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Activation-induced deoxycytidine deaminase (AID) generates antibody diversity in B cells by initiating somatic hypermutation (SHM) and class-switch recombination (CSR) during transcription of immunoglobulin variable (IgV) and switch region (IgS) DNA. Using single-molecule FRET, we show that AID binds to transcribed dsDNA and translocates unidirectionally in(More)
How to properly account for polyvalent counterions in a molecular dynamics simulation of polyelectrolytes such as nucleic acids remains an open question. Not only do counterions such as Mg(2+) screen electrostatic interactions, they also produce attractive intrachain interactions that stabilize secondary and tertiary structures. Here, we show how a simple(More)
  • C. H. Mak
  • 2008
We consider the loop-closure problem for nucleic acids and describe an efficient numerical algorithm for closing single-nucleotide loops in nucleic acids. Using six new internal coordinates to represent the nucleotide conformation, which we call the R-representation, the original closure problem with six free torsion angles in each nucleotide can be reduced(More)
We report a theoretical study of superfluidity in CH(4)-doped para-H(2) nanoclusters. Path integral simulations for clusters of 12-16 H(2) around a single CH(4) molecule were carried out at temperatures between 0.5 and 2 K to study the superfluid response of the cluster. The results indicate that a rapid increase in the superfluid response is expected to(More)
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