Nucleic acid database


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Nucleic acid database

  1. 1. Nucleic Acid Database
  2. 2. Database Utilities • Provides structural references in the form of base pair annotation for DNA, RNA, and some proteins • Contains search engine to find data on many DNA and RNA strcuctures • Depicts these structures through systematic design based on biological data • Includes innovative methods of examining DNA structures
  3. 3. NDB Tools • RNA Viewer • Base Pair Viewer •Given NDB files •Files uploaded in PDB format •Results are 2-D structure or 3-D structure (RASMOL)
  4. 4. DNA & RNA: Nucleic Acids • Nucleic acids of DNA: A, G, C, T • Nucleic acids of RNA: A, G, C, U • While DNA forms double helix, RNA is single stranded, as in t-RNA
  5. 5. Ideal Geometries Defined by Parameters adenine cytosine guanine thymine uracil
  6. 6. DNA Conformations • DNA exists as double helix with base pairs C&G and A&T • Most common conformation is B- DNA, a right handed helix • Other, irregular conformations exist
  7. 7. Other DNA Conformations • A form: major groove deep; minor groove shallow • Z-DNA: left handed helix; forms crystals • Mismatched strands
  8. 8. Base Pair List Instructions • Column 1, 2, 3 are Chain ID, residue sequence number, and residue name. • The standard Watson-Crick pairs are annotated as -/- (AU,AT) or +/+ (GC). • The three base edges: W (Watson-Crick edge); H (Hoogsteen edge); S (sugar edge). • Glycosidic bond orientation is annotated as (cis or trans). • For each nucleic acid, syn sugar-base conformation is annotated as (syn). • Stacked base pairs are annotated as (stack). • Non-identified edges are annotated as (.) or (?) or (X). • Tertiary interactions are marked by (!) in the line.
  9. 9. Nucleic Acid Database: Search Engine • Author • Title • Year • Publication • Volume • Page • Citation Complex NDB Search
  10. 10. Structure Reports • Nucleotide chain • Citations: research bibliography • Cell dimensions • Structure summary • Base Modifier Summary • Phosphate Modifier Summary
  11. 11. Other Database Functions • NDB Integrated Search An alternate NDB search application which provides more flexible searching and report generation. • NDB Status Search Provides a report on the processing status of crystal structures. • Tutorials Instructional aid for the various search capabilities. • Download Data • Deposit Data
  12. 12. ATLAS • Created by a group of Rutgers students • Generated from various software: Blockview, RNAview, MaxIT • Summary and images for structures seen in database • Images from biological and structural data (ideal geometries/ parameters) • Crystal packing picture from x-ray crytalography for nucleic acid structures • NMR experimental structures • Tables of derived data • Secondary and tertiary structures of RNA
  13. 13. Atlas • X-Ray Atlas Gallery Index Index Listing  • NMR Atlas Gallery Index Index Listing  • Sorted Galleries • Musical Atlas
  14. 14. Musical Atlas • Different musical algorithms to view DNA structures in an innovative manner, through instrumental song A-DNA A-DNA with mismatches B-DNA B-DNA with mismatches Z-DNA
  15. 15. Project 1 of Musical ATLAS • In each melody, each base in the sequence is played for one beat. If there are four adenines in a row, the note A will be played four (separated) times. If there is only one cytosine, it will be played for one beat, etc. The sequence for each structure is played once. • Melody is derived from sequence of molecules (repeated 4 times in a sequence • Bass line is the complimentary sequence to the initial sequence
  16. 16. Project 2 of Musical ATLAS • Each piece of DNA music consists of 15 measures. • Measure length is determined by the number of bases in the DNA strand. (Each base is equal to one beat.) For example, a strand which is 10 base pairs long will have 10-beat measures, while a 4 base pair strand will be represented by 4 beats per measure, and so on. • In the time signature there are (# of nitrogenous bases) beats per measure with the eighth note getting the beat. The eighth note was arbitrarily chosen. • The sequence is repeated in each measure.
  17. 17. Database Utilities- Conclusion • Provides structural references in the form of base pair annotation for DNA, RNA, and some proteins- RNA Viewer & Base Pair Viewer • Contains search engine to find data on many DNA and RNA strcuctures- Search Engine • Depicts these structures through systematic design based on biological data- ATLAS • Includes innovative methods of examining DNA structures- Musical Atlas