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