3 - BIF352 Comparison of DNA and RNA
3 - BIF352 Comparison of DNA and RNA
3 - BIF352 Comparison of DNA and RNA
Figure 8.3.1 : Common modifications of bases in DNA. Matthew K.Bilyard et al. Current Opinion in Chemical Biology. Volume
57, August 2020, Pages 1-7. https://doi.org/10.1016/j.cbpa.2020.01.014. Under a Creative Commons license
Likewise, RNA is chemically modified. Figure 8.3.2 shows common modifications of bases in RNA. Methylation and subsequent
hydroxylation to hydroxymethyl are common to both DNA and RNA. Methylation of DNA often represses the transcription of the
DNA into RNA. Hence it has huge potential to alter gene transcription. Such changes to the DNA are called epigenetic
modifications. These changes can be passed down to future generations as well and affect the phenotype of a cell. Histone proteins
involved in DNA packing into nucleosomes can also be methylated and acetylated, altering the interaction of the DNA with the
nucleosome core and further packing, again affecting transcription.
CH3 CH3
HN HN O
N N N N
N NH
N N N N N
HO HO N
HO
O O O
OH O OH OH OH OH
CH3
N6,2'-O-dimethyladenosine N6-methyladenosine ionsine (from adenosine)
O OH NH2 NH2
HN NH H 3C
N N
O N O
HO N O
HO HO
O O O
OH OH OH OH OH OH
Pseudouridine
5-hydroxylmethylcytidine 5-methylcytidine
(from uridine)
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8.3.2: Mutations
Mutation can arise from the chemical modification of bases. Uracil in RNA is a demethylated form of thymine in DNA. In RNA,
AU base pairs replace AT base pairs. Why the need for uracil in RNA? The question could be rephrased as to why the need for
thymine, with its extra methyl group, in DNA. It's useful to think about the consequence of replacing a single H in a molecule with
a -CH3. Take HOH, water, as an example. Our bodies are over 60% water. We drink liters of water of concentration 55 M each day.
Yet if we drink 0.07 L of methanol, CH3OH, half of us would die! Let's probe some consequences of the U (no -CH3) and T (with -
CH3) changes in DNA. It can get confusing but just remember that the normal base pairs in DNA are AT, but AU base pairs also
form (they norm in RNA). The -CH3 substituent on thymine does not affect its base pairing.
a. Spontaneous deamination of cytosine in DNA
Why are we now discussing cytosine in DNA? One reason is that the most common mutation in DNA is a C to T replacement. One
way that happens is through the spontaneous hydrolytic deamination of cytosine in DNA to uracil, which we have presumed to be
found only in RNA. The mechanism for this deamination and subsequence conversion of a GC to an AT base pair is shown in
Figure 8.3.3. The inset box shows a simplified mechanism for spontaneous deamination.
H H
N
O
N H H
N
O NH
N O
H H H
cytosine N N
N GC base pair
H
cytosine N N guanine
H H
N O
H
H H
H
N O spontaneous
H H 2O deamination
N
NH3
N O
H NH3
N
O NH
X
O N N
H
XH
uracil N N guanine
H H
N O
H
H N
N N
replication O NH
O N H H
N N N N
H adenine H
N N
uracil H H cytosine N N guanine
N O H H
H N O
AU basepair H
(similar to RNA)
DNA replication
if not repaired
H
N N
AT base pair
O N
N
H
N N adenine
H H
thymine N O
H
Figure 8.3.3 : GC to AT base pair mutation on spontaneous hydrolytic deamination of cytosine in DNA.
Hence a possible consequence of the deamination reaction is a GC to AT base pair mutation if the uracil in DNA is not removed
before DNA replication. Fortunately, the enzyme uracil-DNA glycosylases can remove any uracils found in DNA, leaving an
abasic site, which can be fixed with DNA repair enzymes.
We can now ask the question, why T and not U in DNA? Pretend you are a DNA repair enzyme and you see a UA base pair in
DNA. How can you tell if the UA base pair is correct and intended to be there or if it should be a CG base pair that underwent
deamination? The most common uracil-DNA glycosylases remove the uracil whether it is across from guanine, the correct base but
which can not hydrogen bond with uracil (in the green oval in Figure 8.3.3), or if is across from adenine, the wrong base (in red
oval), which is present after a round of replication. Evolution has addressed this problem by adding a methyl group to uracil to
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form thymine and using that base, which forms a base pair with adenine. Now no decision on which base across from a uracil
(guanine if the uracil arose from deamination) or across from a "uracil-like" thymine (adenine) is correct.
b. Other mutations
Since we are considering chemical modifications to DNA and mutations, it is appropriate to give a more expanded background on
them. In addition to mutations caused by spontaneous hydrolytic deamination of cytosine, mutations can also arise through the
addition of a wrong base during DNA replication, by chemical damages caused by radiation or chemical modifying agents. How
many mistakes in replication are made? If you received a 99% on an examination, you would be ecstatic. That's not good enough
for DNA replication. In Cell Biology by the Numbers, they calculate it this way. Assume the replication /repair is so good that it
takes 108 replications to make a mistake (an error rate of 10-8/BP). Assume also there are 3 x 109 base pairs in the human genome.
This leads to a mutation rate 10-100 mutations/genome/generation or about 0.1-1 mutations/genome/replication. Not bad!
Figure 8.3.4 shows how common point mutations might arise just randomly.
A. from base pairing with wrong partner: Example
A-T
H
A-T
O N
H H
H H
A-T
T N C A-T
N N N N N A-T
H A* - T
C1 N C1 H
N
N
N G-C
O A O A*
N N cytosine
N N
C1
C1
rare imino tautomer
of adenine
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R1
H N N O
R2
O N
H H oxidative H
T N deamination C A-T G -C
N N O
N N
C1 H C1 H
N N
N N
O A O HA
N cytosine
N N N
C1 hypoxanthine C1
H
in main tautomer
N
H O
C oxidative H H
N N O
deamination U N G-C A -T
C1 H N N
N H
O N C1 N
G N
O A
H N
N N N
uracil N
C1
H C1
- alkylating agents
H
N
O CH3
H H
C alkylation
N N O T* O G-C A -T
N N
C1 H H
N C1 N
O N N
G O G*
H
rare H
N N N N
N tautomer N
C1 C1
H H O6-meG
Cl
O O
insertion
translocation
chromo 20
chromo 20
chromo4
chromo 4
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Given that RNA expresses catalytic activities and can carry genetic information (some viruses have ds and ss RNA as their
genome), it has been suggested that early life might have been based on RNA. DNA would evolve later as a more secure carrier of
genetic information. An inspection of the chemical properties of DNA, RNA, and proteins shows them to have attributes needed for
their expressed function. Let's examine each for structural features that might be important for function.
a. Why does DNA lack a 2' OH group (found in RNA), which has been replaced with hydrogen? This required the evolutionary
creation of a new enzyme, ribonucleotide reductase, to catalyze the replacement of the OH in a ribonucleotide monomer to form the
deoxyribonucleotide form. One possible explanation is offered in the figure below. DNA, the main carrier of genetic information,
must be an extremely stable molecule. An OH present on C'2 could act as a nucleophile and attack the proximal P in the
phosphodiester bond, leading to a nucleophilic substitution reaction and potential cleavage of the link. RNA, an intermediary
molecule, whose concentration (at least as mRNA) should rise and fall based on the need for a potential transcript, should be more
labile to such hydrolysis. Figure 8.3.8 shows a possible reaction diagram for the internal cleavage of RNA. (The reaction would
probably proceed with no actual intermediate, but just a transition state.
Base Base
RO RO
O O
O O O O
H
O P O
O P O Base
Base
O
O
O
O
OR OH
OR OH
+
H
Base
RO Base
O HO
+ O
O O
P OR OH
O O
Figure 8.3.8 : Internal cleave of RNA using the C'2-OH as an intramolecular nucleophile
b. Why do both DNA and RNA contain a phosphodiester link between adjacent monomers instead of more "traditional" links such
as carboxylic acid esters, amides, or anhydrides? One possible explanation is given below. Nucleophilic attack on the sp3
hybridized P in a phosphodiester is much more difficult than for a more open sp2 hybridized carboxylic acid derivative. In addition,
the negative charge on the O in the phosphodiester link would decrease the likelihood of a nucleophilic attack. The negative
charges on both strands in ds-DNA probably help keep the strands separated allowing the traditional base pairing and double-
stranded helical structure observed. The cleavage of the phosphodiester link in DNA and a hypothetic ester link is shown in Figure
8.3.9. Again, the reaction of the phosphodiester shows a pentavalent intermediate, but most like the reaction proceeds directly from
8.3.5 https://bio.libretexts.org/@go/page/72660
Base Base
RO RO
O O
pentavalent
O H intermediate O H
Phosphodiester O P O Base
O
P O sp3d Base
HO
O O
O O O
H
H
OR H OR H
RO RO
Base Base
O O
tetrahedral
intermediate
carboxylic acid O H O H
ester sp3
C O Base C O Base
H O
O O O
H H H H H
H H H H
OR H OR H
Figure 8.3.9 : cleavage of the phosphodiester link in DNA and a hypothetic ester link
c. Why is DNA found as a repetitive double-stranded helix but RNA is usually found as a single-stranded molecule that can form
complicated tertiary structures with some ds-RNA motifs?
Another reason for the absence of the 2' OH in DNA is that it allows the deoxyribose ring in DNA to pucker in just the right way to
sterically allow extended ds-DNA helices (B type). The pucker in deoxyribose and ribose can be visualized by visualizing a single
plane in the sugar ring defined by the ring atoms C1', O, and C4'. If a ring atom is pointing in the same direction as the C4'-C5'
bond, the ring atom is defined as endo. If it is pointing in the opposite direction, it is defined as exo. In the most common form of
double-stranded DNA, B-DNA, which is the iconic extended double helix you know so well, C2' is in the endo form. It can also
adopt the C3' endo form, leading to the formation of another less common helix, a more open ds-A helix. In contrast, steric
interference prevents ribose in RNA from adopting the 2'endo conformation, and allows only the 3'endo form, precluding the
occurrences of extended ds-B-RNA helices but allowing more open, A-type helices.
Figure 8.3.10 shows another comparison between the A-RNA and B-DNA double helices and the C'3 and C'2 endo forms of the
ribose
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Figure 8.3.10 : after Zhou et al Nature Structural and Molecular Biology. doi:10.1038/nsmb.3270
Figure 8.3.5 shows interactive iCn3D models of the pentoses in a strand of A-RNA (413D), double-stranded, left, and B-DNA
(1BNA), double-stranded, right.
C'3-endo ribose, A-RNA (413D, double stranded) C'2 endo ribose, B-DNA (1BNA, double stranded)
Click the image for a popup or use this external link: Click the image for a popup or use this external link:
https://structure.ncbi.nlm.nih.gov/i...KPueqrBADczh26 https://structure.ncbi.nlm.nih.gov/i...BEn5nqsCQG2JH6
8.3.7 https://bio.libretexts.org/@go/page/72660
The increased flexibility in DNA allows rotation around the C1'-N glycosidic bond connecting the deoxyribose and base in DNA,
allowing different orientations of AT and GC base pairs with each other. The normal "anti" orientation allows "Watson-Crick"
(WC) base pairing between AT and GC base pairs while the altered rotation allows "Hoogsteen" (Hoog) base pairs. The different
orientations for an AT base pair are shown in Figure 8.3.11.
Watson-Crick Hoogsteen
Major groove
Major groove
O N1 NH2 O
NH2
N7 A
N3
H N3 T N3 T
A N7 H
N9 N1 N1
10.4 Å N9 N1
R N3 R 8.5 Å
anti O anti R O R
syn anti
Minor groove
Minor groove
pWC ~99.6% pHG ~0.4%
Major groove
Major groove
H
H2N H 2N N1
O O H 2N
N7 G
N3 C N3 +
N9 G N1 H N1 N7 H N3 C
10.6 Å R N9 N1
R N3
O 8.3 Å
anti NH2 anti R O R
syn anti
Minor groove
Minor groove
pWC ~99.99% pHG ~0.01%
Figure 8.3.11 : Xu, Y., McSally, J., Andricioaei, I. et al. Modulation of Hoogsteen dynamics on DNA recognition. Nat Commun 9,
1473 (2018). https://doi.org/10.1038/s41467-018-03516-1Creative Commons Attribution 4.0 International License.
http://creativecommons.org/licenses/by/4.0/.
The Watson-Crick (WC) and Hoogsteen (HG) base pairs in B-DNA are in a dynamic equilibrium with the equilibrium greatly
favoring the WC form as indicated by the arrows in the figure above. In a DNA:protein complex, the WC ↔ HG equilibrium can
favor the WG form for AT and GC+ forms (in the latter, the C is protonated) when those base pairs are also involved in protein
recognition. They can also occur more frequently in damaged DNA. In contrast, molecular dynamic studies show that the HG base
pairs A-U and GC+ are strongly disfavored in ds A-RNA.
One type of DNA damage is methylation on N1-adenosine and N1-guanosine. This modification prevents normal Watson-Crick
base pairing but for DNA, these modified bases can still engage in Hoogsteen base pairing, preserving the overall structure of
dsDNA and its ability to stably carry genetic information. This same methylation occurs normally in post-transcriptional modified
RNA. Hence, N1 adenosine and N1 guanosine methylation prevent any type of base pairing in the modified RNA. These properties
make DNA a better carrier of molecular information and offer another way to regulate the structural and functional properties of
RNA.
Hoogsteen base pairs can be found in distorted dsDNA structures (caused by protein:DNA interactions) but also in normal B-DNA.
Figure 8.3.12 shows a Hoogsteen base pair between dA7 and dT37 in the MAT α 2 homeodomain:DNA complex (pdb 1K61).
Note that the dA base in the Hoogsteen base pair is rotated syn (with respect to the deoxyribose ring) instead of the usual anti,
allowing the Hoogsteen base pair.
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Figure 8.3.12 : Hoogsteen base pair between dA7 and dT37 in the MAT α 2 homeodomain:DNA complex (pdb 1K61)
8.3.4: A Structural Comparison
Now let's review the kinds of structures adopted by the 3 major macromolecules, DNA, RNA, and proteins. DNA predominately
adopts the classic ds-BDNA structure, although this structure is wound around nucleosomes and "supercoiled" in cells since it must
be packed into the nucleus. This extended helical form arises in part from the significant electrostatic repulsions of two strands of
this polyanion (even in the presence of counter-ions). Given its high charge density, it is not surprising that it forms complexes with
positive proteins and does not adopt complex tertiary structures. RNA, on the other hand, can not form long B-type double-stranded
helices (due to steric constraints of the 2'OH and the resulting 3'endo ribose pucker). Rather it can adopt complex tertiary
conformations (albeit with significant counter-ion binding to stabilize the structure) and in doing so can form regions of secondary
structure (ds-A RNA) in the form of stem/hairpin forms. Proteins, with their combination of polar charged, polar uncharged, and
nonpolar side chains have little electrostatic hindrance in the adoption of secondary and tertiary structures. RNA and proteins can
both adopt tertiary structures with potential binding and catalytic sites, making them ideal catalysts for chemical reactions. RNA,
given its 4 nucleotide alphabet, can also carry genetic information, making it an ideal candidate for the first evolved
macromolecules enabling the development of life. Proteins with a great abundance of organic functionalities would eventually
supplant RNA as a better choice for life's catalyst. DNA, with its greater stability, would supplant RNA as the choice for the main
carrier of genetic information (Figure 8.3.13):
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function. On one hand that could be deleterious or even fatal to the organism. On the other hand, the new protein structure might
have new functionalities that allow adaptation to new environments or allow new types of reactions. Evolution would favor the
latter.
8.3.5: References
Börner, R., Kowerko, D., Miserachs, H.G., Shaffer, M., and Sigel, R.K.O. (2016) Metal ion induced heterogeneity in RNA folding
studied by smFRET. Coordination Chemistry Reviews 327 DOI: 10.1016/j.ccr.2016.06.002 Available at:
https://www.researchgate.net/publication/303846502_Metal_ion_induced_heterogeneity_in_RNA_folding_studied_by_smFRET
Hardison, R. (2019) B-Form, A-Form, and Z-Form of DNA. Chapter in: R. Hardison’s Working with Molecular Genetics.
Published by LibreTexts. Available at:
https://bio.libretexts.org/Bookshelves/Genetics/Book%3A_Working_with_Molecular_Genetics_(Hardison)/Unit_I%3A_Genes%2
C_Nucleic_Acids%2C_Genomes_and_Chromosomes/2%3A_Structures_of_Nucleic_Acids/2.5%3A_B-Form%2C_A-
Form%2C_and_Z-Form_of_DNA
Lenglet, G., David-Cordonnier, M-H., (2010) DNA-destabilizing agents as an alternative approach for targeting DNA: Mechanisms
of action and cellular consequences. Journal of Nucleic Acids 2010, Article ID: 290935, DOI: 10.4061/2010/290935 Available at:
https://www.hindawi.com/journals/jna/2010/290935/
Mechanobiology Institute (2018) What are chromosomes and chromosome territories? Produced by the National University of
Singapore. Available at: https://www.mechanobio.info/genome-regulation/what-are-chromosomes-and-chromosome-territories/
National Human Genome Research Institute (2019) The Human Genome Project. National Institutes of Health. Available at:
https://www.genome.gov/human-genome-project
Wikipedia contributors. (2019, July 8). DNA. In Wikipedia, The Free Encyclopedia. Retrieved 02:41, July 22, 2019, from
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This page titled 8.3: Nucleic Acids - Comparison of DNA and RNA is shared under a CC BY-SA 4.0 license and was authored, remixed, and/or
curated by Henry Jakubowski and Patricia Flatt.
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