title: Cheminformatics methods for novel nanopore analysis of HIV DNA termini.
abstract: BACKGROUND
  Channel current feature extraction methods, using Hidden Markov Models (HMMs) have been designed for tracking individual-molecule conformational changes. This information is derived from observation of changes in ionic channel current blockade "signal" upon that molecule's interaction with (and occlusion of) a single nanometer-scale channel in a "nanopore detector". In effect, a nanopore detector transduces single molecule events into channel current blockades. HMM analysis tools described are used to help systematically explore DNA dinucleotide flexibility, with particular focus on HIV's highly conserved (and highly flexible/reactive) viral DNA termini. One of the most critical stages in HIV's attack is the binding between viral DNA and the retroviral integrase, which is influenced by the dynamic-coupling induced high flexibility of a CA/TG dinucleotide positioned precisely two base-pairs from the blunt terminus of the duplex viral DNA. This suggests the study of a family of such CA/TG dinucleotide molecules via nanopore measurement and cheminformatics analysis.
  
  
  RESULTS
  HMMs are used for level identification on the current blockades, HMM/EM with boosted variance emissions are used for level projection pre-processing, and time-domain FSAs are used to parse the level-projected waveform for kinetic information. The observed state kinetics of the DNA hairpins containing the CA/TG dinucleotide provides clear evidence for HIV's selection of a peculiarly flexible/interactive DNA terminus.
authors.affiliation: Department of Computer Science, University of New Orleans, New Orleans, LA 70148, USA. winters@cs.uno.edu
authors.forename: Stephen
authors.initials: S
authors.lastname: Winters-Hilt
authors.forename: Matthew
authors.initials: M
authors.lastname: Landry
authors.forename: Mark
authors.initials: M
authors.lastname: Akeson
authors.forename: Maria
authors.initials: M
authors.lastname: Tanase
authors.forename: Iftekhar
authors.initials: I
authors.lastname: Amin
authors.forename: Amy
authors.initials: A
authors.lastname: Coombs
authors.forename: Eric
authors.initials: E
authors.lastname: Morales
authors.forename: John
authors.initials: J
authors.lastname: Millet
authors.forename: Carl
authors.initials: C
authors.lastname: Baribault
authors.forename: Srikanth
authors.initials: S
authors.lastname: Sendamangalam
mesh_terms: D001483:Base Sequence; D002623:Chemistry Techniques, Analytical / Q000379:methods*; D019295:Computational Biology / Q000379:methods*; D004279:DNA, Viral / Q000737:chemistry*; D006678:HIV / Q000235:genetics*; D008958:Models, Molecular; D049329:Nanostructures / Q000032:analysis* / Q000737:chemistry; D009690:Nucleic Acid Conformation; D016062:Porosity
chemical_list: D004279:DNA, Viral