Antiparallel Strand Orientation Research Articles

Photo-induced crosslinking uncovers an antiparallel strand orientation in heterodimeric (EIAALEK)3/(KIAALKE)3 and (EIAALEK)3/(RIAALRE)3 coiled-coil systems.

We describe for the first time the co-existence of the parallel and antiparallel conformation of the heterodimeric E3/K3 and E3/R3 coiled-coil systems in solution. The introduction of a furanylated amino acid in the (EIAALEK)3 sequence allowed, upon photo-induced covalent crosslinking, freezing of the respective coiled-coil complexes present in solution. The occurrence of both parallel and antiparallel conformations in solution was supported by computational simulations and further confirmed by fluorescence experiments based on pyrene-pyrene stacking.

Prebiotic competition and evolution in self-replicating polynucleotides can explain the properties of DNA/RNA in modern living systems

BackgroundWe hypothesize prebiotic evolution of self-replicating macro-molecules (Alberts, Molecular biology of the cell, 2015; Orgel, Crit Rev Biochem Mol Biol 39:99-123, 2004; Hud, Nat Commun 9:5171) favoured the constituent nucleotides and biophysical properties observed in the RNA and DNA of modern organisms. Assumed initial conditions are a shallow tide pool, containing a racemic mix of diverse nucleotide monomers (Barks et al., Chembiochem 11:1240-1243, 2010; Krishnamurthy, Nat Commun 9:5175, 2018; Hirao, Curr Opin Chem Biol 10:622-627), subject to day/night thermal fluctuations (Piccirilli et al., Nature 343:33-37, 1990). Self-replication, like Polymerase Chain Reactions, followed as higher daytime thermal energy “melted” inter-strand hydrogen bonds causing strand separation while solar UV radiation increased prebiotic nucleobase formation (Szathmary, Proc Biol Sci 245:91-99, 1991; Materese et al., Astrobiology 17:761-770, 2017; Bera et al., Astrobiology 17:771-785, 2017). Lower night energies allowed free monomers to form hydrogen bonds with their template counterparts leading to daughter strand synthesis (Hirao, Biotechniques 40:711, 2006).ResultsEvolutionary selection favoured increasing strand length to maximize auto-catalytic function in RNA and polymer stability in double stranded DNA (Krishnamurthy, Chemistry 24:16708-16715, 2018; Szathmary, Nat Rev Genet 4:995-1001, 2003). However, synthesis of the full daughter strand before daytime temperatures produced strand separation, longer polymer length required increased speed of self-replication. Computer simulations demonstrate optimal polynucleotide autocatalytic speed is achieved when the constituent nucleotides possess a left-right asymmetry that decreases the hydrogen bond kinetic barrier for the free nucleotide attachment to the template on one side and increases bond barrier on the other side preventing it from releasing prior to covalent bond formation. This phenomenon is similar to asymmetric kinetics observed during polymerization of the front and the back ends of linear cytoskeletal proteins such as actin and microtubules (Orgel, Nature 343:18-20, 1990; Henry, Curr Opin Chem Biol 7:727-733, 2003; Walker et al., J Cell Biol 108:931-937, 1989; Crevenna et al., J Biol Chem 288:12102-12113, 2013). Since rotation of the nucleotide would disrupt the asymmetry, the optimal nucleotides must form two or more hydrogen bonds with their counterpart on the template strand. All nucleotides in modern RNA and DNA have these predicted properties. Our models demonstrate these constraints on the properties of constituent monomers result in biophysical properties found in modern DNA and RNA including strand directionality, anti-parallel strand orientation, homochirality, quadruplet alphabet, and complementary base pairing. Furthermore, competition between RNA and DNA auto-replicators for 3 nucleotides in common permit states coexistence and possible cooperative interactions that could be incorporated into nascent living systems.ConclusionOur findings demonstrate the molecular properties of DNA/RNA could have emerged from Darwinian competition among macromolecular replicators that selected nucleotide monomers that maximized the speed of autocatalysis.

Evolutionary advantage of anti-parallel strand orientation of duplex DNA

DNA in all living systems shares common properties that are remarkably well suited to its function, suggesting refinement by evolution. However, DNA also shares some counter-intuitive properties which confer no obvious benefit, such as strand directionality and anti-parallel strand orientation, which together result in the complicated lagging strand replication. The evolutionary dynamics that led to these properties of DNA remain unknown but their universality suggests that they confer as yet unknown selective advantage to DNA. In this article, we identify an evolutionary advantage of anti-parallel strand orientation of duplex DNA, within a given set of plausible premises. The advantage stems from the increased rate of replication, achieved by dividing the DNA into predictable, independently and simultaneously replicating segments, as opposed to sequentially replicating the entire DNA, thereby parallelizing the replication process. We show that anti-parallel strand orientation is essential for such a replicative organization of DNA, given our premises, the most important of which is the assumption of the presence of sequence-dependent asymmetric cooperativity in DNA.

Symmetry in Nucleic-Acid Double Helices

In nature and in the test tube, nucleic acids occur in many different forms. Apart from single-stranded, coiled molecules, DNA and RNA prefer to form helical arrangements, in which the bases are stacked to shield their hydrophobic surfaces and expose their polar edges. Focusing on double helices, we describe the crucial role played by symmetry in shaping DNA and RNA structure. The base pairs in nucleic-acid double helices display rotational pseudo-symmetry. In the Watson–Crick base pairs found in naturally occurring DNA and RNA duplexes, the symmetry axis lies in the base-pair plane, giving rise to two different helical grooves. In contrast, anti-Watson–Crick base pairs have a dyad axis perpendicular to the base-pair plane and identical grooves. In combination with the base-pair symmetry, the syn/anti conformation of paired nucleotides determines the parallel or antiparallel strand orientation of double helices. DNA and RNA duplexes in nature are exclusively antiparallel. Watson–Crick base-paired DNA or RNA helices display either right-handed or left-handed helical (pseudo-) symmetry. Genomic DNA is usually in the right-handed B-form, and RNA double helices adopt the right-handed A-conformation. Finally, there is a higher level of helical symmetry in superhelical DNA in which B-form double strands are intertwined in a right- or left-handed sense.

7-Deaza-2'-deoxyguanosine: Selective Nucleobase Halogenation, Positional Impact of Space-Occupying Substituents, and Stability of DNA with Parallel and Antiparallel Strand Orientation.

The positional impact of phenyl or phenyltriazolyl residues on the properties of 7-deaza-2'-deoxyguanosine, such as fluorescence, sugar conformation, and stability in DNA and DNA-RNA double helixes was studied. To this end, regioselective iodination protocols were developed for 7-deaza-2'-deoxyguanosine affording the 7- and 8-iodo isomers. The aromatic side chains were introduced by Suzuki-Miyaura cross-coupling or click reaction. Only the 8-phenyl nucleoside shows strong fluorescence in polar aprotic solvents accompanied by solvatochromism. The conformation of the sugar moiety was shifted toward S due to the bulky 8-substituent. Phosphoramidite building blocks and oligonucleotides were synthesized. 8-Substituted 7-deaza-2'-deoxyguanosines destabilize canonical (aps) DNA as well as DNA with parallel strand (ps) orientation. The base pair stability was maintained when the space-occupying substitutes were located at the 7-position. Unexpectedly, the bulky phenyltriazolyl "click" residue is well-accommodated at the 7-position of ps DNA and even led to a stabilization of the parallel double helix. CD spectra indicate that functionalization leads only to local distortion of the double helix while the overall structure of aps and ps DNA is maintained.

2'-O-Methyl- and 2'-O-propargyl-5-methylisocytidine: synthesis, properties and impact on the isoCd-dG and the isoCd-isoGd base pairing in nucleic acids with parallel and antiparallel strand orientation.

Oligonucleotides containing 2'-O-methylated 5-methylisocytidine (3) and 2'-O-propargyl-5-methylisocytidine (4) as well as the non-functionalized 5-methyl-2'-deoxyisocytidine (1b) were synthesized. MALDI-TOF mass spectra of oligonucleotides containing 1b are susceptible to a stepwise depyrimidination. In contrast, oligonucleotides incorporating 2'-O-alkylated nucleosides 3 and 4 are stable. This is supported by acid catalyzed hydrolysis experiments performed on nucleosides in solution. 2'-O-Alkylated nucleoside 3 was synthesized from 2'-O-5-dimethyluridine via tosylation, anhydro nucleoside formation and ring opening. The corresponding 4 was obtained by direct regioselective alkylation of 5-methylisocytidine (1d) with propargyl bromide under phase-transfer conditions. Both compounds were converted to phosphoramidites and employed in solid-phase oligonucleotide synthesis. Hybridization experiments resulted in duplexes with antiparallel or parallel chains. In parallel duplexes, methylation or propargylation of the 2'-hydroxyl group of isocytidine leads to destabilization while in antiparallel DNA this effect is less pronounced. 2'-O-Propargylated 4 was used to cross-link nucleosides and oligonucleotides to homodimers by a stepwise click ligation with a bifunctional azide.

A switch from parallel to antiparallel strand orientation in a coiled-coil X-ray structure via two core hydrophobic mutations.

The coiled-coil is one of the most ubiquitous and well studied protein structural motifs. Significant effort has been devoted to dissecting subtle variations of the typical heptad repeat sequence pattern that can designate larger topological features such as relative α-helical orientation and oligomer size. Here we report the X-ray structure of a model coiled-coil peptide, HA2-Del-L2seM, which forms an unanticipated core antiparallel dimer with potential sites for discrete higher-order multimerization (trimer or tetramer). In the X-ray structure, a third, partially-ordered α-helix is weakly associated with the antiparallel dimer and analytical ultracentrifugation experiments indicate the peptide forms a well-defined tetramer in solution. The HA2-Del-L2seM sequence is closely related to a parent model peptide, HA2-Del, which we previously reported adopts a parallel trimer; HA2-Del-L2seM differs by only hydrophobic leucine to selenomethione mutations and thus this subtle difference is sufficient to switch both relative α-helical topology and number of α-helices participating in the coiled-coil. Comparison of the X-ray structures of HA2-Del-L2seM (reported here) with the HA2-Del parent (reported previously) reveals novel interactions involving the selenomethionine residues that promote antiparallel coiled-coil configuration and preclude parallel trimer formation. These novel atomic insights are instructive for understanding subtle features that can affect coiled-coil topology and provide additional information for design of antiparallel coiled-coils.

Duplex DNA and DNA-RNA hybrids with parallel strand orientation: 2'-deoxy-2'-fluoroisocytidine, 2'-deoxy-2'-fluoroisoguanosine, and canonical nucleosides with 2'-fluoro substituents cause unexpected changes on the double helix stability.

Oligonucleotides with parallel or antiparallel strand orientation incorporating 2'-fluorinated 2'-deoxyribonucleosides with canonical nucleobases or 2'-deoxy-2'-fluoroisocytidine ((F)iCd, 1c) and 2'-deoxy-2'-fluoroisoguanosine ((F)iGd, 3c) were synthesized. To this end, the nucleosides 1c and 3c as well as the phosphoramidite building blocks 19 and 23 were prepared and employed in solid-phase oligonucleotide synthesis. Unexpectedly, (F)iCd is not stable during oligonucleotide deprotection (55 °C, aq NH3) and was converted to a cyclonucleoside (14). Side product formation was circumvented when oligonucleotides were deprotected under mild conditions (aq ammonia-EtOH, rt). Oligonucleotides containing 2'-fluoro substituents ((F)iCd, (F)iGd and fluorinated canonical 2'-deoxyribonucleosides) stabilize double-stranded DNA, RNA, and DNA-RNA hybrids with antiparallel strand orientation. Unexpected strong stability changes are observed for oligonucleotide duplexes with parallel chains. While fluorinated oligonucleotides form moderately stable parallel stranded duplexes with complementary DNA, they do not form stable hybrids with RNA. Furthermore, oligoribonucleotide duplexes with parallel strand orientation are extremely unstable. It is anticipated that nucleic acids with parallel chains might be too rigid to accept sugar residues in the N-conformation as observed for ribonucleosides or 2'-deoxy-2'-fluororibonucleosides. These observations might explain why nature has evolved the principle of antiparallel chain orientation and has not used the parallel chain alignment.

Robust silver-mediated imidazolo-dC base pairs in metal DNA: dinuclear silver bridges with exceptional stability in double helices with parallel and antiparallel strand orientation.

A new unprecedented metal-mediated base pair was designed that stabilizes reverse Watson-Crick DNA (parallel strand orientation, ps) as well as canonical Watson-Crick DNA (antiparallel strand orientation, aps). This base pair contains two imidazolo-dC units decorated with furan residues. Tm measurements and spectroscopic studies reveal that each silver-mediated furano-imidazolo-dC forms exceptionally stable duplexes with ps and aps chain orientation. This stability increase by a silver-mediated base pair is the highest reported so far for ps and aps DNA helices.

ChemInform Abstract: Parallel Stranded DNA Stabilized with Internal Sugar Cross‐Links: Synthesis and Click Ligation of Oligonucleotides Containing 2′‐Propargylated Isoguanosine.

Internal sugar cross-links were introduced for the first time into oligonucleotides with parallel chain orientation by click ligation. For this, the 2'- or 3'-position of the isoguanosine ribose moiety was functionalized with clickable propargyl residues, and the synthesis of propargylated cytosine building blocks was significantly improved. Phosphoramidites were prepared and employed in solid-phase synthesis. A series of oligo-2'-deoxyribonucleotides with parallel (ps) and antiparallel (aps) strand orientation were constructed containing isoguanine-cytosine, isoguanine-isocytosine, and adenine-thymine base pairs. Complementary oligonucleotides with propargylated sugar residues were ligated in a stepwise manner with a chelating bis-azide under copper catalysis. Cross-links were introduced within a base pair or in positions separated by two base pairs. From T(m) stability studies it is evident that cross-linking stabilizes DNA with parallel strand orientation strongly (ΔT(m) from +16 to +18.5 °C) with a similar increase as for aps DNA.

Stabilities and structures of islet amyloid polypeptide (IAPP22–28) oligomers: From dimer to 16-mer

BackgroundThe formation of amyloid fibrils is associated with many age-related degenerative diseases. Nevertheless, the molecular mechanism that directs the nucleation of these fibrils is not fully understood. MethodsHere, we performed MD simulations for the NFGAILS motif of hIAPP associated with the type II diabetes to estimate the stabilities of hIAPP22–28 protofibrils with different sizes: from 2 to 16 chains. In addition, to study the initial self-assembly stage, 4 and 8 IAPP22–28 chains in explicit solvent were also simulated. ResultsOur results indicate that the ordered protofibrils with no more than 16 hIAPP22–28 chains will be structurally stable in two layers, while one-layer or three-layer models are not stable as expected. Furthermore, the oligomerization simulations show that the initial coil structures of peptides can quickly aggregate and convert to partially ordered β-sheet-rich oligomers. ConclusionsBased on the obtained results, we found that the stability of an IAPP22–28 oligomer was not only related with its size but also with its morphology. The driving forces to form and stabilize an oligomer are the hydrophobic effects and backbone H-bond interaction. Our simulations also indicate that IAPP22–28 peptides tend to form an antiparallel strand orientation within the sheet. General significanceOur finding can not only enhance the understanding about potential mechanisms of hIAPP nuclei formation and the extensive structural polymorphisms of oligomers, but also provide valuable information to develop potential β-sheet formation inhibitors against type II diabetes.

Parallel Stranded DNA Stabilized with Internal Sugar Cross-Links: Synthesis and Click Ligation of Oligonucleotides Containing 2′-Propargylated Isoguanosine

Internal sugar cross-links were introduced for the first time into oligonucleotides with parallel chain orientation by click ligation. For this, the 2'- or 3'-position of the isoguanosine ribose moiety was functionalized with clickable propargyl residues, and the synthesis of propargylated cytosine building blocks was significantly improved. Phosphoramidites were prepared and employed in solid-phase synthesis. A series of oligo-2'-deoxyribonucleotides with parallel (ps) and antiparallel (aps) strand orientation were constructed containing isoguanine-cytosine, isoguanine-isocytosine, and adenine-thymine base pairs. Complementary oligonucleotides with propargylated sugar residues were ligated in a stepwise manner with a chelating bis-azide under copper catalysis. Cross-links were introduced within a base pair or in positions separated by two base pairs. From T(m) stability studies it is evident that cross-linking stabilizes DNA with parallel strand orientation strongly (ΔT(m) from +16 to +18.5 °C) with a similar increase as for aps DNA.

A TT Dinucleotide with a Nonionic Silyl Backbone: Impact on Conformation and H-Bond Mediated Base Pairing as Studied by Low-Temperature NMR

Abstract A TSiT dinucleotide linked through a nonionic diisopropylsilyl backbone has been synthesized and studied for its self-association through base–base recognition together with a free thymidine nucleoside. To characterize hydrogen-bonded associates in more detail, NMR measurements were performed in a freonic solvent at temperatures as low as 113 K in the slow hydrogen bond exchange regime. For the thymidine, TT base pairs with both the 2- and 4-carbonyl engaged in hydrogen bonds to the imino proton were observed. Whereas hydrogen bonds to the O4 acceptor are stronger as evidenced by a more deshielded proton in the hydrogen bridge when compared to hydrogen bonds to the O2 acceptor, the latter is nevertheless slightly favored over O4 in the H-bond formation of TT base pairs. The diisopropylsilyl linkage of the TSiT dinucleotide has no significant impact on the geometry and strength of formed NH–O2 and NH–O4 hydrogen bonds indicating, that the silyl backbone does not compromise the alignment of bases and does not pose any restrictions to the cyclic hydrogen bond formation between thymidines of the two strands. However, NMR results point to an exclusive formation of TSiT duplexes with an antiparallel strand orientation.

Autonomously Pairing Cysteinyl-Linked Nucleotide Analogues with a Unique Architecture

We report the efficient pairing in water of the first representative of oligonucleotide analogues in which the backbone is replaced by linking elements between the nucleobases. The architecture of the new analogue demonstrates that the structural differentiation of oligonucleotides into a contiguous backbone and nucleobases, as embodied by the natural nucleic acids and all nucleotide analogues analyzed to date, is not a prerequisite for pairing. UV and circular dichroism analyses of self-complementary and non-self-complementary octanucleotide analogues strongly suggest the fully reversible, sequence-specific association of our new analogues to form a left-handed double helix with an antiparallel strand orientation that is characterized by melting temperatures and free enthalpies higher than those of natural RNA and DNA of the same sequence. The linking element incorporates an L-cysteine moiety that allows a short and efficient synthesis of the monomeric building blocks and, through the choice of either L- or D-cysteine, gives access to either one of the enantiomeric oligomers and thus to left- or right-handed helices.

The Utilization of the Anomalous Intensity Enhancement of the Amide I Couplet for Probing the Formation of Peptide Fibrils in Solution

Knowledge of the architecture of amyloid-like fibrils is necessary for understanding the mechanism of fibril formation. Some amyloid fibrils give rise to an intensity-enhanced amide I couplet in their VCD spectra [Ma et al. J. Am. Chem. Soc.2007, 129, 12364 and Measey et al. J. Am. Chem. Soc. 2009, 131, 18218]. An understanding of the structural basis for this enhancement would facilitate the use of VCD spectroscopy for the structural characterization of amyloid fibrils. To this end we developed a simplified model, which describes amide I modes in the fibrillar stacking of -sheets by a three-dimensional lattice of transition dipole moments. The lattice contains 2 dipoles per strand and variable numbers of sheets and strands per sheet. Thus, we showed that the VCD intensity enhancement requires either helically twisted sheets with parallel oriented strands or a special antiparallel arrangements of adjacent sheets with antiparallel strand orientation in a fibril, in which the strands in one sheet are rotated around their axes by 180o compared with a canonical antiparallel orientation. The sign of the VCD signal of amyloid-like fibrils can be used to distinguish between right and left handed helical twists of parallel oriented -sheets. We compare the results of our simulation to experimental spectra of GNNQQNY, a fragment of the yeast prion protein Sup35, and an alanine-rich peptide, AKY8. For the latter, we use IR, VCD and polarized Raman spectroscopy as well as atomic force microscopy to probe and analyze the nucleation phase as well as the fibril formation phase. Our results demonstrate the advantages of using vibrational spectroscopy to probe the kinetics of peptide and protein aggregation as well as the chirality of the resulting supramolecular structure.

Probing the Strand Orientation and Registry Alignment in the Propagation of Amyloid Fibrils

Detailed knowledge of the structure and growth mechanism of amyloid fibrils is important for understanding the disease process. Recently, solid-state NMR and other spectroscopic data have revealed the equilibrium organization of the tertiary structure of fibrils formed by various segments of beta-amyloid peptides. A three-step "dock-and-lock" mechanism for fibril growth has been proposed on the basis of the kinetic data. Here we use all-atom replica-exchange molecular dynamics simulations in generalized-Born implicit solvent to probe the mechanism of tertiary structure propagation in fibrils of Abeta(16-22) modeled as an oligomer consisting of two beta-sheets each having four strands. The data show that following association with the oligomer, but before being fully locked onto the existing beta-sheet, the added monomer predominantly samples states with the antiparallel strand orientation, but both in- and one-residue shifted backbone hydrogen bond alignments. The in-register state, which is the experimentally observed equilibrium alignment, is marginally more stable than the registry-shifted one. These results suggest that, following the fast docking step, the added monomer dynamically slides in the backbone registry, and stabilization of the preferential alignment must occur in the second locking step as the monomer becomes fully integrated with the fibril. We also delineate the electrostatic and hydrophobic effects in directing the registry alignment during monomer addition. Surprisingly, the in-register alignment provides both increased cross-strand electrostatic attraction and hydrophobic surface burial. Finally, our data support the notion that side chain hydrophobic burial is a major driving force for beta-sheet assembly.

Double helix formation in α‐peptides: a theoretical study

A complete overview on all possible hydrogen bonding patterns of double helices with antiparallel and parallel strand orientation in alpha-peptide sequences is provided on the basis of ab initio molecular orbital theory. The most stable representatives belong to the group of antiparallel helices. The study on side chain influence shows that these double helices can only be realized if the strands are composed of L- and D-amino acids in alternate order. The stability of the double helices is compared with that of competing single-stranded helices. The data contribute to an understanding of secondary structure formation in peptides and provide a basis for a rational design of membrane channels.

Luminescence study of G-quadruplex formation in the presence of Tb 3+ ion

The interactions of Tb 3+ with the quadruplex-forming oligonucleotide bearing human telomeric repeat sequence d(G 3T 2AG 3T 2AG 3T 2AG 3), (htel21), have been studied using luminescence spectroscopy and circular dichroism (CD). Enhanced luminescence of Tb 3+, resulting from energy transfer from guanines, indicated encapsulation of Tb 3+ ion in the central cavity of quadruplex core. The ability of lanthanide ions (Eu 3+ and Tb 3+) to mediate formation of quadruplex structure has been further evidenced by the fluorescence energy transfer measurements with the use of oligonucleotide probe labeled with fluorescein and rhodamine FRET partners, FAM-htel21-TAMRA. The CD spectra revealed that Tb 3+/htel21 quadruplex possesses antiparallel strand orientation, similarly as sodium quadruplex. Tb 3+ binding equilibria have been investigated in the absence and the presence of competing metal cations. At low Tb 3+ concentration (8 μM) Tb 3+/htel21 quadruplex stability is very high (5 × 10 6 M −1) and stoichiometry of 5–7 Tb 3+ ions per one quadruplex molecule is observed. Luminescence and CD titration experiments suggested that the cavity of quadruplex accommodates two Tb 3+ ions and the remaining Tb 3+ ions bind probably to TTA loops of quadruplex. Higher concentration of Tb 3+ (above 10 μM) results in the excessive binding of Tb 3+ ions that finally destabilizes quadruplex, which undergoes transformation into differently organized assemblies. Such assemblies (probably possessing multiple positive charge) exhibit kinetic stability, which is manifested by a very slow kinetics of displacement of Tb 3+ ion by competing cations (Li +, Na +, K +).

Short Peptide Amyloid Organization: Stabilities and Conformations of the Islet Amyloid Peptide NFGAIL

Experimentally, short peptides have been shown to form amyloids similar to those of their parent proteins. Consequently, they present useful systems for studies of amyloid conformation. Here we simulate extensively the NFGAIL peptide, derived from the human islet amyloid polypeptide (residues 22–27). We simulate different possible strand/sheet organizations, from dimers to nonamers. Our simulations indicate that the most stable conformation is an antiparallel strand orientation within the sheets and parallel between sheets. Consistent with the alanine mutagenesis, we find that the driving force is the hydrophobic effect. Whereas the NFGAIL forms stable oligomers, the NAGAIL oligomer is unstable, and disintegrates very quickly after the beginning of the simulation. The simulations further identify a minimal seed size. Combined with our previous simulations of the prion-derived AGAAAAGA peptide, AAAAAAAA, and the Alzheimer A β fragments 16–22, 24–36, 16–35, and 10–35, and the solid-state NMR data for A β fragments 16–22, 10–35, and 1–40, some insight into the length and the sequence matching effects may be obtained.

Crystal structure of a B-form DNA duplex containing (L)-alpha-threofuranosyl (3'-->2') nucleosides: a four-carbon sugar is easily accommodated into the backbone of DNA.

(L)-alpha-Threofuranosyl-(3'-->2')-oligonucleotides (TNA) containing vicinally connected phosphodiester linkages undergo informational base pairing in an antiparallel strand orientation and are capable of cross-pairing with RNA and DNA. TNA is derived from a sugar containing only four carbon atoms and is one of the simplest potentially natural nucleic acid alternatives investigated thus far in the context of a chemical etiology of nucleic acid structure. Compared to DNA and RNA that contain six covalent bonds per repeating nucleotide unit, TNA contains only five. We have determined the atomic-resolution crystal structure of the B-form DNA duplex [d(CGCGAA)Td(TCGCG)](2) containing a single (L)-alpha-threofuranosyl thymine (T) per strand. In the modified duplex base stacking interactions are practically unchanged relative to the reference DNA structure. The orientations of the backbone at the TNA incorporation sites are slightly altered in order to accommodate fewer atoms and covalent bonds. The conformation of the threose is C4'-exo with the 2'- and 3'-substituents assuming quasi-diaxial orientation.