Biomaterial Database

Symmetrical base preferences surrounding HIV-1, avian sarcoma/leukosis virus, and murine leukemia virus integration sites. 2005

Alexander G Holman, and John M Coffin

Department of Molecular Microbiology, Sackler School of Graduate Biomedical Sciences, Tufts University School of Medicine, Boston, MA 02111, USA.

To investigate retroviral integration targeting on a nucleotide scale, we examined the base frequencies directly surrounding cloned in vivo HIV-1, murine leukemia virus, and avian sarcoma/leukosis virus integrations. Base preferences of up to 2-fold the expected frequencies were found for three viruses, representing P values down to <10(-100) and defining what appear to be preferred integration sequences. Offset symmetry reflecting the topology of the integration reaction was found for HIV-1 and avian sarcoma/leukosis virus but not murine leukemia virus, suggesting fundamental differences in the way different retroviral integration complexes interact with host-cell DNA.

UI	MeSH Term	Description	Entries
D003001	Cloning, Molecular	The insertion of recombinant DNA molecules from prokaryotic and/or eukaryotic sources into a replicating vehicle, such as a plasmid or virus vector, and the introduction of the resultant hybrid molecules into recipient cells without altering the viability of those cells.	Molecular Cloning
D006367	HeLa Cells	The first continuously cultured human malignant CELL LINE, derived from the cervical carcinoma of Henrietta Lacks. These cells are used for, among other things, VIRUS CULTIVATION and PRECLINICAL DRUG EVALUATION assays.	Cell, HeLa,Cells, HeLa,HeLa Cell
D006801	Humans	Members of the species Homo sapiens.	Homo sapiens,Man (Taxonomy),Human,Man, Modern,Modern Man
D001355	Alpharetrovirus	A genus of the family RETROVIRIDAE with type C morphology, that causes malignant and other diseases in wild birds and domestic fowl.	Avian Erythroblastosis Virus,Retroviruses Type C, Avian,Type C Avian Retroviruses,Avian Leukosis-Sarcoma Viruses,Erythroblastosis Virus, Avian,Retroviruses, ALV-Related,ALV-Related Retrovirus,ALV-Related Retroviruses,Alpharetroviruses,Avian Erythroblastosis Viruses,Avian Leukosis Sarcoma Viruses,Avian Leukosis-Sarcoma Virus,Erythroblastosis Viruses, Avian,Leukosis-Sarcoma Virus, Avian,Leukosis-Sarcoma Viruses, Avian,Retrovirus, ALV-Related,Retroviruses, ALV Related,Virus, Avian Erythroblastosis,Virus, Avian Leukosis-Sarcoma,Viruses, Avian Erythroblastosis,Viruses, Avian Leukosis-Sarcoma
D001482	Base Composition	The relative amounts of the PURINES and PYRIMIDINES in a nucleic acid.	Base Ratio,G+C Composition,Guanine + Cytosine Composition,G+C Content,GC Composition,GC Content,Guanine + Cytosine Content,Base Compositions,Base Ratios,Composition, Base,Composition, G+C,Composition, GC,Compositions, Base,Compositions, G+C,Compositions, GC,Content, G+C,Content, GC,Contents, G+C,Contents, GC,G+C Compositions,G+C Contents,GC Compositions,GC Contents,Ratio, Base,Ratios, Base
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
D015497	HIV-1	The type species of LENTIVIRUS and the etiologic agent of AIDS. It is characterized by its cytopathic effect and affinity for the T4-lymphocyte.	Human immunodeficiency virus 1,HIV-I,Human Immunodeficiency Virus Type 1,Immunodeficiency Virus Type 1, Human
D016662	Virus Integration	Insertion of viral DNA into host-cell DNA. This includes integration of phage DNA into bacterial DNA; (LYSOGENY); to form a PROPHAGE or integration of retroviral DNA into cellular DNA to form a PROVIRUS.	Integration, Provirus,Integration, Virus,Provirus Integration,Viral integration,Integrations, Provirus,Integrations, Virus,Provirus Integrations,Viral integrations,Virus Integrations,integration, Viral,integrations, Viral