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Nucleic Acid Database

Nucleic Acid Database. By Pooja Awatramani. 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

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Nucleic Acid Database

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  1. Nucleic Acid Database By Pooja Awatramani

  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. 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. 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. Ideal Geometries Defined by Parameters uracil adenine guanine cytosine thymine

  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. Other DNA Conformations • A form: major groove deep; minor groove shallow • Z-DNA: left handed helix; forms crystals • Mismatched strands

  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. Nucleic Acid Database: Search Engine • Author • Title • Year • Publication • Volume • Page • Citation Complex NDB Search

  10. Structure Reports • Nucleotide chain • Citations: research bibliography • Cell dimensions • Structure summary • Base Modifier Summary • Phosphate Modifier Summary

  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. 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. Atlas • X-Ray AtlasGallery IndexIndex Listing • NMR AtlasGallery IndexIndex Listing • Sorted Galleries • Musical Atlas

  14. Musical Atlas • Different musical algorithms to view DNA structures in an innovative manner, through instrumental song A-DNAA-DNA with mismatchesB-DNAB-DNA with mismatches Z-DNA

  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. 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. 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

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