Scanning Force Microscopy Study on a Single-Stranded DNA: The Genome of Parvovirus B19

Abstract

The genome of parvovirus B19 is a 5600-base-long single-stranded DNA molecule with peculiar sequence symmetries. Both complementary forms of this single-stranded DNA are contained in distinct virions and they hybridize intermolecularly to double-stranded DNA if extracted from the capsids with traditional methods, thus losing some of their native structural features. A scanning force microscopy analysis of these double-stranded DNA molecules after thermal denaturation and renaturation gave us the chance to study the possible states that this DNA can assume in both its single-stranded and double-stranded forms. A novel but still poorly reproducible in situ lysis experiment that we have conducted on single virions with the scanning force microscope made it possible to image the totally unpaired state that the single-stranded DNA molecule most likely assumes inside the viral particle. Structural considerations on single molecules offer the opportunity for the formulation of plausible hypotheses on the interaction between the DNA and the viral structural proteins that could prove important for the DNA packaging in the capsid and, possibly, the viral infection mechanisms.

Parvovirus B19 Achievements and Challenges

“…Different combinations of these alternative sequences at both termini can therefore give rise to four different genome isomers. The presence of self-complementary sequences in the terminal regions allows for the single-stranded DNA molecule to adopt terminal loop and stem structures [8]. The presence of mismatched bases within the self-complementary regions necessarily introduces distortions in such doublestranded structures, so that different isomers might differ depending on the distortion introduced.…”