RNA polymerise (Pot) II is a fundamental and important enzyme in the transcription process. However, two mysterious questions have remained unsolved: how an unwound bubble of DNA is established and maintained, and how the enzyme moves along the DNA. To answer these questions, we constructed a model structure of the Pot II elongation complex with the 50 base pairs of DNA-24 bases of RNA including the unwound bubble of DNA and performed a molecular dynamics simulation. We obtained a reliable model structure of the Pot II elongation complex in the pre-translocation state which has not yet been determined by the X-ray crystallographic study. The model structure revealed that multiple protein loops work concertedly to form and maintain the bubble structure. We also found that the conformational change of a loop in the Pot II, fork loop 1, couples with the unidirectional movement of the Pot II along the DNA. (c) 2006 Elsevier Inc. All rights reserved.