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Qu GR, Li Y, Han SH. Microwave Assisted Synthesis of N-(ethoxycarbonylmethyl)-nucleobases: Building Blocks for PNAs. JOURNAL OF CHEMICAL RESEARCH 2019. [DOI: 10.3184/0308234054213627] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The synthesis of N1/N9- (Ethoxycarbonylmethyl)pyrimidine/purine using as synthons for peptide nucleic acids has been described. Microwave irradiation provided the desired products by alkylation of the appropriately protected natural and substituted nucleobases with ethyl bromoacetate within 4–7 min in 48–85% yields.
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Affiliation(s)
- Gui-Rong Qu
- College of Chemistry and Environmental Science, Henan Normal University, Xinxiang 453007, Henan, P. R. China
| | - Yong Li
- College of Chemistry and Environmental Science, Henan Normal University, Xinxiang 453007, Henan, P. R. China
| | - Su-Hui Han
- College of Chemistry and Environmental Science, Henan Normal University, Xinxiang 453007, Henan, P. R. China
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Wu JC, Meng QC, Ren HM, Wang HT, Wu J, Wang Q. Recent advances in peptide nucleic acid for cancer bionanotechnology. Acta Pharmacol Sin 2017; 38:798-805. [PMID: 28414202 DOI: 10.1038/aps.2017.33] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 02/04/2017] [Indexed: 02/07/2023] Open
Abstract
Peptide nucleic acid (PNA) is an oligomer, in which the phosphate backbone has been replaced by a pseudopeptide backbone that is meant to mimic DNA. Peptide nucleic acids are of the utmost importance in the biomedical field because of their ability to hybridize with neutral nucleic acids and their special chemical and biological properties. In recent years, PNAs have emerged in nanobiotechnology for cancer diagnosis and therapy due to their high affinity and sequence selectivity toward corresponding DNA and RNA. In this review, we summarize the recent progresses that have been made in cancer detection and therapy with PNA biotechnology. In addition, we emphasize nanoparticle PNA-based strategies for the efficient delivery of drugs in anticancer therapies.
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Wang Q, Chen L, Long Y, Tian H, Wu J. Molecular beacons of xeno-nucleic acid for detecting nucleic acid. Theranostics 2013; 3:395-408. [PMID: 23781286 PMCID: PMC3677410 DOI: 10.7150/thno.5935] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Accepted: 04/10/2013] [Indexed: 12/24/2022] Open
Abstract
Molecular beacons (MBs) of DNA and RNA have aroused increasing interest because they allow a continuous readout, excellent spatial and temporal resolution to observe in real time. This kind of dual-labeled oligonucleotide probes can differentiate between bound and unbound DNA/RNA in homogenous hybridization with a high signal-to-background ratio in living cells. This review briefly summarizes the different unnatural sugar backbones of oligonucleotides combined with fluorophores that have been employed to sense DNA/RNA. With different probes, we epitomize the fundamental understanding of driving forces and these recognition processes. Moreover, we will introduce a few novel and attractive emerging applications and discuss their advantages and disadvantages. We also highlight several perspective probes in the application of cancer therapeutics.
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DNA-, RNA- and self-pairing properties of a pyrrolidinyl peptide nucleic acid with a (2′R,4′S)-prolyl-(1S,2S)-2-aminocyclopentanecarboxylic acid backbone. Tetrahedron Lett 2010. [DOI: 10.1016/j.tetlet.2010.08.102] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Vilaivan T, Srisuwannaket C. Hybridization of pyrrolidinyl peptide nucleic acids and DNA: selectivity, base-pairing specificity, and direction of binding. Org Lett 2007; 8:1897-900. [PMID: 16623579 DOI: 10.1021/ol060448q] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
[structure: see text] A mixed-base, beta-amino acid containing, pyrrolidinyl peptide nucleic acid (PNA) binds strongly and selectively to complementary DNA in an exclusively antiparallel fashion. The PNA-DNA binding specificity strictly follows the Watson-Crick base-pairing rules.
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Affiliation(s)
- Tirayut Vilaivan
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok 10330, Thailand.
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Pandit UK. Biomolecular approach to the design of potential drugs. PURE APPL CHEM 2007. [DOI: 10.1351/pac200779122119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
The approach to drug design on the basis of molecular-level information on biological processes is being driven by the expanding knowledge of the details of molecular events in biological systems. We have directed attention to the design of potentially active compounds based on the aforementioned "biomolecular" concepts. Selected examples from our studies are discussed. This paper presents three case studies of approaches to the development of potential medicinal agents whose design has evolved from considerations of molecular mechanisms of processes in selected biological systems.
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Affiliation(s)
- Upendra K. Pandit
- Van't Hoff Institute of Molecular Sciences, University of Amsterdam, Nieuwe Achtergracht 129, 1018 WS Amsterdam, The Netherlands
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Topham CM, Smith JC. Orientation preferences of backbone secondary amide functional groups in peptide nucleic acid complexes: quantum chemical calculations reveal an intrinsic preference of cationic D-amino acid-based chiral PNA analogues for the P-form. Biophys J 2006; 92:769-86. [PMID: 17071666 PMCID: PMC1779963 DOI: 10.1529/biophysj.105.079723] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Geometric descriptions of nonideal interresidue hydrogen bonding and backbone-base water bridging in the minor groove are established in terms of polyamide backbone carbonyl group orientation from analyses of residue junction conformers in experimentally determined peptide nucleic acid (PNA) complexes. Two types of interresidue hydrogen bonding are identified in PNA conformers in heteroduplexes with nucleic acids that adopt A-like basepair stacking. Quantum chemical calculations on the binding of a water molecule to an O2 base atom in glycine-based PNA thymine dimers indicate that junctions modeled with P-form backbone conformations are lower in energy than a dimer comprising the predominant conformation observed in A-like helices. It is further shown in model systems that PNA analogs based on D-lysine are better able to preorganize in a conformation exclusive to P-form helices than is glycine-based PNA. An intrinsic preference for this conformation is also exhibited by positively charged chiral PNA dimers carrying 3-amino-D-alanine or 4-aza-D-leucine residue units that provide for additional rigidity by side-chain hydrogen bonding to the backbone carbonyl oxygen. Structural modifications stabilizing P-form helices may obviate the need for large heterocycles to target DNA pyrimidine bases via PNA.DNA-PNA triplex formation. Quantum chemical modeling methods are used to propose candidate PNA Hoogsteen strand designs.
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Affiliation(s)
- Christopher M Topham
- Institut de Pharmacologie et de Biologie Structurale, Centre National de la Recherche Scientifique UMR 5089, Toulouse, France.
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Suparpprom C, Srisuwannaket C, Sangvanich P, Vilaivan T. Synthesis and oligodeoxynucleotide binding properties of pyrrolidinyl peptide nucleic acids bearing prolyl-2-aminocyclopentanecarboxylic acid (ACPC) backbones. Tetrahedron Lett 2005. [DOI: 10.1016/j.tetlet.2005.02.126] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Monitor – chemistry. Drug Discov Today 2004. [DOI: 10.1016/s1359-6446(04)03219-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Demidov VV, Frank-Kamenetskii MD. Two sides of the coin: affinity and specificity of nucleic acid interactions. Trends Biochem Sci 2004; 29:62-71. [PMID: 15102432 DOI: 10.1016/j.tibs.2003.12.007] [Citation(s) in RCA: 144] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
During the past decade, synthetic nucleobase oligomers have found wide use in biochemical sciences, biotechnology and molecular medicine, both as research and/or diagnostic tools and as therapeutics. Numerous applications of common and modified oligonucleotides and oligonucleotide mimics rely on their ability to sequence-specifically recognize nucleic acid targets (DNA or RNA) by forming duplexes or triplexes. In general, these applications would benefit significantly from enhanced binding affinities of nucleobase oligomers in the formation of various secondary structures. However, for high-affinity probes, the selectivity of sequence recognition must also be improved to avoid undesirable associations with mismatched DNA and RNA sites. Here, we review recent progress in understanding the molecular mechanisms of nucleic acid interactions and the development of new high-affinity plus high-specificity oligonucleotides and their mimics, with particular emphasis on peptide nucleic acids.
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Affiliation(s)
- Vadim V Demidov
- Center for Advanced Biotechnology, Boston University, Boston, MA 02215, USA.
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Abstract
In some aspects, homogeneous (all-in-solution) nucleic acid hybridization assays are superior to the traditionally used heterogeneous (solution-to-surface) alternatives. Profluorescent probes, which reveal fluorescence enhancement or fluorescence polarization upon their binding to DNA and RNA targets, are a paradigm for the real-time sequence-specific homogeneous detection of nucleic acids. A variety of such DNA or RNA-derived probes of different constructs has already been developed with numerous applications. However, the recent additions to the field - locked nucleic acids (LNAs) and peptide nucleic acids (PNAs) - significantly increase the potential of profluorescent probes and provide a robust impulse for their new uses.
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Affiliation(s)
- Vadim V Demidov
- Center for Advanced Biotechnology, Boston University, 36 Cummington Street, Boston, MA 02215, USA.
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Falkiewicz B. Application of Mitsunobu reaction to solid-phase peptide nucleic acid (PNA) monomer synthesis. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2002; 21:883-9. [PMID: 12537028 DOI: 10.1081/ncn-120016612] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
PNA type I monomer backbone with a reduced peptide bond was synthesized on a Merrifield resin in Mitsunobu reaction of Boc-aminoethanol with resin-bound o-nitrobenzenesulfonylglycine. The pseudodipeptide secondary amine group was deprotected by thiolysis and acylated with thymin-1-ylacetic acid. The monomer was released as a methyl ester. The procedure seems to be of general applicability and allows various modifications of PNA structure by using diverse alcohols and amino acid esters.
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Protozanova E, Demidov VV, Soldatenkov V, Chasovskikh S, Frank-Kamenetskii MD. Tailoring the activity of restriction endonuclease PleI by PNA-induced DNA looping. EMBO Rep 2002; 3:956-61. [PMID: 12231505 PMCID: PMC1307623 DOI: 10.1093/embo-reports/kvf192] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
DNA looping is one of the key factors allowing proteins bound to different DNA sites to signal one another via direct contacts. We demonstrate that DNA looping can be generated in an arbitrary chosen site by sequence-directed targeting of double-stranded DNA with pseudocomplementary peptide-nucleic acids (pcPNAs). We designed pcPNAs to mask the DNA from cleavage by type IIs restriction enzyme PleI while not preventing the enzyme from binding to its primary DNA recognition site. Direct interaction between two protein molecules (one bound to the original recognition site and the other to a sequence-degenerated site) results in a totally new activity of PleI: it produces a nick near the degenerate site. The PNA-induced nicking efficiency varies with the distance between the two protein-binding sites in a phase with the DNA helical periodicity. Our findings imply a general approach for the fine-tuning of proteins bound to DNA sites well separated along the DNA chain.
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Affiliation(s)
- Ekaterina Protozanova
- Center for Advanced Biotechnology, Boston University, 36 Cummington Street, Boston, MA 02215
| | - Vadim V. Demidov
- Center for Advanced Biotechnology, Boston University, 36 Cummington Street, Boston, MA 02215
- V.V. Demidov and M.D. Frank-Kamenetskii should be regarded as senior authors
| | - Viatcheslav Soldatenkov
- Department of Radiation Medicine, Georgetown University Medical Center, 3970 Reservoir Road N.W., Washington, DC 20007, USA
| | - Sergey Chasovskikh
- Department of Radiation Medicine, Georgetown University Medical Center, 3970 Reservoir Road N.W., Washington, DC 20007, USA
| | - Maxim D. Frank-Kamenetskii
- Center for Advanced Biotechnology, Boston University, 36 Cummington Street, Boston, MA 02215
- V.V. Demidov and M.D. Frank-Kamenetskii should be regarded as senior authors
- Tel: +1 617 353 8498; Fax: +1 617 353 8501;
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