Sequence specificity of alternating hydroyprolyl/phosphono peptide nucleic acids against zebrafish embryo mRNAs.
Identifieur interne : 002358 ( PubMed/Corpus ); précédent : 002357; suivant : 002359Sequence specificity of alternating hydroyprolyl/phosphono peptide nucleic acids against zebrafish embryo mRNAs.
Auteurs : E. Wickstrom ; M. Choob ; K A Urtishak ; X. Tian ; N. Sternheim ; S. Talbot ; J. Archdeacon ; V A Efimov ; S A FarberSource :
- Journal of drug targeting [ 1061-186X ] ; 2004.
English descriptors
- KwdEn :
- Animals, Base Sequence, Embryo, Nonmammalian (drug effects), Embryo, Nonmammalian (metabolism), Hydroxyproline (chemistry), Molecular Mimicry, Oligoribonucleotides, Antisense (chemistry), Oligoribonucleotides, Antisense (pharmacology), Organophosphonates (chemistry), Peptide Nucleic Acids (chemistry), RNA, Messenger (antagonists & inhibitors), RNA, Messenger (biosynthesis), Zebrafish (embryology).
- MESH :
- chemical , antagonists & inhibitors : RNA, Messenger.
- chemical , biosynthesis : RNA, Messenger.
- chemical , chemistry : Hydroxyproline, Oligoribonucleotides, Antisense, Organophosphonates, Peptide Nucleic Acids.
- drug effects : Embryo, Nonmammalian.
- embryology : Zebrafish.
- metabolism : Embryo, Nonmammalian.
- chemical , pharmacology : Oligoribonucleotides, Antisense.
- Animals, Base Sequence, Molecular Mimicry.
Abstract
Morpholino phosphorodiamidate (MO) DNA mimics display excellent water solubility and hybridization properties toward DNA and RNA, and have been utilized in the model vertebrate zebrafish (Danio rerio) for genome-wide, sequence-based, reverse genetic screens during embryonic development. Peptide nucleic acids (PNAs) exhibit excellent mismatch discrimination, nuclease resistance, and protease resistance, but low solubility. Negatively charged DNA mimics composed of alternating residues of trans-4-hydroxy-L-proline peptide nucleic acid monomers and phosphono peptide nucleic acid monomers (HypNA-pPNA) combine all of the positive features of both MOs and PNAs. Thus, we evaluated PNA oligomers and HypNA-pPNA oligomers as an alternative to MOs for oligonucleotide inhibition of gene expression in zebrafish embryos. We observed that HypNA-pPNA 18-mers displayed comparable potency to MO 25-mers as knockdown agents against chordin, notail and uroD, with greater mismatch stringency. Furthermore, we observed that a specific HypNA-pPNA 18-mer elicited the dharma (bozozok)(-/-) phenotype in zebrafish embryos, which MO 25-mers do not. These observations validate HypNA-pPNAs as an alternative to MO oligomers for reverse genetic studies. The stronger hybridization and greater specificity of HypNA-pPNAs enable knockdown of mRNAs unaffected by MO oligomers.
DOI: 10.1080/10611860412331285242
PubMed: 15545086
Links to Exploration step
pubmed:15545086Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Sequence specificity of alternating hydroyprolyl/phosphono peptide nucleic acids against zebrafish embryo mRNAs.</title><author><name sortKey="Wickstrom, E" sort="Wickstrom, E" uniqKey="Wickstrom E" first="E" last="Wickstrom">E. Wickstrom</name><affiliation><nlm:affiliation>Department of Biochemistry and Molecular Pharmacology, Thomas Jefferson University, Philadelphia, PA 19107, USA. eric@tesla.jci.tju.edu</nlm:affiliation></affiliation></author><author><name sortKey="Choob, M" sort="Choob, M" uniqKey="Choob M" first="M" last="Choob">M. Choob</name></author><author><name sortKey="Urtishak, K A" sort="Urtishak, K A" uniqKey="Urtishak K" first="K A" last="Urtishak">K A Urtishak</name></author><author><name sortKey="Tian, X" sort="Tian, X" uniqKey="Tian X" first="X" last="Tian">X. Tian</name></author><author><name sortKey="Sternheim, N" sort="Sternheim, N" uniqKey="Sternheim N" first="N" last="Sternheim">N. Sternheim</name></author><author><name sortKey="Talbot, S" sort="Talbot, S" uniqKey="Talbot S" first="S" last="Talbot">S. Talbot</name></author><author><name sortKey="Archdeacon, J" sort="Archdeacon, J" uniqKey="Archdeacon J" first="J" last="Archdeacon">J. Archdeacon</name></author><author><name sortKey="Efimov, V A" sort="Efimov, V A" uniqKey="Efimov V" first="V A" last="Efimov">V A Efimov</name></author><author><name sortKey="Farber, S A" sort="Farber, S A" uniqKey="Farber S" first="S A" last="Farber">S A Farber</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2004">2004</date><idno type="RBID">pubmed:15545086</idno><idno type="pmid">15545086</idno><idno type="doi">10.1080/10611860412331285242</idno><idno type="wicri:Area/PubMed/Corpus">002358</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">002358</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Sequence specificity of alternating hydroyprolyl/phosphono peptide nucleic acids against zebrafish embryo mRNAs.</title><author><name sortKey="Wickstrom, E" sort="Wickstrom, E" uniqKey="Wickstrom E" first="E" last="Wickstrom">E. Wickstrom</name><affiliation><nlm:affiliation>Department of Biochemistry and Molecular Pharmacology, Thomas Jefferson University, Philadelphia, PA 19107, USA. eric@tesla.jci.tju.edu</nlm:affiliation></affiliation></author><author><name sortKey="Choob, M" sort="Choob, M" uniqKey="Choob M" first="M" last="Choob">M. Choob</name></author><author><name sortKey="Urtishak, K A" sort="Urtishak, K A" uniqKey="Urtishak K" first="K A" last="Urtishak">K A Urtishak</name></author><author><name sortKey="Tian, X" sort="Tian, X" uniqKey="Tian X" first="X" last="Tian">X. Tian</name></author><author><name sortKey="Sternheim, N" sort="Sternheim, N" uniqKey="Sternheim N" first="N" last="Sternheim">N. Sternheim</name></author><author><name sortKey="Talbot, S" sort="Talbot, S" uniqKey="Talbot S" first="S" last="Talbot">S. Talbot</name></author><author><name sortKey="Archdeacon, J" sort="Archdeacon, J" uniqKey="Archdeacon J" first="J" last="Archdeacon">J. Archdeacon</name></author><author><name sortKey="Efimov, V A" sort="Efimov, V A" uniqKey="Efimov V" first="V A" last="Efimov">V A Efimov</name></author><author><name sortKey="Farber, S A" sort="Farber, S A" uniqKey="Farber S" first="S A" last="Farber">S A Farber</name></author></analytic><series><title level="j">Journal of drug targeting</title><idno type="ISSN">1061-186X</idno><imprint><date when="2004" type="published">2004</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Animals</term><term>Base Sequence</term><term>Embryo, Nonmammalian (drug effects)</term><term>Embryo, Nonmammalian (metabolism)</term><term>Hydroxyproline (chemistry)</term><term>Molecular Mimicry</term><term>Oligoribonucleotides, Antisense (chemistry)</term><term>Oligoribonucleotides, Antisense (pharmacology)</term><term>Organophosphonates (chemistry)</term><term>Peptide Nucleic Acids (chemistry)</term><term>RNA, Messenger (antagonists & inhibitors)</term><term>RNA, Messenger (biosynthesis)</term><term>Zebrafish (embryology)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="antagonists & inhibitors" xml:lang="en"><term>RNA, Messenger</term></keywords><keywords scheme="MESH" type="chemical" qualifier="biosynthesis" xml:lang="en"><term>RNA, Messenger</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Hydroxyproline</term><term>Oligoribonucleotides, Antisense</term><term>Organophosphonates</term><term>Peptide Nucleic Acids</term></keywords><keywords scheme="MESH" qualifier="drug effects" xml:lang="en"><term>Embryo, Nonmammalian</term></keywords><keywords scheme="MESH" qualifier="embryology" xml:lang="en"><term>Zebrafish</term></keywords><keywords scheme="MESH" qualifier="metabolism" xml:lang="en"><term>Embryo, Nonmammalian</term></keywords><keywords scheme="MESH" type="chemical" qualifier="pharmacology" xml:lang="en"><term>Oligoribonucleotides, Antisense</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Animals</term><term>Base Sequence</term><term>Molecular Mimicry</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Morpholino phosphorodiamidate (MO) DNA mimics display excellent water solubility and hybridization properties toward DNA and RNA, and have been utilized in the model vertebrate zebrafish (Danio rerio) for genome-wide, sequence-based, reverse genetic screens during embryonic development. Peptide nucleic acids (PNAs) exhibit excellent mismatch discrimination, nuclease resistance, and protease resistance, but low solubility. Negatively charged DNA mimics composed of alternating residues of trans-4-hydroxy-L-proline peptide nucleic acid monomers and phosphono peptide nucleic acid monomers (HypNA-pPNA) combine all of the positive features of both MOs and PNAs. Thus, we evaluated PNA oligomers and HypNA-pPNA oligomers as an alternative to MOs for oligonucleotide inhibition of gene expression in zebrafish embryos. We observed that HypNA-pPNA 18-mers displayed comparable potency to MO 25-mers as knockdown agents against chordin, notail and uroD, with greater mismatch stringency. Furthermore, we observed that a specific HypNA-pPNA 18-mer elicited the dharma (bozozok)(-/-) phenotype in zebrafish embryos, which MO 25-mers do not. These observations validate HypNA-pPNAs as an alternative to MO oligomers for reverse genetic studies. The stronger hybridization and greater specificity of HypNA-pPNAs enable knockdown of mRNAs unaffected by MO oligomers.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">15545086</PMID><DateCompleted><Year>2005</Year><Month>04</Month><Day>14</Day></DateCompleted><DateRevised><Year>2019</Year><Month>11</Month><Day>09</Day></DateRevised><Article PubModel="Print"><Journal><ISSN IssnType="Print">1061-186X</ISSN><JournalIssue CitedMedium="Print"><Volume>12</Volume><Issue>6</Issue><PubDate><Year>2004</Year><Month>Jul</Month></PubDate></JournalIssue><Title>Journal of drug targeting</Title><ISOAbbreviation>J Drug Target</ISOAbbreviation></Journal><ArticleTitle>Sequence specificity of alternating hydroyprolyl/phosphono peptide nucleic acids against zebrafish embryo mRNAs.</ArticleTitle><Pagination><MedlinePgn>363-72</MedlinePgn></Pagination><Abstract><AbstractText>Morpholino phosphorodiamidate (MO) DNA mimics display excellent water solubility and hybridization properties toward DNA and RNA, and have been utilized in the model vertebrate zebrafish (Danio rerio) for genome-wide, sequence-based, reverse genetic screens during embryonic development. Peptide nucleic acids (PNAs) exhibit excellent mismatch discrimination, nuclease resistance, and protease resistance, but low solubility. Negatively charged DNA mimics composed of alternating residues of trans-4-hydroxy-L-proline peptide nucleic acid monomers and phosphono peptide nucleic acid monomers (HypNA-pPNA) combine all of the positive features of both MOs and PNAs. Thus, we evaluated PNA oligomers and HypNA-pPNA oligomers as an alternative to MOs for oligonucleotide inhibition of gene expression in zebrafish embryos. We observed that HypNA-pPNA 18-mers displayed comparable potency to MO 25-mers as knockdown agents against chordin, notail and uroD, with greater mismatch stringency. Furthermore, we observed that a specific HypNA-pPNA 18-mer elicited the dharma (bozozok)(-/-) phenotype in zebrafish embryos, which MO 25-mers do not. These observations validate HypNA-pPNAs as an alternative to MO oligomers for reverse genetic studies. The stronger hybridization and greater specificity of HypNA-pPNAs enable knockdown of mRNAs unaffected by MO oligomers.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Wickstrom</LastName><ForeName>E</ForeName><Initials>E</Initials><AffiliationInfo><Affiliation>Department of Biochemistry and Molecular Pharmacology, Thomas Jefferson University, Philadelphia, PA 19107, USA. eric@tesla.jci.tju.edu</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Choob</LastName><ForeName>M</ForeName><Initials>M</Initials></Author><Author ValidYN="Y"><LastName>Urtishak</LastName><ForeName>K A</ForeName><Initials>KA</Initials></Author><Author ValidYN="Y"><LastName>Tian</LastName><ForeName>X</ForeName><Initials>X</Initials></Author><Author ValidYN="Y"><LastName>Sternheim</LastName><ForeName>N</ForeName><Initials>N</Initials></Author><Author ValidYN="Y"><LastName>Talbot</LastName><ForeName>S</ForeName><Initials>S</Initials></Author><Author ValidYN="Y"><LastName>Archdeacon</LastName><ForeName>J</ForeName><Initials>J</Initials></Author><Author ValidYN="Y"><LastName>Efimov</LastName><ForeName>V A</ForeName><Initials>VA</Initials></Author><Author ValidYN="Y"><LastName>Farber</LastName><ForeName>S A</ForeName><Initials>SA</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType><PublicationType UI="D013487">Research Support, U.S. Gov't, P.H.S.</PublicationType><PublicationType UI="D016454">Review</PublicationType></PublicationTypeList></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>J Drug Target</MedlineTA><NlmUniqueID>9312476</NlmUniqueID><ISSNLinking>1026-7158</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D020320">Oligoribonucleotides, Antisense</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D063065">Organophosphonates</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D020135">Peptide Nucleic Acids</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D012333">RNA, Messenger</NameOfSubstance></Chemical><Chemical><RegistryNumber>RMB44WO89X</RegistryNumber><NameOfSubstance UI="D006909">Hydroxyproline</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D000818" MajorTopicYN="N">Animals</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D001483" MajorTopicYN="N">Base Sequence</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D004625" MajorTopicYN="N">Embryo, Nonmammalian</DescriptorName><QualifierName UI="Q000187" MajorTopicYN="Y">drug effects</QualifierName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D006909" MajorTopicYN="N">Hydroxyproline</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D018716" MajorTopicYN="N">Molecular Mimicry</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D020320" MajorTopicYN="N">Oligoribonucleotides, Antisense</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName><QualifierName UI="Q000494" MajorTopicYN="Y">pharmacology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D063065" MajorTopicYN="N">Organophosphonates</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D020135" MajorTopicYN="N">Peptide Nucleic Acids</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName></MeshHeading><MeshHeading><DescriptorName 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