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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
Depicts these structures through systematic design based on biological data
Includes innovative methods of examining DNA structures
NDB Tools
RNA ViewerBase Pair Viewer
• Given NDB files• Files uploaded in
PDB format• Results are 2-D
structure or 3-D structure (RASMOL)
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
Ideal Geometries Defined by Parameters
adenine
cytosine
guanine
thymine
uracil
DNA Conformations
DNA exists as double helix with base pairs C&G and A&TMost common conformation is B-DNA, a right handed helixOther, irregular conformations exist
Other DNA Conformations
A form: major groove deep; minor groove shallow
Z-DNA: left handed helix; forms crystals
Mismatched strands
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.
Nucleic Acid Database: Search Engine
Author
Title
Year
Publication
Volume
Page
Citation
Complex NDB Search
Structure Reports
Nucleotide chain
Citations: research bibliography
Cell dimensions
Structure summary
Base Modifier Summary
Phosphate Modifier Summary
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
ATLAS
Created by a group of Rutgers studentsGenerated from various software: Blockview, RNAview, MaxITSummary and images for structures seen in databaseImages from biological and structural data (ideal geometries/ parameters)Crystal packing picture from x-ray crytalography for nucleic acid structuresNMR experimental structuresTables of derived dataSecondary and tertiary structures of RNA
Atlas
X-Ray Atlas Gallery Index Index Listing
NMR Atlas Gallery Index Index Listing
Sorted Galleries
Musical Atlas
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
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
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.
Database Utilities- Conclusion
Provides structural references in the form of base pair annotation for DNA, RNA, and some proteins- RNA Viewer & Base Pair ViewerContains search engine to find data on many DNA and RNA strcuctures- Search EngineDepicts these structures through systematic design based on biological data- ATLASIncludes innovative methods of examining DNA structures- Musical Atlas