Nucleic Acid Nomenclature and Structure

compiled by

Christoph Schneider, -- Biocomputing -- Group at IMB Jena

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Contents

  1. base numbering system
  2. backbone torsion angles
  3. pucker
  4. chi angle
  5. base pair structures
  6. base triples
  7. movements of bases

    more detailed information on B-DNA and A-RNA

  8. secondary structural elements
  9. pseudoknots


1. base numbering

structures of the five major purine (R) and pyrimidine (Y) bases of nucleic acids in their dominant tautomeric forms and with the IUPAC numbering system


Source: Blackburn and Gait, Nucleic acids in chemistry and biology, Oxford University Press New York 1996.

2. backbone torsion angles in nucleic acid structures

atomic numbering scheme and definition of torsion angles for a polyribonucleotide chain
For other information on backbone torsional angles click here.

backbone torsions
Source: Saenger,W., Principles of Nucleic Acid Structure, Springer Verlag New York 1984.


Source: Blackburn and Gait, Nucleic acids in chemistry and biology, Oxford University Press New York 1996.

Average torsion angles (in °) for nucleic acid helices

Structure type

alpha

beta

gamma

delta

epsilon

zeta

chi

A-DNA (fibres) -50 172 41 79 -146 -78 -154
GGCCGGCC -75 185 56 91 -166 -75 -149
B-DNA (fibres) -41 136 38 139 -133 -157 -102
CGCGAATTCGCG -63 171 54 123 -169 -108 -117
Z-DNA (C residues) -137 -139 56 138 -95 80 -159
Z-DNA (G residues) 47 179 -169 99 -104 -69 68
DNA-RNA decamer -69 175 55 82 -151 -75 -162
A-RNA -68 178 54 82 -153 -71 -158



3. pucker

pseudorotation cycle of the furanose ring in nucleosides.
Source: Saenger,W., Principles of Nucleic Acid Structure, Springer Verlag New York 1984.

ideal B-DNA is C2'-endo (South), ideal A-RNA is C3'-endo (North)



4. chi angle

anti and syn conformational ranges for glycosydic bonds in pyrimidine (left) and purine (right) nucleosides
Source: Blackburn and Gait, Nucleic acids in chemistry and biology, Oxford University Press New York 1996.

5. Structures of base pairs involving at least two hydrogen bonds

(More detailed information on base pairs can be found in the Base Pair Directory).


The 28 possible base pairs that involve at least two hydrogen bonds as compiled by I. Tinoco Jr.

Watson-Crick, Reverse Watson-Crick, Hoogsteen, Reverse Hoogsteen, Wobble, Reverse Wobble

the ten possible purine-pyrimidine base pairs

Homo purines

the seven possible homo purine-purine base pairs

Hetero purines

the four possible hetero purine-purine base pairs

Homo- and hetero pyrimidines

the seven possible pyrimidine-pyrimidine base pairs
Source: Ignacio Tinoco, Jr. in Gesteland, R. F. and Atkins, J. F. (1993) THE RNA WORLD. Cold Spring Harbor Laboratory Press.

6. base triples

proposed hydrogen-bonding schemes for base triples. nucleotide triples occur when single-stranded nucleotides form hydrogen bonds with nucleotides that are already base paired (see also pseudoknots).

Proposed hydrogen-bonding schemes for base triples.
Source: Chastain, M. and Tinoco Jr., I., (1991) Prog. Nucleic Acid Res. Mol. Biol. 41, 131-177.

7. movement of bases

more detailed information

  1. moving in concert
  2. moving in opposition
  3. steps between two base-pairs
  4. translocational movement of base-pairs relative to the helix axis

movements of bases in sequence-dependent structures (tip, inclination, opening, propeller, buckle, twist, roll, tilt, slide, rise, shift and tilt).


Source: Blackburn and Gait, Nucleic acids in chemistry and biology, Oxford University Press New York 1996.
R.E. Dickerson et al. (1989) Nucleic Acids Res. 17, 1797-1803.



8. secondary structures of RNA

  1. duplexes
  2. single stranded regions
  3. hairpins
  4. bulges
  5. internal loops
  6. junctions

secondary structure of RNA consists of duplex and loop regions that can be divided into six different types: duplexes, single-stranded regions, hairpins, internal loops or bubbles, bulge loops or bulges and junctions.
Source: Chastain, M. and Tinoco Jr., I., (1991) Prog. Nucleic Acid Res. Mol. Biol. 41, 131-177.

9. pseudoknots

RNA pseudoknots are tertiary structural elements that result when a loop in a secondary structure pairs with a complementary sequence outside the loop

  1. loop at the top crosses the major groove and the loop at the bottom crosses the minor groove
  2. one loop crosses the major groove and the other loop bridges the whole helix
  3. one loop crosses the minor groove and the other loop bridges the whole helix


Source: Chastain, M. and Tinoco Jr., I., (1991) Prog. Nucleic Acid Res. Mol. Biol. 41, 131-177.

The H-type pseudoknot. A pseudoknot is always defined by two stems (S1 and S2) and by two or three loop regions (L1-L3). Dashed lines indicate base-pairing. LD is the loop crossing the deep groove, LS is the loop crossing the shallow groove, and LP is the loop spanning the sugar-phosphate backbone

  1. two alternative presentations of the generalized H-pseudoknot
  2. pseudoknot with coaxial stacking of the two stems when loop (L2) is zero
  3. pseudoknot with coaxial stacking of the two stems when loop (L3) is zero
  4. pseudoknot with coaxial stacking of the two stems when loop (L1) is zero


Source: Cornelis W. A. Pleij in Gesteland, R. F. and Atkins, J. F. (1993) THE RNA WORLD. Cold Spring Harbor Laboratory Press.



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