The document discusses the conformational analysis of cyclic systems and their relevance to the structure of nucleic acids, particularly focusing on deoxyribose sugar puckering in DNA. It highlights key conformations of cycloalkanes, the impact of sugar puckers on DNA structure, and provides case studies on factors influencing puckering, including methylation and kinase activity. Additionally, it addresses the understanding of different DNA forms (A, B, and Z) and their respective conformational characteristics.

1. Organic Pedagogical Electronic
Network
Cyclic Conformation and Nucleic
Acid Sugar Puckering
Roland Jones, Dane Brankle, and Peter Stevenson
University of Utah
https://commons.wikimedia.org/wiki/File:A-B-Z-DNA_Side_View.png

2. Conformation of cyclic systems and illustration
Ansyln, E.V.; Dougherty, D.A. Modern Physical Organic Chemistry. University Science Books, 2006. Saenger, W. Principles of Nucleic Acid Structure,
Springer-Verlag, 1984. http://x3dna.org/highlights/sugar-pucker-correlates-with-phosphorus-base-distance. http://casegroup.rutgers.edu/lnotes/dnab.pdf.
Model cyclic systems: Cyclic systems are ubiquitous. Establishing an understanding of the
shape preferences (e.g., strain and energetics) regarding representative cyclic models is a
powerful tool in conformational analysis. The expanded review of fundamental cycloalkanes can
further assist in preferential conformational analysis of associated derivatives.
Much of the resulting conformational preferences can be attributed to bond angle strain and/or
C-H interactions (e.g., torsional strain). Some general systems are depicted here. (1)
Cyclopropane is planar (as a result of the carbon framework) with a strain energy of 27.5
kcal/mol. (2) Cyclobutane is not planar and assumes a puckered conformation to relieve C-H
eclipsing. It has a strain energy of 26.5 kcal/mol. (3) Cyclopentane is also puckered to relieve C-
H eclipsing. It has a strain energy of 6.2 kcal/mol. Finally, (4) cyclohexane predominantly
assumes a rigid chair conformation providing a commonly assigned strain energy of 0 kcal/mol.
(1) Cycloproane (2) Cyclobutane (3) Cyclopentane (4) Cyclohexane

3. Conformation of cyclic systems and illustration
Ansyln, E.V.; Dougherty, D.A. Modern Physical Organic Chemistry. University Science Books, 2006. Saenger, W. Principles of Nucleic Acid Structure,
Springer-Verlag, 1984. http://x3dna.org/highlights/sugar-pucker-correlates-with-phosphorus-base-distance. http://casegroup.rutgers.edu/lnotes/dnab.pdf.
Illustrative Effect: Resulting conformational dynamics can easily be illustrated upon review of the
biological ramifications concerning cyclopentane in DNA conformations. The favored conformation of
DNA building blocks plays a crucial role in defining the resulting structure (or global conformation) of
DNA. As discussed above (i.e., a five-membered ring), deoxyribose sugar rings contain five atoms that
cannot lie in one plane: at least one must be out of plane. It can then be anticipated that the alternating
conformations of deoxyribose rings influence overall DNA conformation.
Conformation: There are two predominate deoxyribose ring conformations that strongly influence the
global conformation of DNA: C3’-endo and C2’-endo sugar puckers.
C2’-endo is an S-type
conformation
(S for south)
C3’-endo is an N-type
conformation
(N for north)

4. Nucleic acid sugar puckering
History: Over 60 years ago, analysis of the diffraction pattern of DNA was consistent with a double
helix conformation. However, what was not immediately answered was why there were various forms of
DNA observed: predominately A-form and B-form. Over the subsequent years, the resulting
conformation of the deoxyribose sugar ring provided insight into the global conformation of DNA.
Saenger, W. Principles of Nucleic Acid Structure, Springer-Verlag, 1984. Rich, A. Nat. Struct. Bio. 2003. 10, 247-249. Patel, D.; et al. Proc. Natl. Acad. Sci.
1978. 75, 6, 2533-2557. Williams, A.A.: et al. Biochemistry. 2009. 48, 11994-12004. https://commons.wikimedia.org/wiki/File:A-B-Z-DNA_Side_View.png.
A-form B-form
Puckering Impact: With continued analysis, it became
apparent that the B-form contains a ring pucker in which
the C2’ atom is out of plane on the same side as the
base (C2’-endo).
Consequently, the phosphate groups are about 7 Å
apart. Subsequent evaluation of the A-form determined
that the C3’ atom is out of plane (C3’-endo). The
resulting conformation positions the phosphate groups
at about 5.9 Å apart. Consequently, the sugar
phosphate backbone is shorter in comparison to the
C2’-endo conformation, resulting in a double helix in
which the base pairs are somewhat displaced.

5. Nucleic acid sugar puckering
Saenger, W. Principles of Nucleic Acid Structure, Springer-Verlag, 1984. Rich, A. Nat. Struct. Bio. 2003. 10, 247-249. Patel, D.; et al. Proc. Natl. Acad. Sci.
1978. 75, 6, 2533-2557. Williams, A.A.: et al. Biochemistry. 2009. 48, 11994-12004. https://commons.wikimedia.org/wiki/File:A-B-Z-DNA_Side_View.png.
Z-form
Left-Handed DNA: As the conformational impacts were
understood, additional efforts led to the evaluation of an
unusual left-handed double helix. Still held together with
Watson-Crick base pairs (i.e., d(CGCGCG)), it is somewhat
elongated and thinner with only one grove in comparison to A-
and B-forms. It is related to B-form by flipping the bases
upside down so that the upper surface of a base pair in B-DNA
becomes the lower surface of a the base pair when it changes
to Z-DNA. This inversion results in rotating the purine bases
about their C-N glycosyl bond (depicted in red below), so that
it assumes the syn conformation.
NH
N
N
O
NH2
N
O
HOH
HH
HH
HO
Anti
HN
N
N
O
H2N N
O
HOH
HH
HH
HO
Syn

6. Supplementary and illustrative studies
Moreau, C.; et al. Org. Biomol. Chem. 2011. 1, 278-290.
Case Study I
DNA sugar pucker is sensitive to many substituents that are placed on the deoxyribose
nitrogenous base. A common substituent placed on the base Is a methyl group on the C5’
carbon. This is often done naturally by the cell as an epigenetic marker for many cellular
processes in both, prokaryotes and eukaryotes. Studies show that the addition of the methyl
group on the cytosine as shown below causes increased contribution of C2’-endo pucker.

7. Supplementary and illustrative studies
Marquez, V.E; et al. J. Am. Chem. Soc. 2004. 126, 2, 543-549
Case Study II
A kinase is an enzyme that phosphorylates a certain molecule (such as the phosphorylation of
the 5’ hydroxyl group depicted here). Shown below is the pseudorotation conformation cycle of a
of an unrestricted furanose ring (defined by the value of P which depends on the associated
torsional angles (n0 to n4)). Crystallographic data indicates that puckering preference is between
the 3’-endo and 2’-endo conformations.

8. Supplementary and illustrative studies
Santos, R.A; et al. Biochemistry. 1989. 28, 9372-9378. Banway, M.; et al. J. Mol. Biol. 2002. 324, 667-676. Wu,
Z.; et al. J. Biomol. NMR. 2003. 26, 297-315
Case Study III
Solid-state NMR is a spectroscopy method that employs assessment of anisotropic (directionally
specific) interactions. These interactions modify spin energy levels for all sites in a molecule
(which changes the resonance frequency).
Solid-state 13C NMR has been used with a series of crystalline nucleosides and nucleotides.
Characterization provided the measurement of dexoyribose ring conformation relative to the
carbon chemical shift. It was observed that 3’-endo conformers have 3’ and 5’ chemical shifts
more upfield in comparison to 2’-endo conformers.
DNA C1’ C2’ C3’ C4’ C5’
A-
form
81.6 38.7 68.2 83.6 60.9
B-
form
84.4 36.3 77.3 84.4 66.2
Average chemical shift in ppm for two principle forms of DNA.

9. Problems
1) Rank the illustrated representative cycloalkane molecules in order from most to least stable and most to least acidic.
2) If a double bond were added to each of the illustrated representative cycloalkane molecules, how would the resulting strain
energies be affected? Why?
3) Draw the most likely conformation of the deoxyribonucleoside shown here.
4) Propose an explanation for why methylation of cytosine causes an increase in the contribution of C2’-endo pucker versus C3’-
endo pucker (see Case Study I).
5) Predict the preferred puckered conformation of the 5’ hydroxyl ring shown below in the presence of a catalyzing kinase
enzyme under characteristic reaction conditions (see Case Study II).
6) Describe how 13C NMR can be used as a probe for DNA ring puckering. Suggest alternative probes in characterizing and
analyzing sugar ring puckering (see Case Study III and references).
NH
N
N
O
NH2
N
O
HOH
HH
HH
HO
O
B
HO

10. Solutions
1) Stability: cyclohexane > cyclopentane > cyclobutane > cyclopropane. Acidity: cyclopropane > cyclobutane > cyclopropane >
cyclohexane.
2) Incorporating an olefin into a small ring generally increases the strain energy. Olefins prefer larger angles over alkanes
resulting in more destabilized cyclic systems (with a more noticeable effect seen in cyclopropene, cyclobutane, and
cyclohexane). However, the strain energy is lower in cyclopentene as it has only one set of C-H bonds eclipsed versus two
sets in cyclopentane. The preferred (rigid) chair conformation is disrupted in cyclohexane with the addition of an olefin
resulting in a slight strain energy increase (about 0.4 kcal/mol).
3) In five membered rings, the anomeric effect is less pronounced. Consequently, the purine substituent will be in more of an
equatorial position with either C2’- or C3’-endo conformation upon puckering. The least torsional strain is seen when the
purine (or base) substituent is in the anti orientation. Rotation about the C-N glycosyl bond will contribute to modifications in
resulting DNA conformation (such as Z-DNA).
4) As discussed in the overview, a C3’-endo pucker causes the sugar backbone to shorten compared a C2’-endo pucker. This
also causes the base substituents to be slightly displaced. Therefore, a bigger base (such as methylated cytosine) prefers
more space due to steric repulsions.
5) Studies show that kinase activity often prefers the C2’-endo (south) pucker because the hydroxyl group is more easily
accessed through a sense of steric activity.
6) The 13C chemical shift will vary relative to the puckering conformation. Additionally, functionalization could be evaluated via
FTIR (such as DNA methylation which has significance in transcription). Depending on synthetic difficulties, isotopic labeling
could be employed relative to the desired assessment (e.g., conformation, mechanism, etc.).
See previously cited references for further details and review.
H
H
H
H
H
H

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Contributed by:
Roland Jones, Dane Brankle, and Peter Stevenson
University of Utah
2015