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When retroviral reverse transcriptases reach the end of their RNA templates. 1992

T B Fu, and J Taylor
Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111.

Luo and Taylor (J. Virol. 64:4321-4328, 1990) have previously shown that when, during RNA-directed DNA synthesis, a retroviral reverse transcriptase comes to a halt at the end of an RNA template, the associated RNase H produces a specific oligonucleotide that contains the 5' end of that template; in those studies the length of the oligonucleotide was predominantly 17 nucleotides. We have now investigated variables that might affect the formation and length of such a terminal oligonucleotide. We found small but significant variations in the length could be caused by the choice of reaction conditions and also the sources of reverse transcriptase and RNA template. Nevertheless, the general finding in all these situations was that RNase H acted at or about 14 to 18 nucleotides from the 5' end, thereby supporting the interpretation that in the reverse transcriptase, the cleavage site for the RNase H is held at around this distance behind the DNA polymerase activity. In other words, it appears that for the intact protein, the RNase H and reverse transcriptase activities may work in a coupled or coordinate manner. We also found that more than 80% of the residual 5' oligonucleotides remained base paired to the RNA-directed DNA product. Furthermore, under certain conditions, these short RNAs could act as efficient primers for an associated DNA-directed DNA synthesis in the reverse direction.

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
D009841 Oligonucleotides Polymers made up of a few (2-20) nucleotides. In molecular genetics, they refer to a short sequence synthesized to match a region where a mutation is known to occur, and then used as a probe (OLIGONUCLEOTIDE PROBES). (Dorland, 28th ed) Oligonucleotide
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
D012194 RNA-Directed DNA Polymerase An enzyme that synthesizes DNA on an RNA template. It is encoded by the pol gene of retroviruses and by certain retrovirus-like elements. EC 2.7.7.49. DNA Polymerase, RNA-Directed,RNA-Dependent DNA Polymerase,Reverse Transcriptase,RNA Transcriptase,Revertase,DNA Polymerase, RNA Directed,DNA Polymerase, RNA-Dependent,RNA Dependent DNA Polymerase,RNA Directed DNA Polymerase
D012367 RNA, Viral Ribonucleic acid that makes up the genetic material of viruses. Viral RNA
D013698 Templates, Genetic Macromolecular molds for the synthesis of complementary macromolecules, as in DNA REPLICATION; GENETIC TRANSCRIPTION of DNA to RNA, and GENETIC TRANSLATION of RNA into POLYPEPTIDES. Genetic Template,Genetic Templates,Template, Genetic
D014158 Transcription, Genetic The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION. Genetic Transcription
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
D016914 Ribonuclease H A ribonuclease that specifically cleaves the RNA moiety of RNA:DNA hybrids. It has been isolated from a wide variety of prokaryotic and eukaryotic organisms as well as RETROVIRUSES. Endoribonuclease H,RNase H,Ribonuclease H, Calf Thymus,RNAase H

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