Biomaterial Database

Inhibition of phage phi 29 assembly by antisense oligonucleotides targeting viral pRNA essential for DNA packaging. 1995

C Zhang, and K Garver, and P Guo

Department of Pathobiology, Purdue University, West Lafayette, Indiana 47907, USA.

A sensitive and efficient system for the functional assay of antisense oligonucleotides (oligos) was developed based on an in vitro viral assembly system. A 120-base RNA (pRNA), which indispensably participates in bacteriophage phi 29 DNA packaging, was the target for antisense action. Antisense oligos bound to pRNA, as revealed by a slower electrophoretic mobility of pRNA/oligo complexes in comparison with native pRNA. Infectious viruses were assembled in vitro with synthetic pRNA and DNA, as well as with viral proteins produced from cloned genes. Up to 10(7) plaque-forming units per milliliter were obtained in the absence of antisense oligos, while as few as zero plaques were detected in the presence of certain antisense oligos. A 1-base mismatch greatly influenced the inhibitory effect of the antisense oligos, but this 1-based mismatch was not important when the mismatch was placed at the end of the oligo. Five oligos did not bind pRNA or inhibit the assembly of the virion, suggesting that the RNA sequences complementary to these oligos are nonessential or buried internally in the RNA. Viral assembly was strongly inhibited by antisense oligos P15 and P10, targeting either the 5'- or the 3'-end of the pRNA, respectively. Viral assembly was also strongly inhibited by oligo P6, targeting an internal region, residues 75-91, of pRNA. Oligo P6 inhibited DNA packaging activity by blocking the binding of pRNA to the procapsid, while P10 and P15 inhibited DNA packaging activity but did not block the binding of pRNA to the procapsid, suggesting that in addition to the reported internal domain for procapsid binding, pRNA contains another domain at the paired 5'/3'-ends with a yet to be defined role in DNA translocation.

UI	MeSH Term	Description	Entries
D008969	Molecular Sequence Data	Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.	Sequence Data, Molecular,Molecular Sequencing Data,Data, Molecular Sequence,Data, Molecular Sequencing,Sequencing Data, Molecular
D009690	Nucleic Acid Conformation	The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.	DNA Conformation,RNA Conformation,Conformation, DNA,Conformation, Nucleic Acid,Conformation, RNA,Conformations, DNA,Conformations, Nucleic Acid,Conformations, RNA,DNA Conformations,Nucleic Acid Conformations,RNA Conformations
D002213	Capsid	The outer protein protective shell of a virus, which protects the viral nucleic acid. Capsids are composed of repeating units (capsomers or capsomeres) of CAPSID PROTEINS which when assembled together form either an icosahedral or helical shape.	Procapsid,Prohead,Capsids,Procapsids,Proheads
D004279	DNA, Viral	Deoxyribonucleic acid that makes up the genetic material of viruses.	Viral DNA
D001483	Base Sequence	The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.	DNA Sequence,Nucleotide Sequence,RNA Sequence,DNA Sequences,Base Sequences,Nucleotide Sequences,RNA Sequences,Sequence, Base,Sequence, DNA,Sequence, Nucleotide,Sequence, RNA,Sequences, Base,Sequences, DNA,Sequences, Nucleotide,Sequences, RNA
D001665	Binding Sites	The parts of a macromolecule that directly participate in its specific combination with another molecule.	Combining Site,Binding Site,Combining Sites,Site, Binding,Site, Combining,Sites, Binding,Sites, Combining
D012367	RNA, Viral	Ribonucleic acid that makes up the genetic material of viruses.	Viral RNA
D014779	Virus Replication	The process of intracellular viral multiplication, consisting of the synthesis of PROTEINS; NUCLEIC ACIDS; and sometimes LIPIDS, and their assembly into a new infectious particle.	Viral Replication,Replication, Viral,Replication, Virus,Replications, Viral,Replications, Virus,Viral Replications,Virus Replications
D016376	Oligonucleotides, Antisense	Short fragments of DNA or RNA that are used to alter the function of target RNAs or DNAs to which they hybridize.	Anti-Sense Oligonucleotide,Antisense Oligonucleotide,Antisense Oligonucleotides,Anti-Sense Oligonucleotides,Anti Sense Oligonucleotide,Anti Sense Oligonucleotides,Oligonucleotide, Anti-Sense,Oligonucleotide, Antisense,Oligonucleotides, Anti-Sense
D017103	Bacillus Phages	Viruses whose host is Bacillus. Frequently encountered Bacillus phages include bacteriophage phi 29 and bacteriophage phi 105.	Bacteriophage phi 105,Bacteriophage phi 29,Phage phi 105,Phage phi 29,Bacillus Bacteriophages,Bacillus Bacteriophage,Bacillus Phage,Bacteriophage, Bacillus,Bacteriophages, Bacillus