Recognition of T-rich single-stranded DNA by the cold shock protein Bs-CspB in solution

Abstract

Cold shock proteins (CSP) belong to the family of single-stranded nucleic acid binding proteins with OB-fold. CSP are believed to function as 'RNA chaperones' and during anti-termination. We determined the solution structure of Bs -CspB bound to the single-stranded DNA (ssDNA) fragment heptathymidine (dT7) by NMR spectroscopy. Bs -CspB reveals an almost invariant conformation when bound to dT 7 with only minor reorientations in loop β1-β2 and β3-β4 and of few aromatic side chains involved in base stacking. Binding studies of protein variants and mutated ssDNA demonstrated that Bs -CspB associates with ssDNA at almost diffusion controlled rates and low sequence specificity consistent with its biological function. A variation of the ssDNA affinity is accomplished solely by changes of the dissociation rate. 15N NMR relaxation and H/D exchange experiments revealed that binding of dT 7 increases the stability of Bs-CspB and reduces the sub-nanosecond dynamics of the entire protein and especially of loop β3-β4. © 2006 Oxford University Press.