VIBRATIONAL LOCAL MODES IN DNA POLYMER

Where the translational symmetry of a long polymer chain is interrupte d, characteristic vibrations of the molecule are possible in which onl y those atoms at or relatively near the defect site partake of the mot ion. This contrasts with the more common vibrational states in which t he motion propagates along the chain as a sound wave. Examples of read ily producible local defects include broken bonds, missing atoms or gr oups, and extra links as are found, e.g., in thymine dimers. For each different defect. the spectrum of local mode frequencies is characteri stic of its structure. Hence the local modes give direct information a bout the nature of the defect and can serve as a diagnostic signature of the polymer chain lesion. We have developed and are using algorithm s and fortran code to predict the existence and nature of local modes based on their atomic structures. We have studied examples of differen t defects and found their eigenfrequencies and eigenvectors. For the s implest case of a broken hydrogen bond in a single A-T unit in a long homopolymer dA.dT chain, we display stereo views of the vibrating unit side-by-side with the undisturbed molecule for the three local modes occurring below 300 cm(-1) in frequency.