Model systems for understanding DNA base pairing

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The fact that nucleic acid bases recognize each other to form pairs is a canonical part of the dogma of biology. However, they do not recognize each other well enough in water to account for the selectivity and efficiency that is needed in the transmission of biological information through a cell. Thus proteins assist in this recognition in multiple ways, and recent data suggest that these mechanisms of recognition can vary widely with context. To probe how the chemical differences of the four nucleobases are defined in various biological contexts, chemists and biochemists have developed modified versions that differ in their polarity, shape, size, and functional groups. This brief review covers recent advances in this field of research.

Introduction

The information that is stored and transferred in a cell is carried in the structure and sequence of nucleic acid bases. These heterocycles must be distinguished from one another by the cellular machinery, and this recognition and discrimination is carried out both by nucleobases themselves, and by proteins as well. For successful cellular function, the genetic information as a base sequence must be recognized accurately during many processes, including DNA replication, transcription, DNA repair, recombination, translation, and RNA interference. All of these processes involve the pairing of one base with another in a selective way. Errors in this pairing can lead to medically serious outcomes such as cancer and drug resistance; but at the same time, such errors also make the process of evolution, and thus life on earth, possible.

A central and basic question is what chemically defines the nucleobases as different from one another, and how does the answer vary in the different biological processes mentioned above. The four bases adenine, guanine, thymine, and cytosine vary from one another in their size, shape, polarity, local electrostatics, and functional groups (Figure 1). In principle, all of these differences can be used in the identification of a base, and yet which of these are most important is often not clear. We know from many solution studies that the bases have some ability to recognize each other in nonpolar solvents by complementary hydrogen bonding, and of course we also know that short molecules of DNA and RNA can self-assemble into double helices in water. However, studies have also shown that simple base–base recognition is not strong or selective enough on its own to account for the selectivities observed in many biological processes, which suggests that proteins act to enhance the specificity and efficiency of nucleobase recognition.

Understanding the mechanisms of accurate genetic pairing matters in both basic and practical ways. Since this transfer of information is central to many diseases, a full understanding of its origin and propagation in living systems will require a better grasp of these recognition processes. In addition, design of therapeutic agents aimed at disrupting or enhancing this recognition also can benefit from such knowledge. Finally, the development of improved tools for postgenomic analysis can result from better understanding of the recognition of genetic sequences as well.

This brief review describes recent work in which non-natural nucleobases are used as tools to study base recognition and pairing mechanisms. It covers only very recent work, mainly carried out in the past two to three years, because multiple reviews have addressed related topics recently. In addition, because of the large increase in work in this field lately, it focuses mainly on studies aimed at basic science, and only briefly notes some designed systems, which have been already reviewed in this journal.

Section snippets

Testing electrostatic effects in pairing

Electrostatic effects can be important in DNA since the structure is highly polar. This is of course tempered by the fact that the solvent is water, which is not only highly polar itself (providing a high dielectric that suppresses electrostatic attractions) but also competes directly for electrostatic interactions such as with hydrogen-bonding groups. One of the main electrostatic interactions to be studied recently is base–base hydrogen bonding, and the question of the role of Watson–Crick

Probes for minor groove effects

Studies in several laboratories have shown that polar interactions in the minor groove of DNA are exceedingly important in pairing stability and structure. All natural DNA bases have minor groove hydrogen-bond acceptors in similar positions, and these are typically well solvated. McLaughlin has developed a number of base analogs lacking minor groove hydrogen-bond acceptors, which have shown a strong destabilizing effect on DNA [19]. Minor groove carbonyl groups of thymine have also been

Testing shape and size effects

The canonical pairs adopt very similar geometries, occupying space that overlaps to a large extent (Figure 2). Since both correctly and incorrectly matched base pairs in DNA are hydrogen-bonded, it is clear that the nonstandard geometry of mismatches plays a substantial role in pairing selectivity. An important question is how much do steric effects alone (in the absence of hydrogen bonds) affect pairing selectivity in the double helix? And secondly, it is clear that pairing selectivity in DNA

Probes for recognition of damaged bases

DNA analogs have also been recently implemented as probes of damage in DNA. Sturla has demonstrated selective and stable base pairing between the biologically relevant damage adduct O6-benzyldeoxyguanosine and a designed diaminonaphthyl-derived nucleoside [34]. In addition, two laboratories have constructed analogs of oxidized purines as probes for how such damage is recognized by repair and polymerase enzymes. Hamm et al. used 8-haloguanines to measure the steric effect of the 8-substituent on

Structural studies

Structural studies of nucleobase analogs in DNA or RNA yield the benefit of helping to understand how the helix adjusts to changes in structure or interactions. Manoharan, Frank-Kamenetskii, and Egli (as part of their siRNA studies) published the X-ray crystal structure of an RNA–RNA duplex containing a non-H-bonded pair between adenine and difluorotoluene. The majority of the RNA and local base pair structure was unaffected by this pair, although small local adjustments to pair geometry were

Alternative principles for base pairing

Some of the insights gained from studies of pairing have led to the development and testing of other, non-natural principles for design of new base pairs. For example, Sekine recently tested the interesting idea of using ‘halogen bonds’ to help pairs associate [41]. Saito examined the use of Schiff base linkage to connect opposing bases [42]. Purine–purine pairs were examined by Battersby et al. [43]. A number of laboratories have recently described metal-bridged base pairs; in this light,

Conclusions

There are multiple points in the transmission of cellular genetic information where accurate base pairing is crucial, and the growing complement of DNA base analogs developed by researchers (Figure 4) will be essential in evaluating how this recognition occurs. It is no doubt the case that both steric and electrostatic effects have important influences on base pairing, but the relative importance of these factors will vary depending on the context, whether it is DNA or RNA. In addition, it is

References and recommended reading

Papers of particular interest, published within the annual period of review, have been highlighted as:

  • • of special interest

  • •• of outstanding interest

Acknowledgement

This work was supported by the U.S. National Institutes of Health (GM072705 and GM63587).

References (48)

  • G.T. Hwang et al.

    Substituent effects on the pairing and polymerase recognition of simple unnatural base pairs

    Nucleic Acids Res

    (2006)
  • A. Zivkovic et al.

    RNA recognition by fluor-aromatic substituted

    Nucleosides Nucleotides Nucleic Acids

    (2005)
  • Z. Yang et al.

    Enzymatic incorporation of a third nucleobase pair

    Nucleic Acids Res

    (2007)
  • A.M. Sismour et al.

    The use of thymidine analogs to improve the replication of an extra DNA base pair: a synthetic biological system

    Nucleic Acids Res

    (2005)
  • S.A. Benner et al.

    Synthetic biology

    Nat Rev Genet

    (2005)
  • C.L. Moore et al.

    Human DNA primase uses Watson–Crick hydrogen bonds to distinguish between correct and incorrect nucleoside triphosphates

    Biochemistry

    (2004)
  • W.T. Wolfle et al.

    Evidence for a Watson–Crick hydrogen bonding requirement in DNA synthesis by human DNA polymerase kappa

    Mol Cell Biol

    (2005)
  • S. Mizukami et al.

    Varying DNA base-pair size in subangstrom increments: evidence for a loose, not large, active site in low-fidelity Dpo4 polymerase

    Biochemistry

    (2006)
  • O. Potapova et al.

    DNA polymerase catalysis in the absence of Watson–Crick hydrogen bonds: analysis by single-turnover kinetics

    Biochemistry

    (2006)
  • J. Xia et al.

    Gene silencing activity of siRNAs with a ribo-difluorotoluyl nucleotide

    ACS Chem Biol

    (2006)
  • A. Somoza et al.

    The roles of hydrogen bonding and sterics in RNA interference

    Angew Chem Int Ed Engl

    (2006)
  • Z. Sun et al.

    Effects of the minor groove pyrimidine nucleobase functional groups on the stability of duplex DNA: the impact of uncompensated minor groove amino groups

    Biopolymers

    (2007)
  • Meena et al.

    Removal of a single minor-groove functional group eliminates A-tract curvature

    J Am Chem Soc

    (2006)
  • J.C. Morales et al.

    Minor groove interactions between polymerase and DNA: more essential than Watson–Crick bonds

    J Am Chem Soc

    (1999)
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