RNA–DNA Molecules


RNA–DNA chimaeric molecules are important intermediates in many essential biological processes, including DNA replication and reverse transcription by retroviruses.

Keywords: DNA replication; primer RNAs; B‐form DNA; A‐form RNA; reverse transcription

Figure 1.

The synthesis of Okazaki fragments in DNA replication. In eukaryotic cells, RNA primers are made at intervals spaced by about 200 nucleotides on the lagging strand by DNA primase, and each RNA primer is about 10 nucleotides long. This RNA primer is degraded by RNAase H and/or 5′‐3′ exonuclease activities; this leaves a gap that is filled by DNA polymerase and DNA ligase.

Figure 2.

A schematic representation of reverse transcription of a retroviral genomic RNA into full‐length double‐stranded DNA. The blue‐coloured line refers to the genomic RNA, and the red‐coloured lines refer to the DNA strand synthesized by reverse transcriptase. R, U3 and U5 are repetitive sequences in the long terminal repeats located at both 5′ and 3′ ends of the genomic RNA. PBS is the binding site for tRNA primer, and PPT is the binding site for polypurine tract primer.



Baltimore D (1970) RNA‐dependent DNA polymerase in virions of RNA tumor viruses. Nature 226: 1209–1211.

Denis D and Bullock P (1993) Primer‐DNA formation during simian virus 40 DNA replication in vitro. Molecular and Cellular Biology 13: 2882–2890.

Fedoroff OY, Salazar M and Reid BR (1993) Structure of a DNA:RNA hybrid duplex. Why RNase H does not cleave pure RNA? Journal of Molecular Biology 233: 509–523.

Fedoroff OY, Salazar M and Reid BR (1996) Structural variation among retroviral primer‐DNA junctions: solution structure of the HIV‐1 (−)‐strand Okazaki fragment r(gcca)d(CTGC)• d(GCAGTGGC). Biochemistry 35: 11070–11080.

Fedoroff OY, Ge Y and Reid BR (1997) Solution structure of r(gaggacug):d(CAGTCCTC)hybrid: implications for the initiation of HIV‐1 (+)‐strand synthesis. Journal of Molecular Biology 269: 225–239.

Gyi JI, Lane AN, Conn GL and Brown T (1998) Solution structure of DNA•RNA hybrids with purine‐rich and pyrimidine‐rich strands: comparison with the homologous DNA and RNA duplexes. Biochemistry 37: 73–80.

Murante RS, Henricksen LA and Bambara RA (1998) Junction ribonuclease: an activity in Okazaki fragment processing. Proceedings of the National Academy of Sciences of the USA 95: 2244–2249.

Ogawa T and Okazaki T (1980) Discontinuous DNA replication. Annual Review of Biochemistry 49: 421–457.

Prichard MN, Jairath S, Penfold MET et al. (1998) Identification of persistent RNA–DNA hybrid structures within the origin of replication of human cytomegalovirus. Journal of Virology 72: 6997–7004.

Salazar M, Fedoroff OY and Reid BR (1996) Structure of chimeric duplex junctions: solution conformation of the retroviral Okazaki‐like fragment r(ccca)d(AATGA)•d(TCATTTGGG) from moloney murine leukemia virus. Biochemistry 35: 8126–8135.

Szyperski T, Gotte M, Billeter M et al. (1999) NMR structure of the chimeric hybrid duplex r(gcaguggc)•r(gcca)d(CTGC) comprising the tRNA–DNA junction formed during initiation of HIV‐1 reverse transcription. Journal of Biomolecular NMR 13: 343–355.

Temin HM and Mizutani S (1970) RNA‐dependent DNA polymerase in virions of Rous sarcoma virus. Nature 226: 1211–1213.

Further Reading

Goff SP (1990) Retroviral reverse transcriptase: synthesis, structure, and function. Journal of Acquired Immune Deficiency Syndrome 3: 817–831.

Litvak S (1996) Retroviral Reverse Transcriptases. New York: Chapman & Hall.

Salas M, Miller JT, Leis J and DePamphilis ML (1996) Mechanisms for priming DNA synthesis. In: DePamphilis ML (eds) DNA Replication in Eukaryotic Cells. Cold Spring Harbor, New York: Cold Spring Harbor Laboratory Press.

Sinden RR (1994) DNA Structure and Function. San Diego: Academic Press.

Zubay G (1988) Biochemistry, 2nd edn. London: Macmillan Press.

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How to Cite close
Chen, Yahua, and Reddy, Ramanchandra(May 2001) RNA–DNA Molecules. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1038/npg.els.0001493]