The Nucleic Acid Database provides structural references and a search engine for DNA and RNA structures. It depicts structures through systematic design based on biological data in tools like the RNA Viewer, Base Pair Viewer, and ATLAS. It also examines structures through innovative methods like the Musical Atlas, which uses musical algorithms to represent DNA structures as instrumental songs.

1. Nucleic Acid
Database

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
adenine
cytosine
guanine
thymine
uracil

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 Atlas
Gallery Index
Index Listing
• NMR Atlas
Gallery Index
Index Listing
• Sorted Galleries
• Musical Atlas

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. 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