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
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.
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
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
