DNA and RNA Base Pair Stacking Structures

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Mol color: "high contrast" CPK 		Bkg color: white black blue
Mol color: "high contrast" CPK
The starting images show computer-generated structures of B-form DNA and A-form RNA*. The nucleotides are colored "Shapely"; a thin Ribbon trace is drawn along the backbone.
The sequences include the 10 possible base pair stacking interactions. Each dinucleotide stack can be viewed using the buttons below.
The dinucleotide stacks are designated, N1N2/N1'N2', corresponding to the N1-N1' bp (Ball & Stick) stacked on top of the N2-N2' bp (Sticks). Each button leaves the indicated bp stack "Selected" for display and/or color manipulation.

Dinucleotide stacks in DNA:
AT/TA   TA/AT   AA/TT
AC/TG   CA/GT   AG/TC
GG/CC   GC/CG   CG/GC
GA/CT
The DNA sequence is:

BSeq
Each chain is numbered from the 5' end. Thus, the "AT/TA" stack corresponds to nucleotides 1 & 2 of chain A and nucleotides 10 & 11 of chain B.

Dinucleotide stacks in RNA:
AU/UA   UA/AU   AA/UU
AC/UG     CA/GU   AG/UC
GG/CC     GC/CG   CG/GC
GA/CU
The RNA sequence is:

ASeq
Each chain is numbered from the 5' end. Thus, the "AU/UA" stack corresponds to nucleotides 1 & 2 of chain A and nucleotides 10 & 11 of chain B.

*The structures of the double helices were generated from a link on the PSC Web Tools page at the Pittsburgh Supercomputing Center. The coordinate files are B11mer.pdb (DNA) and A11mer.pdb (RNA). The PDB files used here include hydrogens.

Refer to the tables that compile the Thermodynamic Parameters for each of the dinucleotide stacks shown above.

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