novel antibiotics based on DNA analogues or mimics.
Collapse
Affiliation(s)
- L Good
- Center for Biomolecular Recognition, Departments of Medical Biochemistry and Genetics, Biochemistry B, The Panum Institute, University of Copenhagen, Blegdamsvej 3, 2200 Copenhagen N, Copenhagen, Denmark
| | | |
Collapse
|
167
|
Cherny DI, Fourcade A, Svinarchuk F, Nielsen PE, Malvy C, Delain E. Analysis of various sequence-specific triplexes by electron and atomic force microscopies. Biophys J 1998; 74:1015-23. [PMID: 9533714 PMCID: PMC1302582 DOI: 10.1016/s0006-3495(98)74026-3] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Sequence-specific interactions of 20-mer G,A-containing triple helix-forming oligonucleotides (TFOs) and bis-PNAs (peptide nucleic acids) with double-stranded DNA was visualized by electron (EM) and atomic force (AFM) microscopies. Triplexes formed by biotinylated TFOs are easily detected by both EM and AFM in which streptavidin is a marker. AFM images of the unlabeled triplex within a long plasmid DNA show a approximately 0.4-nm height increment of the double helix within the target site position. TFOs conjugated to a 74-nt-long oligonucleotide forming a 33-bp-long hairpin form extremely stable triplexes with the target site that are readily imaged by both EM and AFM as protruding DNA. The short duplex protrudes in a perpendicular direction relative to the double helix axis, either in the plane of the support or out of it. In the latter case, the apparent height of the protrusion is approximately 1.5 nm, when that of the triplex site is increased by 0.3-0.4 nm. Triplex formation by bis-PNA, in which two decamers of PNA are connected via a flexible linker, causes deformations of the double helix at the target site, which is readily detected as kinks by both EM and AFM. Moreover, AFM shows that these kinks are often accompanied by an increase in the DNA apparent height of approximately 35%. This work shows the first direct visualization of sequence-specific interaction of TFOs and PNAs, with their target sequences within long plasmid DNAs, through the measurements of the apparent height of the DNA double helix by AFM.
Collapse
Affiliation(s)
- D I Cherny
- Institute of Molecular Genetics, Moscow, Russia.
| | | | | | | | | | | |
Collapse
|
168
|
Sen S, Nilsson L. Molecular Dynamics of Duplex Systems Involving PNA: Structural and Dynamical Consequences of the Nucleic Acid Backbone. J Am Chem Soc 1998. [DOI: 10.1021/ja972234x] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Srikanta Sen
- Contribution from the Centre for Structural Biochemistry, Karolinska institutet, Department of Bioscience, S-141 57 HUDDINGE, Sweden
| | - Lennart Nilsson
- Contribution from the Centre for Structural Biochemistry, Karolinska institutet, Department of Bioscience, S-141 57 HUDDINGE, Sweden
| |
Collapse
|
169
|
Sequence-specific recognition of double-stranded DNA by peptide nucleic acids. ACTA ACUST UNITED AC 1998. [DOI: 10.1016/s1067-568x(98)80012-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
|
170
|
Haaima G, Hansen HF, Christensen L, Dahl O, Nielsen PE. Increased DNA binding and sequence discrimination of PNA oligomers containing 2,6-diaminopurine. Nucleic Acids Res 1997; 25:4639-43. [PMID: 9358176 PMCID: PMC147079 DOI: 10.1093/nar/25.22.4639] [Citation(s) in RCA: 88] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The synthesis of a diaminopurine PNA monomer, N-[N6-(benzyloxycarbonyl)-2,6-diaminopurine-9-yl] acetyl-N-(2-t-butyloxycarbonylaminoethyl)glycine, and the incorporation of this monomer into PNA oligomers are described. Substitution of adenine by diaminopurine in PNA oligomers increased the T m of duplexes formed with complementary DNA, RNA or PNA by 2.5-6.5 degrees C per diaminopurine. Furthermore, discrimination against mismatches facing the diaminopurine in the hybridizing oligomer is improved. Finally, a homopurine decamer PNA containing six diaminopurines is shown to form a (gel shift) stable strand displacement complex with a target in a 246 bp double-stranded DNA fragment.
Collapse
Affiliation(s)
- G Haaima
- Center for Biomolecular Recognition, Department of Chemistry, The H. C.Orsted Institute, Universitetsparken 5, DK-2100 Copenhagen O, Denmark
| | | | | | | | | |
Collapse
|
171
|
Abstract
The biophysical and biological properties of PNA (peptide nucleic acid) is briefly reviewed with special emphasis on recent three dimensional structures of PNA-nucleic acid complexes and on structure-activity relations in terms of nucleic acid hybridization properties. 1997 Elsevier Science B.V.
Collapse
Affiliation(s)
- P E Nielsen
- Biochemistry Laboratory B, Center for Biomolecular Recognition, Department of Medical Biochemistry and Genetics, The Panum Institute, Copenhagen N, Denmark
| |
Collapse
|
172
|
Leijon M, Sehlstedt U, Nielsen PE, Gräslund A. Unique base-pair breathing dynamics in PNA-DNA hybrids. J Mol Biol 1997; 271:438-55. [PMID: 9268670 DOI: 10.1006/jmbi.1997.1153] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Kinetic and thermodynamic parameters, derived from 1H-NMR measurements of the imino proton exchange rates upon titration with the exchange catalyst ammonia, are reported for two mixed-sequence peptide nucleic acid (PNA)-DNA hybrids and their counterpart DNA duplex. The exchange times of the imino protons in the PNA strands extrapolate to very short base-pair lifetimes in the limit of infinite exchange catalyst concentration. This is not due to generally less stable base-pairs in PNA-DNA hybrids, since the lifetimes, apparent dissociation constants and thermodynamic stability (DeltaG degrees ) of the innermost DNA guanine imino protons are similar in the hybrid duplexes and in the DNA duplex. In addition, the apparent dissociation constants determined for PNA bases of the hybrids are of the same order as those of the corresponding bases in the DNA duplex. An exchange process from the closed state was found to be inconsistent with the experimental data. From these results, we conclude that opening and closing rates of the PNA guanine and thymine bases are at least two orders of magnitude higher than those of the corresponding bases in the DNA duplex. Unusual kinetics in the hybrids is also evident from the destabilization of the complementary DNA strand thymine bases, which exhibit base-pair dissociation constants increased by approximately two orders of magnitude compared to what is observed in the DNA duplex, while the DNA strand guanine bases are largely unaffected. The general pattern of the base-pair dynamics in the hybrids obtained when using trimethylamine as an exchange catalyst is the same as when using ammonia. However, the long base-pair lifetimes i. e. those of the DNA duplex and the guanine bases of the DNA strands in the hybrids, are approximately three to five times longer than when using ammonia. Thus, all opening events sensed by ammonia are not accessible to trimethylamine. These observations are discussed in regard to the mechanism of base-pair opening and the nature of the open state.
Collapse
Affiliation(s)
- M Leijon
- Department of Biophysics Arrhenius Laboratory, Stockholm University, Stockholm, S-106 91, Sweden
| | | | | | | |
Collapse
|
173
|
Kool ET. Preorganization of DNA: Design Principles for Improving Nucleic Acid Recognition by Synthetic Oligonucleotides. Chem Rev 1997; 97:1473-1488. [PMID: 11851456 PMCID: PMC2790533 DOI: 10.1021/cr9603791] [Citation(s) in RCA: 226] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Eric T. Kool
- Department of Chemistry and Department of Biochemistry and Biophysics, University of Rochester, Rochester, New York 14627
| |
Collapse
|
174
|
Giovannangeli C, Hélène C. Progress in developments of triplex-based strategies. ANTISENSE & NUCLEIC ACID DRUG DEVELOPMENT 1997; 7:413-21. [PMID: 9303193 DOI: 10.1089/oli.1.1997.7.413] [Citation(s) in RCA: 96] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Recognition of B-DNA by oligonucleotides that form triple helices is a unique method to specifically recognize sequences of double-stranded DNA. Recently, some significant limitations of the triple-based applications have been overcome. Stable intermolecular triplexes can be formed under physiologic conditions. Binding affinities of modified oligonucleotides to their target sequence due to Hoogsteen or reverse Hoogsteen hydrogen bonding interactions are now in the range of those obtained for duplex formation via Watson-Crick hydrogen bonding interactions even if the kinetics may be quite different. Progress has been made toward developing general procedures to determine the molecular mechanisms of action of triplex-forming oligonucleotides (TFO) administered to cultured cells to provide a rational proof-of-concept for antigene strategies. The antigene strategy has reached a point where TFOs can be used to interfere with several biologic progresses (replication, transcription, recombination, repair) in relevant systems both in vitro and ex vivo.
Collapse
Affiliation(s)
- C Giovannangeli
- Laboratoire de Biophysique, INSERM U.201, CNRS URA 481, Paris, France
| | | |
Collapse
|
175
|
Good L, Nielsen PE. Progress in developing PNA as a gene-targeted drug. ANTISENSE & NUCLEIC ACID DRUG DEVELOPMENT 1997; 7:431-7. [PMID: 9303195 DOI: 10.1089/oli.1.1997.7.431] [Citation(s) in RCA: 90] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Peptide nucleic acid (PNA) is a DNA mimic in which the nucleobases are attached to a pseudopeptide backbone. This achiral, uncharged, and rather flexible peptide backbone permits more stable hybridization to DNA and RNA oligomers with uncompromised or even improved sequence selectivity. Additional advantages of PNA are stability against nucleases and proteases and convenient solid phase synthesis. At the RNA level, PNA can be targeted to mRNA to block protein synthesis in an antisense strategy. PNA can also be targeted to the RNA component of ribonucleoproteins (RNPs) to inhibit their enzymatic activities. At the DNA level, the unique ability of PNA to bind DNA by duplex invasion can be used to arrest transcription within a gene sequence or to provide an artificial open complex to promote transcription. This review focuses on recent progress toward the development of PNA as a sequence-targeted drug.
Collapse
Affiliation(s)
- L Good
- Department of Medical Biochemistry and Genetics, University of Copenhagen, Panum Institute, Copenhagen, Denmark
| | | |
Collapse
|
176
|
Colombier C, Boudvillain M, Leng M. Interstrand crosslinking reaction in transplatin-modified oligo-2'-O-methyl ribonucleotide-RNA hybrids. ANTISENSE & NUCLEIC ACID DRUG DEVELOPMENT 1997; 7:397-402. [PMID: 9303191 DOI: 10.1089/oli.1.1997.7.397] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
In the context of developing an approach to irreversibly and specifically link oligonucleotides to RNA, the purpose of this work was to determine the factors interfering with the rate of the rearrangement of the transplatin 1,3-intrastrand crosslinks into interstrand crosslinks, rearrangement triggered by the formation of a double helix between platinated oligo-2'-O-methyl-ribonucleotides and their complementary strands. The rate of the rearrangement has been studied as a function of the length of the hybrids, the location of the intrastrand crosslinks, the nature of the oligonucleotide backbone, and the nature of the doublet replacing the triplet complementary to the intrastrand crosslinks. The thermal stability of the platinated hybrids has been determined in various salt conditions. The results are discussed in relation to the mechanism of the rearrangement. It is shown that the cellular proteins present weaker nonspecific interactions with single-stranded platinated oligo-2'-O-methyl-nucleotides than with the isosequential oligodeoxyribonucleotides.
Collapse
Affiliation(s)
- C Colombier
- Centre de Biophysique Moléculaire, CNRS, Orléans, France
| | | | | |
Collapse
|
177
|
Jankowsky E, Strunk G, Schwenzer B. Peptide nucleic acid (PNA) is capable of enhancing hammerhead ribozyme activity with long but not with short RNA substrates. Nucleic Acids Res 1997; 25:2690-3. [PMID: 9207013 PMCID: PMC146807 DOI: 10.1093/nar/25.14.2690] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Long RNA substrates are inefficiently cleaved by hammerhead ribozymes in trans. Oligonucleotide facilitators capable of affecting the ribozyme activity by interacting with the substrates at the termini of the ribozyme provide a possibility to improve ribozyme mediated cleavage of long RNA substrates. We have examined the effect of PNA as facilitator in vitro in order to test if even artificial compounds have facilitating potential. Effects of 12mer PNA- (peptide nucleic acid), RNA- and DNA-facilitators of identical sequence were measured with three substrates containing either 942, 452 or 39 nucleotides. The PNA facilitator enhances the ribozyme activity with both, the 942mer and the 452mer substrate to a slightly smaller extent than RNA and DNA facilitators. This effect was observed up to PNA facilitator:substrate ratios of 200:1. The enhancement becomes smaller as the PNA facilitator:substrate ratio exceeds 200:1. With the 39mer substrate, the PNA facilitator decreases the ribozyme activity by more than 100-fold, even at PNA facilitator:substrate ratios of 1:1. Although with long substrates the effect of the PNA facilitator is slightly smaller than the effect of identical RNA or DNA facilitators, PNA may be a more practical choice for potential applications in vivo because PNA is much more resistant to degradation by cellular enzymes.
Collapse
Affiliation(s)
- E Jankowsky
- Institut für Biochemie, Technische Universität Dresden, Mommsenstrasse 13, 01069 Dresden, Germany
| | | | | |
Collapse
|
178
|
Lagriffoule P, Eriksson M, Jensen KK, Nielsen PE, Wittung P, Nordén B, Buchardt O. Peptide Nucleic Acids with a Conformationally Constrained Chiral Cyclohexyl-Derived Backbone. Chemistry 1997. [DOI: 10.1002/chem.19970030613] [Citation(s) in RCA: 79] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
179
|
Koppelhus U, Zachar V, Nielsen PE, Liu X, Eugen-Olsen J, Ebbesen P. Efficient in vitro inhibition of HIV-1 gag reverse transcription by peptide nucleic acid (PNA) at minimal ratios of PNA/RNA. Nucleic Acids Res 1997; 25:2167-73. [PMID: 9153317 PMCID: PMC146729 DOI: 10.1093/nar/25.11.2167] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
We have tested the inhibitory potential of peptide nucleic acid (PNA) on in vitro reverse transcription of the HIV-1 gag gene. PNA was designed to target different regions of the HIV-1 gag gene and the effect on reverse transcription by HIV-1, MMLV and AMV reverse transcriptases (RTs) was investigated. We found that a bis-PNA (parallel antisense 10mer linked to antiparallel antisense 10mer) was superior to both the parallel antisense 10mer and antiparallel antisense 10mer in inhibiting reverse transcription of the gene, thus indicating triplex formation at the target sequence. A complete arrest of reverse transcription was obtained at approximately 6-fold molar excess of the bis-PNA with respect to the gag RNA. At this molar ratio we found no effect on in vitro translation of gag RNA. A 15mer duplex-forming PNA was also found to inhibit reverse transcription at very low molar ratios of PNA/ gag RNA. Specificity of the inhibition of reverse transcription by PNA was confirmed by RNA sequencing, which revealed that all tested RTs were stopped by the PNA/RNA complex at the predicted site. We propose that the effect of PNA is exclusively due to steric hindrance, as we found no signs of RNA degradation that would indicate PNA-mediated RNase H activation of the tested RTs. In conclusion, PNA appears to have a potential to become a specific and efficient inhibitor of reverse transcription in vivo , provided sufficient intracellular levels are achievable.
Collapse
Affiliation(s)
- U Koppelhus
- Department of Virus and Cancer, Danish Cancer Society, Gustav Wieds Vej 10, DK-8000 Aarhus C, Denmark.
| | | | | | | | | | | |
Collapse
|
180
|
Abstract
Peptide nucleic acids (PNAs) are DNA analogs containing neutral amide backbone linkages. PNAs are stable to degradation by enzymes and hybridize to complementary sequences with higher affinity than analogous DNA oligomers. PNA synthesis employs protocols derived from solid-phase peptide synthesis, making the methodology straightforward and flexible. PNAs are being incorporated into an expanding set of applications, including genome mapping, the identification of mutations and measurement of telomere length. The growth in the popularity of PNAs as a tool for nucleic acid recognition should accelerate as the properties of PNAs become more familiar.
Collapse
Affiliation(s)
- D R Corey
- Howard Hughes Medical Institute, Dallas, TX, USA.
| |
Collapse
|
181
|
Heidenreich O, Gryaznov S, Nerenberg M. RNase H-independent antisense activity of oligonucleotide N3 '--> P5 ' phosphoramidates. Nucleic Acids Res 1997; 25:776-80. [PMID: 9016628 PMCID: PMC146512 DOI: 10.1093/nar/25.4.776] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Oligonucleotide N3'-->P5'phosphoramidates are a new and promising class of antisense agents. Here we report biological properties of phosphoramidate oligonucleotides targeted against the human T cell leukemia virus type-I Tax protein, the major transcriptional transactivator of this human retrovirus. Isosequential phosphorothioate oligodeoxynucleotides and uniformly modified and chimeric phosphoramidate oligodeoxynucleotides containing six central phosphodiester linkages are all quite stable in cell nuclei. The uniformly modified anti-tax phosphoramidate oligodeoxynucleotide does not activate nuclear RNase H, as was shown by RNase protection assay. In contrast, the chimeric phosphoramidate-phosphodiester oligodeoxynucleotide is an efficient activator of RNase H. The presence of one or two mismatched nucleotides in the phosphodiester portion of oligonucleotides affected this activation only negligibly. When introduced into tax-transformed fibroblasts ex vivo, only the uniformly modified anti-tax phosphoramidate oligodeoxynucleotide caused a sequence-dependent reduction in the Tax protein level. Neither the chimeric phosphoramidate nor the phosphorothioate oligodeoxynucleotides significantly reduced tax expression under similar experimental conditions.
Collapse
|
182
|
Rasmussen H, Kastrup JS, Nielsen JN, Nielsen JM, Nielsen PE. Crystal structure of a peptide nucleic acid (PNA) duplex at 1.7 A resolution. NATURE STRUCTURAL BIOLOGY 1997; 4:98-101. [PMID: 9033585 DOI: 10.1038/nsb0297-98] [Citation(s) in RCA: 200] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The crystal structure of a PNA duplex reveals both a right- and a left-handed helix in the unit cell. The helices are wide (28A), large pitched (18bp) with the base pairs perpendicular to the helix axis, thereby demonstrating that PNA besides adapting to oligonucleotide partners also has a unique structure by itself.
Collapse
|
183
|
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
|
184
|
|
185
|
|
186
|
Smulevitch SV, Simmons CG, Norton JC, Wise TW, Corey DR. Enhancement of strand invasion by oligonucleotides through manipulation of backbone charge. Nat Biotechnol 1996; 14:1700-4. [PMID: 9634855 DOI: 10.1038/nbt1296-1700] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The ability of DNA oligonucleotides, neutral peptide nucleic acids (PNAS), and oligonucleotide conjugates to hybridize to inverted repeat sequences within supercoiled double-stranded DNA by Watson-Crick base-pairing is examined. PNAs and oligonucleotide conjugates initiate and maintain strand invasion under more stringent conditions than do unmodified DNA oligonucleotides. PNAs hybridize rapidly and, once bound, hold open a target site allowing oligonucleotides to base-pair to the displaced strand under conditions that would otherwise preclude hybridization. The ability to manipulate hybridization efficiency through different options for the alteration of oligomer charge should have important implications for optimizing sequence-specific recognition of DNA.
Collapse
Affiliation(s)
- S V Smulevitch
- Howard Hughes Medical Institute, Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, TX 75235, USA
| | | | | | | | | |
Collapse
|