A crystallographic map of the transition from B-DNA to A-DNA

Abstract

The transition between B-and A-DNA was first observed nearly 50 years ago. We have now mapped this transformation through a set of single-crystal structures of the sequence d(GGCGCC)2, with various intermediates being trapped by methylating or brominating the cytosine bases. The resulting pathway progresses through 13 conformational steps, with a composite structure that pairs A-nucleotides with complementary B-nucleotides serving as a distinct transition intermediate. The details of each step in the conversion of B-to A-DNA are thus revealed at the atomic level, placing intermediates for this and other sequences in the context of a common pathway.

Phase transition between A and B forms of DNA: A free-energy perspective

“…This only implies coexistence of phases at the transition point. Further, it may be noted that the DNA molecule, under experimentation in [2,3], being not a long molecule, has a finite region of coexistence in the r-g plane whereas Fig3 shows a line(wiggle) representing the coexistence valid for infinitely long molecule. | α a | = 0 , | α b | = 0 is the most ordered phase and in our problem should reflect a phase that has the lowest symmetry.But such a phase which will have a lower symmetry than both 10 1 and 11 1 is not possible.…”

“…This perhaps tells us that the Fig3 represents the likely phase picture and Fig4 may be ruled out. If we refer to the experimental results of [2,3], it is mentioned that the transition from 'B' DNA to 'A' DNA takes place through 14 conformations. Further, the experimental data in [2,3], where they have measured certain quantities like tilt angle, axial distance etc do not actually tell us whether there has been a phase transition or not.…”

“…Experiments that have been carried out to study the phase transition [2,3] report conformations in which both 'A' type and 'B' type features are there apart from only 'A' type or 'B' type features. We interpret this as coexistence of phases.…”

“…Experimental studies , among other techniques, use crystallography to study the structure of DNA. The various conformations take on different crystallographic structures [2,3] corresponding to different space groups. The space groups depend on the detailed symmetry of the molecule, length of the sequence etc.…”

“…The transition from 'B' form to 'A' form was observed during the first x-ray studies by Franklin and Goslin [1] who characterized the change of the helix structure as ' a substantial re-arrangement of the molecule'. Experiments [2,3] have been performed to observe the transition from 'B' form to 'A' form in a more detailed manner and this report is an attempt to explain the fundamental features of the experiments. Recent experiments [4] to study the dynamics of the transition from 'B' to 'A ' observe that the helical states are clearly separated from one another in terms of activation energy with the time scale of the dynamics of transition being of the order of ms.…”