Stability Of Base Pairs Research Articles

Determinants of Unnatural Nucleobase Stability and Polymerase Recognition

Six new unnatural nucleobases have been synthesized and characterized in terms of stability and selectivity of self-pairing in duplex DNA and efficiency and fidelity of self-pairing during polymerase-mediated replication. Each nucleobase has a conserved ring structure but differs from the others in its specific pattern of substitution with oxygen and sulfur atoms. Heteroatom derivatization within the conserved scaffold is shown to have only moderate effects on unnatural self-pair synthesis by the polymerase; larger effects were observed on the thermal stability and polymerase-mediated extension of the self-pairs. The largest effects of heteroatom substitution were on the stability and synthesis of mispairs between the unnatural and natural bases. Certain heteroatom substitutions were found to have a general effect while others were found to have effects that were specific for a particular unnatural or natural base. The data are useful for designing stable and replicable third base pairs and for understanding the contributions of nucleobase shape, polarity, and polarizability to the stability and replication of DNA.

Computer‐Aided Molecular Design of Hydrogen Bond Equivalents of Nucleobases: Theoretical Study of Substituent Effects on the Hydrogen Bond Energies of Nucleobase Pairs

AbstractSubstituent effects on the hydrogen bond energies of Watson−Crick‐type base pairs, formed between a chemically modified nucleic acid base derivative and an unmodified one, were evaluated by ab initio molecular orbital theory. Different trends were observed in the relationship between the substituent and the hydrogen bond energy in each base pair. The predicted hydrogen bond energies correlated well with the experimentally measured binding properties, and so ab initio calculation appears to be an effective method with which to estimate the stabilities of base pairs between chemically modified nucleic acid bases. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2003)

The effect of minor-groove hydrogen-bond acceptors and donors on the stability and replication of four unnatural base pairs.

The stability and replication of DNA containing self-pairs formed between unnatural nucleotides bearing benzofuran, benzothiophene, indole, and benzotriazole nucleobases are reported. These nucleobase analogues are based on a similar scaffold but have different hydrogen-bond donor/acceptor groups that are expected to be oriented in the duplex minor groove. The unnatural base pairs do not appear to induce major structural distortions and are accommodated within the constraints of a B-form duplex. The differences between these unnatural base pairs are manifest only in the polymerase-mediated extension step, not in base-pair stability or synthesis. The benzotriazole self-pair is extended with an efficiency that is only 200-fold less than a correct natural base pair. The data are discussed in terms of available polymerase crystal structures and imply that further modifications may result in unnatural base pairs that can be both efficiently synthesized and extended, resulting in an expanded genetic alphabet.

Formation of the P1.1 pseudoknot is critical for both the cleavage activity and substrate specificity of an antigenomic trans-acting hepatitis delta ribozyme

Hepatitis delta virus RNAs possess self-cleavage activities that produce 2',3'-cyclic phosphate and 5'-hydroxyl termini (i.e. cis-acting delta ribozyme). Trans-acting delta ribozymes have been engineered by removing a junction from the cis version, thereby producing one molecule possessing the substrate sequence and the other the catalytic domain. According to the pseudoknot model, the secondary structure of the delta ribozyme includes a pseudoknot (i.e. P1.1 stem) formed by two base pairs from residues of the L3 loop and J1/4 junction. A collection of 48 P1.1 stem mutants was synthesized in order to provide an original characterization of both the importance and the structure of this pseudoknot in a trans-acting version of the ribozyme. Several structural differences were noted compared to the results reported for cis-acting ribozymes. For example, a combination of two stable Watson-Crick base pairs composing the essential P1.1 stem was demonstrated to be crucial for a significant level of activity, while the cis version required only one base pair. In addition, we present the first physical evidences revealing that the composition of the P1.1 stem affects the substrate specificity for ribozyme cleavage. Depending on the residues forming the J1/4 junction, non-productive ribozyme-substrate complexes can be observed. This phenomenon is proposed to be important for further development of a gene-inactivation system based on delta ribozyme.

Oligonucleotide duplexes containing N8-glycosylated 8-aza-7-deazaguanine and self-assembly of 8-aza-7-deazapurines on the nucleoside and the oligomeric level

The 8-aza-7-deazaguanine N8-(2'-deoxy-beta-D-ribofuranoside) (1) was synthesized, converted into the phosphoramidite 4 and incorporated into oligonucleotides. Nucleoside 1 forms stable base pairs with 2'-deoxy-5-methylisocytidine in DNA with antiparallel chain orientation (aps) and with 2'-deoxycytidine in duplexes with parallel chains (ps). According to the CD spectra self-complementary oligonucleotides d(1-m5isoC)3 and d(1-C), form autonomous DNA-structures. Neither the nucleoside 1 nor the regularly linked 8-aza-7-deaza-2'-deoxyguanosine form G-like tetrads while the regularly linked 8-aza-7-deaza-2'-deoxyisoguanosine gives higher molecular assemblies which are destroyed by bulky 7-bromo substituents. This was verified on monomeric nucleosides by ESI-MS spectrometry and on oligonucleotides by HPLC analysis.

Propynyl groups in duplex DNA: stability of base pairs incorporating 7-substituted 8-aza-7-deazapurines or 5-substituted pyrimidines.

Oligonucleotides incorporating the 7-propynyl derivatives of 8-aza-7-deaza-2'-deoxyguanosine (3b) and 8-aza-7-deaza-2'-deoxyadenosine (4b) were synthesized and their duplex stability was compared with those containing the 5-propynyl derivatives of 2'-deoxycytidine (1) and 2'-deoxyuridine (2). For this purpose phosphoramidites of the 8-aza- 7-deazapurine (pyrazolo[3,4-d]pyrimidine) nucleosides were prepared and employed in solid-phase synthesis. All propynyl nucleosides exert a positive effect on the DNA duplex stability because of the increased polarizability of the nucleobase and the hydrophobic character of the propynyl group. The propynyl residues introduced into the 7-position of the 8-aza-7-deazapurines are generally more stabilizing than those at the 5-position of the pyrimidine bases. The duplex stabilization of the propynyl derivative 4b was higher than for the bromo nucleoside 4c. The extraordinary stability of duplexes containing the 7-propynyl derivative of 8-aza-7- deazapurin-2,6-diamine (5b) is attributed to the formation of a third hydrogen bond, which is apparently not present in the base pair of the purin-2,6-diamine 2'-deoxyribonucleoside with dT.

6-Aza-2‘-deoxyisocytidine: Synthesis, Properties of Oligonucleotides, and Base-Pair Stability Adjustment of DNA with Parallel Strand Orientation

6-Aza-5-methyl-2'-deoxyisocytidine (1a) and 6-aza-2'-deoxyisocytidine (1b) have been synthesized, converted into phosphoramidite building blocks, and incorporated into oligodeoxynucleotides. The glycosylic bond stability of 1a,b under acidic conditions increases compared to that of 5-methyl-2'-deoxyisocytidine (2a) and 2'-deoxyisocytidine (2b). Oligonucleotides incorporating 1a or 1b show an enhanced stability against the 3'-exonuclease snake-venom phosphodiesterase. The duplexes containing 6-azapyrimidine nucleosides 1a or 1b have lower T(m) values than duplexes containing 2a or 2b with either antiparallel or parallel chain orientation. This was used to adjust the stability of the tridentate m5iCd-dG base pair to the level of the bidentate reverse Watson-Crick dA-dT pair.

Hybridization ability and base pair geometry of modified deoxycytidine derivatives having a 4-N-carbamoyl group.

Modified oligodeoxyribonucleotides incorporating 4-N-carbamoyldeoxycytidine derivatives were synthesized. The 1H-NMR of 4-N-carbamoyldeoxycytidine suggests that the carbamoyl group forms an intramolecular hydrogen bond with the cytosine ring nitrogen atom and this geometry would inhibit formation of the Watson-Crick base pair with a guanine base. However, the Tm analysis of the modified oligodeoxynucleotides revealed that, in the process of their hybridization with the complementary oligodeoxynucleotides, the orientation of the carbamoyl group changed in a manner where the stable Watson-Crick base pair can be formed with the guanine base.

RNA LEGO: magnesium-dependent assembly of RNA building blocks through loop-loop interactions.

We describe the construction of nano-molecular assemblies using RNA building blocks the human immunodeficiency virus type 1 (HIV-1) dimerization initiation site (DIS) RNA, that forms stable base pairing through a magnesium-dependent loop-loop interaction ("kissing"). RNA building blocks containing two DIS or DIS-like hairpins connected by a two nucleotide linker self-assembled to form specific structures as observed by non-denaturing polyacrylamide gel electrophoresis (PAGE). Furthermore, observation of "real time" formation of the molecular assemblies by circular dichroism (CD) spectroscopy was attempted.

Theoretical study of substitution effect of the hydrogen bond stability of 9-methylguanine derivatives and 1-methylcytosine.

The substitution effect on hydrogen bond stability of the Watson-Crick type base pair between 1-methylcytosine (C) and substitution-introduced 9-methylguanine derivatives (Gx) was studied by an ab initio molecular orbital theory. Introduction of an electron-withdrawing group on the 8-position or on the exo-cyclic amino moiety enforced the base pair stability.

Pyrazolylborate-zinc-nucleobase-complexes, 3:(1) base pairing studies.

In solution, the pyrazolylborate-zinc-nucleobase complexes show self-association and base pairing with external nucleobases. The self-association was studied quantitatively for Tp(Cum,Me)Zn-hypoxanthinate and Tp(Cum,Me)Zn-thyminate; the dimerization constants K(D) are 63 +/- 8 and 0.2 +/- 0.1 M(-1), respectively. Of the external nucleobases, 9-ethyladenine forms stable base pairs with the thyminate, uracilate, and xanthinate complexes, 9-isobutylguanine only with the cytosinate complex, 1-methylthymine with the adeninate and diaminopurinate complexes, and 1-methyluracil with the diaminopurinate complex. The association constant for the base pair Tp(Cum,Me)Zn-thyminate:9-ethyladenine was determined by NMR methods as K = 66 +/- 10 M(-1). Structure determinations of the crystalline adducts have confirmed the base pairing for Tp(Cum,Me)Zn-thyminate:9-ethyladenine, Tp(Cum,Me)Zn-cytosinate:9-isobutylguanine, and Tp(Cum,Me)Zn-xanthinate:9-ethyladenine. Both Watson-Crick and Hoogsteen base pairs have been observed. In the solid state, extended base pairing leads to quartet and polymer arrangements.

Protonation of non-Watson–Crick base pairs and encapsidation of turnip yellow mosaic virus RNA

The 5' UTR of turnip yellow mosaic virus RNA contains two conserved hairpins with internal loops consisting of C.C and C.A mismatches. In this article, evidence is presented indicating that the 5' proximal hairpin functions as an encapsidation initiation signal. Extensive mutagenesis studies on this hairpin and sequencing of virus progeny showed a clear preference for C.C and C.A mismatches within the internal loop. The importance of these mismatches lies in their pH-dependent protonation and stable base pair formation. Encapsidation efficiency was found to be severely affected for several mutants lacking the protonatable mismatches in the internal loop of the 5' proximal hairpin. Furthermore, gel mobility-shift assays were performed with various RNA hairpins and empty capsids with a hole. Protonatable hairpins containing C.C and/or C.A pairs were found to bind specifically to the interior of the protein shell under acidic conditions (pH 4.5) in the presence of spermidine. Based on these results we propose that this binding of protonated cytosines to the coat protein of turnip yellow mosaic virus may represent a new motif in RNA-protein interactions.

Multimerization of restriction fragments by magnesium-mediated stable base pairing between overhangs: a cause of electrophoretic mobility shift.

The electrophoretic mobility shift assay (EMSA) or simply the "gel shift assay" is one of the most sensitive methods for studying the ability of a protein to bind to DNA. EMSAs are also widely used to investigate protein- or sequence-dependent DNA bending. Here we report that electrophoresis using physiological concentrations of Mg(2+) can cause a mobility shift of restriction fragments in nondenaturing polyacrylamide gels as the overhangs form stable base pairs. This phenomenon was observed at even 37 degrees C. The retardation was, however, more pronounced at low temperatures, where a three-nucleotide overhang 5'-GAC also caused a mobility shift. The stability of the pairing was generally high when the overhangs of four nucleotides display high GC content, while the mobility shift caused by 5'-AATT was greater than those caused by 5'-GATC, 5'-TCGA, and 5'-CTAG. This observation should be taken into account to avoid misinterpretation of the data when the EMSA, especially the circular permutation gel mobility shift assay, is performed using a running buffer that contains Mg(2+) ions. The stable adhesion between short overhangs may present an important basis for genome stability and many genetic processes occurring in living cells.

The elusive atomic rationale for DNA base pair stability.

A systematic analysis of the electrostatic interaction between 27 natural DNA base pairs was carried out, based on ab initio correlated wave functions and the topology of the electron density. Using high rank multipole moments we show that the atomic partitioning of the interaction energy contains many substantial contributions between distant atoms. Profiles of cumulative energy versus internuclear distance show large fluctuations and provide an electrostatic fingerprint of the partitioning of interaction energy in a complex. A quantified comparison between each pair of energy profiles, one for each base pair, makes clear that there is no correlation between the total base pair interaction energy and the shape of the profile. In other words, base pairs with similar interaction energy are not stable for the same reasons in terms of atomic partitioning. In summary, simple rules to rationalize the pattern of energetic stability of naturally occurring base pairs in terms of subsets of atoms are elusive. Our work cautions against inappropriate use of Jorgensen's secondary interaction hypothesis.

Стабілізація Вотсон-Криківських пар основ ДНК протонуванням: квантово-хімічне дослідження

Стабілізація Вотсон-Криківських пар основ ДНК протонуванням: квантово-хімічне дослідження

사람의 ε-글로빈 프로모트에서 d(CXG)와 d(GXC)의 안정성에 인접한 염기 서열들의 영향 에 관한 연구

온도 기울기 전기영동장치를 이용하여 d(CXG)와 d(GXC) 염기의 열 안정성을 결정하는데 사람의 <TEX>$\varepsilon$</TEX>-글로빈 DNA조각을 사용하였다. 염기 쌍의 안정성은 이웃하는 염기서열에 의한 수소결합과 base stocking 상호작용에 의존한다. 염기 쌍의 안정성은 d(CXG) d(CYG)의 경우에 T.A<A.T<C.G<G.C이고 또한 d(GXC).d(GYC)의 경우는 A.T<T.A<C.G<G.C 이다. 그리고 d(GXC).d(GYC)의 경우에 mismatch 염기 쌍의 안정성은 G.T=T.G>G.A = A.G>C.T>T.C>C.A>A.C이다. Human <TEX>$\varepsilon$</TEX>-globin DNA fragment was used to determine the thermal stabilities of base pairs at d(CXG) and d(GXC) by Temperature Gradient Gel Electrophoresis(TGGE). The base pair stability depends on the hydrogen bonding interaction and base stacking interaction of neighbor base sequence. The orders of base pair stabilities were T.A<A.T<C.G<G.C for d(CXG).d(CYG) and A.T<T.A<C.G<G.C for d(GXC).d(GYC). And also heteroduplex TGGE suggested that the mismatch bases stabilities were G.T = T.G>G.A = A.G>C.T>T.C>C.A>A.C for d(GXC).d(GYC).

Site-resolved energetics in DNA triple helices containing G*TA and T*CG triads.

Recognition of specific sites in double-helical DNA by triplex-forming oligonucleotides has been limited until recently to sites containing homopurine-homopyrimidine sequences. G*TA and T*CG triads, in which TA and CG base pairs are specifically recognized by guanine or by thymine, have now extended this recognition code to DNA target sites of mixed base sequences. In the present work, we have obtained a characterization of the stabilities of G*TA and T*CG triads, and of the effects of these triads upon canonical triads, in triple-helical DNA. The three DNA triplexes investigated are formed by the folding of the 31-mers d(GAAXAGGT(5)CCTYTTCT(5)CTTZTCC) with X = G, T, or C, Y = C, A, or G, and Z = C, G, or T. We have measured the exchange rates of imino protons in each triad of the three triplexes using nuclear magnetic resonance spectroscopy. The exchange rates are used to map the local free energy of structural stabilization in each triplex. The results indicate that the stability of Watson-Crick base pairs in the G*TA and T*CG triads is comparable to that of Watson-Crick base pairs in canonical triads. The presence of G*TA and T*CG triads, however, destabilizes neighboring canonical triads, two or three positions removed from the G*TA/T*CG site. Moreover, the long-range destabilizing effects induced by the T*CG triad are larger than those induced by the G*TA triad. These findings reveal the molecular basis for the lower overall stability of G*TA- and T*CG-containing triplexes.

A critical stem-loop structure in the CR4-CR5 domain of mammalian telomerase RNA.

Telomerase is an enzyme that maintains telomere length by adding telomeric sequence repeats onto chromosome ends. The telomerase ribonucleoprotein complex consists of two essential components, a reverse transcriptase and an RNA molecule that provides the template for telomeric repeat synthesis. A common secondary structure of vertebrate telomerase RNA has been proposed based on a phylogenetic comparative analysis of 35 sequences. Here we report the identification of an additional essential base-paired region in the CR4-CR5 domain of mammalian telomerase RNA, termed P6.1. Mouse telomerase RNAs with mutations that disrupted base pairings in the P6.1 helix were unable to reconstitute telomerase activity in vivo. In contrast, an RNA mutant with compensatory mutations that restored base pairings in the P6.1 helix restored telomerase activity. In an in vitro reconstitution system stable base pairing of the P6.1 stem was required for the RNA-protein interaction between the CR4-CR5 domain and the telomerase reverse transcriptase (TERT) protein. Interestingly, two RNA mutations, one that extends the P6.1 stem and one that alters the conserved nucleotides of the L6.1 loop, allowed RNA-protein binding but significantly impaired telomerase activity. These data establish the presence of the P6.1 stem-loop and its importance for the assembly and enzymatic activity of the mammalian telomerase complex.

2-Amino-7-deazaadenine forms stable base pairs with cytosine and thymine

2-Amino-7-deazaadenine ( ADA) was incorporated into oligodeoxynucleotides (ODN) and their base-pairing properties with natural nucleobases were investigated. In melting temperature ( T m) experiments, the duplex containing an ADA/C base pair showed a high stability comparable to that containing ADA/T base pair. Destabilization of the duplex usually observed for existing degenerate bases was not observed. However, the incorporation efficiency of dCTP was only 1.8% for TTP in single-nucleotide insertion reactions using polymerase.

NMR Study of A Heterochiral DNA Hairpin: Impact of L-Enantiomery in the Loop

We carried out a structural study of the DNA heterochiral strand d (AGCTTATCAT(L)CGATAAGCT), -AT(L)C-, where T(L) (L thymine) replaces T (natural D-thymine). -AT(L)C- is a structural analog of -ATC- that belongs to a strong topoisomerase II DNA cleavage site and which has been shown to resolve into a hairpin structure with a stem formed by eight Waston-Crick base-pairs and a single residue loop closed by an A.C sheared base-pair. Although -AT(L)C-, like its parent -ATC-, folds into a hairpin structure at low and high DNA concentrations it displays a lower stability (Tm of 56 °C versus 58.5 °C). Several NMR features in—AT(L)C- account for the disruption of the A.C pairing in the loop and a weakening of the C.G base-pair stability at the stem-loop junction. For instance, the exchange of the loop imino protons with solvent is accelerated compared with the natural oligonucleotide -ATC-. The higher flexibility of the heterochiral loop is confirmed by the results of NMR restrained molecular dynamics. In the calculated final structures of—AT(L)C-, the T10(L) residue moves the A9 and C11 residues away, thus preventing the loop closure through a C.A sheared base-pair and the achievement of a good base-base or sugarbase stacking. Actually, most of the stabilizing interactions present in -ATC- are lost in the heterochiral -AT(L)C- explaining its weaker stability.