Nucleic Acid Database

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 Viewer• Base 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&T

• Most common conformation is B-DNA, a right handed helix

• Other, 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 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

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 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