Compositions, methods and kits for real-time nucleic acid analysis in live cells

An isolated nucleopeptide conjugate complex for detecting transcription in a biological system, comprising:

• a) a chimeric RNA polymerase comprising a fusion protein comprising
• 1) a RNA polymerase and
• 2) a detector binding domain linked to the N-terminus of the RNA polymerase, wherein the detector binding domain is capable of binding to a chimeric RNA polymerase binding domain (CRPBD);
• and
• b) a detector molecule comprising
• 1) a PNA comprising a tri-nucleotide complementary to a portion of an RNA molecule,
• 2) a CRPBD capable of binding to the detector binding domain, and
• 3) a first fluorescent molecule linked to the PNA and a second fluorescent molecule linked to the CRPBD, wherein the first fluorescent molecule and the second fluorescent molecule interact to emit a fluorescent energy resonance transfer (FRET) signal,
• wherein the CRPBD is specifically bound to the detector binding domain in said nucleopeptide complex such that the detector molecule is positioned at an RNA exit pore of the chimeric RNA polymerase, and the PNA is capable of transiently interacting with an RNA molecule transcribed by the chimeric RNA polymerase, wherein interactions between the PNA and the RNA molecule are capable of causing a transient change in the FRET signal emitted by the first fluorescent molecule and the second fluorescent molecule.