Objective: To screen available 16S rDNA sequences of endophytic bacteria sampled from Chuanxiong Rhizoma for further denaturing gradient gel electrophoresis (DGGE) analysis

and optimize suitable analysis conditions. Method: In order to get DNA sequences of endophytic bacteria gathered from Chuanxiong Rhizoma

polymerase chain reaction (PCR) and nested PCR experiments have been conducted to the V3 region and the V6-V8 region of 16S rDNA respectively.Vertical electrophoresis has been used to ameliorate degeneration gradient of gels

time interval method has been used to figure out electrophoresis time

in addition

some modification of voltage-time context finally been made according to electrophoretograms. Result: The 16S rDNA V6-V8 region was ideal for DGGE analysis

owing to that it's effective to purify DNA of endophytic bacteria from their host of Chuanxiong Rhizoma

as a result makes it easy to get diverse sequences.These conclusive ideal analysis conditions for this region:gradient range of denaturing agent 55%-70% (Gel 6%)

electrophoresis temperature at 60 ℃

voltage of 50 V

electrophoresis time of 16 h. Conclusion: These DGGE analysis conditions can be useful for distinguishing 16S rDNA V6-V8 sequences of endophytic bacteria of Chuanxiong Rhizoma.This research lays a reliable foundation for further study of exploring endophytic bacterium community structure of Chuanxiong Rhizoma

as well as many other medicinal plants.