Short Nascent cDNA Fragments in the Presence of Nucleocapsid Protein during Reverse Transcription

Abstract

Pausing and strand-transfers occur frequently during reverse transcription. To investigate how nucleocapsid protein (NC) affects pausing and strand-transfer of nascent cDNA fragments, we directly cloned and sequenced new reverse transcripts in the presence or absence of NC using our recently develop method that clones cDNA products without their amplification by PCR. The nascent cDNA yield was lower and their lengths were shorter in the presence of NC during reverse transcription than in the absence of NC. Our results showed that NC promoted more frequent pausing of nascent cDNA fragments during reverse transcription and resulted in short reverse transcripts.