Using Artificial DNA Sequence to Suppress Non-specific Bindings in Crude Nuclear Extract During Surface Plasmon Resonance Assay.

OBJECTIVE: Surface plasmon resonance (SPR) has been extensively used to characterize the interactions between molecules in terms of their binding specificity, affinity, and kinetics. Practical procedures, however, for measurement of the protein-DNA association in crude nuclear extract are yet to be defined.

METHODS: Crude nuclear extract was obtained from MCF-7 cells or recombinant estrogen receptor alpha (ERα) was used for analysis. To suppress signal from non-specific bindings in SPR assay using Biacore, DNA fragments with minimal protein binding activity were identified in a database for transcription factors and included in the study.

RESULTS: It is known that when analytes were purified transcription factors, the dissociation curves in Biacore sensorgrams exhibit exponential tendency. Based on statistical analysis, the dissociation phase between the ERα complex from crude nuclear extract and DNA oligonucleotides could be fitted exponentially. Following extrapolation of the dissociation phase, theoretical amount of bound antibodies could be estimated and compared for significant difference.

CONCLUSION: Our procedures made SPR technique such as Biacore a practical technique for measurement of protein-DNA associations in crude nuclear extract with reproducible and reliable results.