Tren-microgonotropen-b (6b) binds 1:1 and 2:1 into the minor groove of d(CGCAAATTTGCG)(2). The solution structure of the 1:1 complex of d(CGCA(3)T(3)GCG)(2) with 6b has been determined by 2D nuclear Overhauser effect H-1 NMR spectroscopy (NOESY) and restrained molecular modeling. An H-1 NMR melting study on d(CGCA(3)T(3)GCG)(2) shows that while the G.C base pairs exist equally as paired and melted forms of 35 degrees C, the A(3)T(3) region maintains base pairing up to 45 degrees C, A total of 206 resonances for the d(CGCA(3)T(3)GCG)(2):6b have been assigned. The signals of both exchangeable and nonexchangeable protons in the NOESY spectra indicate asymmetric binding of 6b in the A + T-rich region involving five base pairs (5’-A(6)T(7)T(8)T(9)G(10)-3’) The terminal acetamide head of 6b is directed toward A(6), while the carboxy terminal dimethylpropylamino tail is directed toward G(10) The protonated tren polyamino substituent residing on the nitrogen of the central pyrrole ring is directed up toward the phosphate backbone, firmly grasping the phosphodiester linkages of P-9 and P-10 on the edge of the major groove. The protonated terminal nitrogen of the dimethylpropylamino tail is adjacent to sugar oxygen C(11)O4’ and a base oxygen C(11)O2 within the minor groove. The off-rate of 6b from the 1:1 complex was found to be 1.3 +/- 0.2 s(-1), corresponding to an activation energy of 17 kcal/mol. Compound 6b binds 3.1-4.5 Angstrom from the bottom of the minor groove and 7.3-9.0 and 5.5-6.3 Angstrom distant from the (-) and (+) strands, respectively when observing the strands of the DNA in a 5’ to 3’ orientation (distances from the pyrrole nitrogens to P-4P-5P-6 and P8P9P10, respectively). Comparisons of the solution structures of d(CGCA(3)T(3)GCG)(2) and the d(CGCA(3)T(3)GCG)(2):6b complex with the crystal structure of the same dsDNA, show that there is a break in the C-2 nu symmetry of the crystallized dsDNA at the A(6)T(7) junction as it goes into aqueous solution. A helical bend, alpha, of 22.2 degrees was found for the solution structure of the d(CGCA(3)T(3)GCG)(2):6b complex; this is an increase of 11.4 degrees relative to the crystallized dodecamer (alpha 10.8 degrees), 8.3 degrees relative to the crystallized d(CGCA(3)T(3)GCG)(2):distamycin complex (alpha = 13.9 degrees) and 5.0 degrees relative to the solution structure of d(CGCA(3)T(3)GCG)(2):5c complex (alpha = 17.2 degrees). In addition, solvation increases the length of the duplex by 0.2 Angstrom/bp for the d(CGCA(3)T(3)GCG)(2):6b complex compared to crystal structures of d(CGCA(3)T(3)GCG)(2) and of the d(CGCA(3)T(3)GCG)(2):distamycin complex. The A.T region of the d(CGCA(3)T(3)GCG)(2):6b complex maintains its B-DNA conformation, while the terminal G C ends appear to exist in an intermediate B- to A-DNA form.