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Objectives: To determine cell-free mitochondrial DNA (mt-cfDNA) levels in tachycardia-induced cardiomyopathy (TIC) and non-TIC among atrial fibrillation (AF) cases., Backgrounds: TIC is a reversible cardiomyopathy resulting from tachyarrhythmias, such as AF. The exact cause of TIC is not fully understood, but mitochondrial dysfunction has been reported in a variety of cardiomyopathies and may be involved in TIC as well. AF is recognized to be associated with systemic inflammation, and studies have shown that in patients with AF have elevated levels of mt-cfDNA increased, and this increase is linked to systemic inflammation., Methods: We enrolled 67 patients with TIC (TIC group) and 671 patients without TIC (non-TIC group), who underwent catheter ablation for AF at our hospital between November 2009 and September 2016 and did not meet the exclusion criteria. We performed quantitative PCR analysis of plasma mt-cfDNA and nuclear-cfDNA and compared clinical factors and these measurements between the two groups., Results: Levels of mt-cfDNA were significantly lower in the TIC group than in the non-TIC group (1110.01 vs. 1918.71 copies/μg plasma, P = 0.027), while levels of nuclear-cfDNA were comparable between these two groups. In particular, mt-cfDNA (P = 0.0003, odds ratio [OR] 2.54), non-paroxysmal AF (P < 0.0001, OR 3.07), and diabetes mellitus (P = 0.006, OR 2.36) were identified as independent factors associated with TIC., Conclusion: There are lower mt-cfDNA in TIC, and decreased plasma levels of circulating mt-cfDNA may be a new biomarker and involve in related mechanisms for AF associated TIC., Condensed Abstract: Tachycardia-induced cardiomyopathy (TIC) is a reversible cardiomyopathy caused by tachyarrhythmias, such as atrial fibrillation (AF) tachycardia. The pathogenesis of TIC remains incompletely understood, and there is currently no method to predict its development in patients. In this study, we show that cell-free mitochondrial DNA (mt-cfDNA) levels were significantly lower in the TIC group than in the non-TIC group. Persistent AF, coexisting diabetes mellitus, and decreased mt-cfDNA levels were independently associated with TIC. Decreased mt-cfDNA levels may serve as a novel biomarker for predicting TIC in patients with AF., Competing Interests: Declaration of competing interest All authors have nothing to disclose., (Copyright © 2024. Published by Elsevier B.V.)

Objective Atrial fibrillation (AF) is the most common cause of tachycardia-induced cardiomyopathy (TIC). However, which patients with AF are prone to developing TIC remains unclear. In this study, we investigated the clinical features of AF patients with TIC. Methods This single-center study included 722 patients with AF (average age, 63.1±10.2 years old; 191 women) who underwent radiofrequency catheter ablation. We defined TIC as an initial left ventricular ejection fraction (LVEF) of <40% and a >20% recovery of the LVEF after successful AF ablation and compared the clinical characteristics between the TIC and control groups. Results The proportions of type 2 diabetes (30.5% vs. 14.7%), renal dysfunction (34.2% vs. 23.8%), hypertension (67.1% vs. 54.8%), and persistent AF (62.2% vs. 32.2%) were significantly higher in the TIC group (n=82) than in the control group (n=640). The atrioventricular nodal effective refractory period (AVNERP) (303±72 ms vs. 332±86 ms; p=0.017) was significantly shorter in the TIC group than in the control group. A multivariable analysis found that persistent AF [odds ratio (OR), 3.19; 95% confidence interval (CI), 1.94-5.24], renal dysfunction (OR, 1.87; 95% CI, 1.06-3.32), and type 2 diabetes (OR, 2.30; 95% CI, 1.31-4.05) were significantly associated with TIC. Conclusion Comorbid renal dysfunction and type 2 diabetes were clinical features of AF patients with TIC. Persistent AF, and short AVNERP may be involved in the development of TIC.

Background: TactiFlex is a next-generation catheter that is being used increasingly in ablation-treatment strategies. The purpose of this study was to investigate the differences in ablation lesions when the ablation power, time, and perfusion flow are varied with TactiFlex and TactiCath catheters., Methods: The TactiFlex and TactiCath catheters were contacted perpendicularly/obliquely/parallel to the swine myocardium at varying powers (30, 40, and 50 W), time points (10, 15, 20, 25, 30, and 40 s), and forces (5, 10, 15, 20, and 30 g); the depth, width, and area of each lesion were measured, and the number of steam pops that occurred was counted., Results: A total of 672 (336 lesions for each catheter) radiofrequency (RF) energy applications were delivered and 648 lesions were analyzed, excluding steam pops. The surface area and volume increased significantly with an increasing contact force for the TactiCath. The TactiCath lesions were significantly deeper than those for TactiFlex in most groups with the same power and seconds. The surface area was significantly larger when the catheters were contacted obliquely/parallel to the myocardium than perpendicularly using TactiCath, whereas the difference was less significant in the case of TactiFlex. In a 10-g contact force ablation experiment, TactiFlex did not cause pops, but TactiCath caused pops in 9.8% of cases., Conclusion: The TactiFlex lesions were shallower than those of TactiCath. However, TactiFlex catheters reduced the steam pops during RF applications. Those data should help clinicians understand the characteristics of the catheters and develop adequate strategies., (© 2024. The Author(s).)

Background: Although left bundle branch area pacing (LBBAP) reportedly results in fewer adverse outcomes after implantation than conventional stylet-guided right ventricular septal pacing (RVSP), previous studies have not compared LBBAP with accurate RVSP using a delivery catheter. The aim of this study was to compare clinical outcomes between LBBAP and accurate RVSP among patients with atrioventricular block (AVB)., Methods: This single-center observational study enrolled 160 patients requiring RV pacing due to symptomatic AVB between September 2018 and December 2021. Primary composite outcomes included all-cause death, hospitalization due to heart failure (HF), and upgrading to biventricular pacing. Secondary composite outcomes included any procedural and postprocedural complications., Results: Overall, 160 patients were analyzed (LBBAP, n = 81; RVSP, n = 79). No significant differences in baseline characteristics were observed between the two groups. The RV pacing burden at 1 year after implantation was 90.8% ± 20.4% and 86.2% ± 22.6%, respectively (p = 0.21). During a mean follow-up of 840 ± 369 days, the incidence of the primary outcome was significantly lower with LBBAP (4.9%) compared to RVSP (22.8%) (Log-rank p = 0.02). There was no significant difference in the incidence of the secondary outcome between the two groups (3.7% vs. 5.1%, p = 0.65). In the multivariate analysis, baseline QRS duration, RV pacing burden, and LBBAP were independently associated with the primary outcome (baseline QRS duration: hazard ratio [HR], 1.01; 95% confidence interval [CI], 1.00-1.02; p < 0.001; RV pacing burden: HR, 1.01; 95% CI, 1.00-1.02; p < 0.001; LBBAP: HR, 0.45; 95% CI, 0.31-0.64; p < 0.001)., Conclusion: In patients requiring frequent RV pacing, LBBAP was associated with reduced adverse clinical outcome compared to accurate RVSP using a delivery catheter., (© 2024. The Author(s).)

Background: Periodontitis has not been recognized as a modifiable risk factor for atrial fibrillation (AF). This prospective nonrandomized study investigated whether periodontal treatment improves the AF ablation outcome., Methods and Results: We prospectively enrolled 288 AF patients scheduled to undergo initial radiofrequency catheter ablation. Each patient underwent periodontal inflamed surface area (PISA; a quantitative index of periodontal inflammation) measurement. All eligible patients were recommended to receive periodontal treatment within the blanking period, and 97 consented. During the mean follow-up period of 507±256 days, 70 (24%) AF recurrences were documented. Patients who exhibited AF recurrences had a higher PISA than those who did not (456.8±403.5 versus 277.7±259.0 mm 2 , P =0.001). These patients were categorized into high-PISA (>615 mm 2 ) and low-PISA (<615 mm 2 ) groups according to the receiver operating characteristic analysis for AF recurrence (area under the curve, 0.611; sensitivity, 39%; specificity, 89%). A high PISA, as well as female sex, AF duration, and left atrial volume, were the statistically significant predicter for AF recurrence (hazard ratio [HR], 2.308 [95% CI, 1.234-4.315]; P =0.009). In patients with a high PISA, those who underwent periodontal treatment showed significantly fewer AF recurrences ( P =0.01, log-rank test). The adjusted HR of periodontal treatment for AF recurrence was 0.393 (95% CI, 0.215-0.719; P =0.002)., Conclusions: Periodontitis may serve as a modifiable risk factor for AF. PISA is a hallmark of AF recurrence, and periodontal treatment improves the AF ablation outcome, especially for those with poor periodontal condition.

Background: Recent studies have shown that atrial slow conduction velocity (CV) is associated with the perpetuation of atrial fibrillation (AF). However, the criteria of CV measurement have not been standardized. The aim of this study was to evaluate the relationship between the slow CV area (SCVA) measured by novel omnipolar technology (OT) and AF recurrence., Methods: This study included 90 patients with AF who underwent initial pulmonary vein isolation (PVI). The segmented surface area of the SCVA was measured by left atrial (LA) electrophysiological mapping using OT before the PVI. The proportion of the SCVA at each cutoff value of CV (from < 0.6 to < 0.9 m/s) was compared between the patients with and without AF recurrence., Results: During a mean follow-up period of 516 ± 197 days, the recurrence of AF after the initial PVI was observed in 23 (25.5%) patients. In patients with AF recurrence, the proportion of the SCVA in the LA posterior, LA appendage (LAA), and LA anterior were significantly higher than those without AF recurrence. The multivariate analysis indicated that the proportion of the low voltage area and the SCVA in the LA anterior (local CV < 0.7 m/s) were independent predictors of AF recurrence (hazard ratio [HR], 1.07; 95% confidence interval [CI], 1.01-1.14; p = 0.03; HR, 1.40; 95% CI, 1.07-1.83; p = 0.01, respectively)., Conclusion: By evaluating the local CV using OT, it was indicated that SCVA with CV < 0.7 m/s in the LA anterior is strongly associated with AF recurrence after PVI., (© 2023 Wiley Periodicals LLC.)

Background: Previously, direct monitoring of local activation at the communicating vein (CV) has been reported to be useful for the ablation of ventricular arrhythmias (VAs) originating from the left ventricular (LV) summit. In this study, we evaluated the performance of the novel over-the-wire (OTW)-type decapolar catheter for VAs originating from the LV summit., Methods: Overall, 17 patients who underwent catheter ablation for idiopathic VAs originating from the LV summit were included in this study. Of these, seven patients underwent mapping of the epicardial LV outflow tract with the novel 2.7 Fr OTW-type decapolar catheter (EPstar FIX AIV), and ten underwent mapping with the standard 2.0 Fr octopolar catheter (EPstar FIX 2F) procedure (AIV group = EPstar FIX AIV and control group = EPstar FIX 2F)., Results: No significant differences in the baseline characteristics were observed between the two groups. In the AIV group, all patients achieved successful catheter positioning in the target CV, whereas in the control group, two patients failed to achieve the same. The novel catheter not only advanced to the target vessels using a 0.014-in guidewire but it was also used for contrast injection from the catheter lumen, which enabled accurate and safe positioning. As a result, the earliest activation time preceding QRS onset during the VA, recorded at the CV, was significantly earlier when compared with the control group (44.66 ± 11.23 ms vs. 32.16 ± 4.26 ms, P = 0.007)., Conclusions: Compared with the conventional electrode catheter, this novel multipolar electrode catheter is more effective for mapping local activation at the CV., (© 2022. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.)

Background: Atrial fibrosis contributes to the onset and persistence of atrial fibrillation (AF) and AF-related stroke. Periodontitis, a common infectious and inflammatory disease, aggravates some systemic diseases. However, the association of periodontitis with AF and with atrial fibrosis has remained unclarified., Objectives: The authors aimed to elucidate the relationship between periodontitis and atrial fibrosis by studying resected left atrial appendages (LAAs)., Methods: Seventy-six patients with AF (55 with nonparoxysmal AF, 25 with mitral valve regurgitation, 18 with LAA thrombus) who were scheduled to undergo LAA excision during cardiac surgery were prospectively enrolled. All patients underwent an oral examination, and the remaining number of teeth, bleeding on probing, periodontal probing depth, and periodontal inflamed surface area (PISA) were evaluated as parameters of periodontitis. The degree of fibrosis in each LAA was quantified by Azan-Mallory staining., Results: Bleeding on probing (R = 0.48; P < 0.0001), periodontal probing depth of ≥4 mm (R = 0.26; P = 0.02), and PISA (R = 0.46; P < 0.0001) were positively correlated with atrial fibrosis. Among patients with >10 remaining teeth, PISA was positively and strongly correlated with atrial fibrosis (R = 0.57; P < 0.0001). After adjustments for age, AF duration, BMI, mitral valve regurgitation, and CHADS₂ (congestive heart failure, hypertension, age, diabetes, previous stroke/transient ischemic attack) score, PISA was significantly associated with atrial fibrosis (β = 0.016; P = 0.0002)., Conclusions: The authors histologically revealed the association of periodontitis with atrial fibrosis. This indicates that periodontitis, which is modifiable, is likely a risk factor for AF., Competing Interests: Funding Support and Author Disclosures This work was supported by the Japan Society for the Promotion of Science (JSPS, Tokyo, Japan) Grant-in-Aid for Research Activity Start-up (Research Project number 21K20924) to Dr Miyauchi and by a Grant-in-Aid for Scientific Research (B) (Research Project number 21H03112) to Dr Miyauchi. The authors have reported that they have no relationships relevant to the contents of this paper to disclose., (Copyright © 2023 American College of Cardiology Foundation. Published by Elsevier Inc. All rights reserved.)

Background: Atrial fibrillation (AF) and recurrence of AF after pulmonary vein isolation (PVI) have been linked to sinus node dysfunction., Objective: The purpose of this study was to investigate the association between the heart rate-associated single nucleotide polymorphisms (SNPs) identified in genome-wide association studies and recurrence of AF after PVI., Methods: In this study, patients with paroxysmal AF who underwent initial PVI, including 522 patients for screening and 172 patients for replication, were recruited and 21 heart rate-associated SNPs identified in genome-wide association studies were genotyped. The association between these SNPs and the recurrence of AF was investigated., Results: Throughout the follow-up period of 21 ± 12 months, 119 patients with paroxysmal AF (22.8%) exhibited AF recurrences in the screening set. The rate of AF recurrence was significantly associated with the minor allele C of the gap junction alpha-1 protein (GJA1) rs1015451 (additive model: odds ratio 2.07; P = 9.32 × 10 -7 ), but not with other SNPs. This association was confirmed in the replication set (allelic model: odds ratio 1.81; P = 2.70 × 10 -2 ). Multivariate analysis revealed that the recurrence of AF after AF ablation was independently related to the GJA1 SNP rs1015451 additive model, duration of AF >1 year, AF from non-pulmonary vein foci, and thicker interventricular septum., Conclusion: The GJA1 SNP rs1015451, coding for a gap junction protein (connexin-43), may be considered a novel genetic marker for AF recurrence after PVI., (Copyright © 2022. Published by Elsevier Inc.)

Background: Brugada syndrome (BrS) can be diagnosed by a type 1 BrS tracing in a 12-lead electrocardiogram (ECG). However, there are daily variations in the ECGs of BrS patients, which presents a challenge when diagnosing BrS. Although many susceptibility genes have been identified, the SCN5A gene is reportedly the main causative gene of BrS. However, most patients do not have an evidence of genetic predisposition to develop BrS. In addition, the diagnosis and risk stratification for ventricular fibrillation (VF) in patients with BrS presents some problems. Meanwhile, circulating micro RNAs (miRNAs) have drawn increased attention as potential biomarkers of various diseases. We hypothesize that circulating miRNAs may be potential diagnostic biomarkers for BrS., Methods: We enrolled 70 Japanese BrS patients and 34 controls for the screening cohort. A total of 2,555 miRNA sequences were detected using the 3D-Gene miRNAs labeling kit and 3D-Gene Human miRNAs Oligo Chip. We compared the expression of the miRNAs between the BrS patients and the controls. We validated whether the miRNA were significantly up- or downregulated in the screening cohort using RT-PCR. We also enrolled 72 Japanese BrS patients and 56 controls to replicate these miRNAs., Results: Eight miRNAs (hsa-miR-223-3p, hsa-miR-22-3p, hsa-miR-221-3p, hsa-miR-4485-5p, hsa-miR-550a-5p, hsa-miR-423-3p, hsa-miR-23a-3p, and hsa-miR-30d-5p) were downregulated, and one miRNA (hsa-miR-873-3p) was upregulated by more than 3-fold in BrS patients. The multivariate logistic regression analysis determined that hsa-miR-423-3p, hsa-miR-223-3p, and hsa-miR-23a-3p were independently associated with BrS (P < 0.0001). The AUC based on cross validation was 0.871 with a sensitivity and specificity of 83.5% and 81.1%, respectively., Conclusions: The plasma miRNAs are potential noninvasive biomarkers of BrS, and the constructed logistic model was useful for discriminating BrS., Competing Interests: NONE.

Introduction: Although recent echocardiographic studies have suggested that left atrial appendage (LAA) remodeling contributes to the development of LAA thrombus (LAAT), histological evidence is absent. The objective of this study was to examine clinical parameters and histological findings to clarify the factors involved in LAAT formation., Methods: A total of 64 patients (no atrial fibrillation [AF], N = 22; paroxysmal AF, N = 16; nonparoxysmal AF, N = 26) who underwent LAA excision during surgery were enrolled. Transthoracic and transesophageal echocardiography were performed before surgery. We evaluated the fibrosis burden (%) in the excised LAA sections with Azan-Mallory staining in patients with a LAAT compared with those without., Results: Patients with paroxysmal and non-paroxysmal AF had a higher LAA fibrosis burden than those without AF (p = .005 and p < .0001, respectively). Among the patients enrolled, 16 had a LAAT and 15 of them had nonparoxysmal AF. Among the nonparoxysmal AF patients, those with a LAAT had significantly higher LAA fibrosis burden than those without (23.8% [14.8%-40.3%] vs. 12.8% [7.4%-18.2%], p = .004) and echocardiographic parameters of the left atrial volume index (R = 0.543, p = .01), LAA depth (R = 0.452, p = .02), and LAA flow velocity (R = - 0.487, p = .01) were correlated with the LAA fibrosis burden., Conclusion: This study provided histological evidence that LAA fibrosis is related to LAAT formation. Echocardiographic parameters of LAA remodeling and function were correlated with the LAA fibrosis burden., (© 2022 Wiley Periodicals LLC.)

Background: Recently, conduction system pacing, including His bundle and left bundle branch area pacing (LBBAP), has emerged as an alternative pacing procedure for right ventricular (RV) pacing. The current study aimed to compare the clinical outcomes of LBBAP and conventional RV midseptal pacing (RVMSP) in patients with heart failure (HF) with preserved ejection fraction (HFpEF) and HF with midrange ejection (HFmrEF) requiring frequency RV pacing due to atrioventricular block (AVB)., Methods: A total of 89 patients with HFpEF and HFmrEF requiring RV pacing due to symptomatic AVB were enrolled between September 2018 and April 2021, among whom 43 and 46 underwent LBBAP and RVMSP, respectively., Results: No significant differences in baseline characteristics were observed between the two groups. The LBBAP group had a significantly shorter paced-QRS duration and paced left ventricular activation time (LVAT) compared to the RVMSP group (123.4 ± 10.4 ms vs. 152.3 ± 12.3 ms, p < .001 and 68.3 ± 10.0 ms vs. 95.2 ± 12.3 ms, p < .001, respectively). The LBBAP group had significantly lower N-terminal pro-B-type natriuretic peptide (NT-proBNP) levels at the 6-month follow-up compared to the RVMSP group [459.6 pg/ml (240.4-678.7) vs. 972.7 pg/ml (629.5-1315.9), p = .01]. More patients in the LBBAP group exhibited a significant improvement in NT-proBNP, defined as a > 50% decreased from baseline levels., Conclusion: LBBAP maintains physiological ventricular activation and contributes to greater improvement in NT-proBNP value 6 months after implantation in patients with HFpEF and HFmrEF compared to RVMSP., (© 2022 Wiley Periodicals LLC.)

Atrial fibrillation (AF) is associated with a fivefold risk of stroke and thrombotic embolism, which are usually derived from the left atrial appendage (LAA). Spontaneous echo contrast (SEC) is known as a risk factor for thrombosis. Porphyromonas gingivalis (P. gingivalis) has some prothrombotic effects and plays a key role in periodontitis and oral-systemic disease connection. We aimed to clarify the relationship between P. gingivalis and LAA SEC among AF patients. A total of 569 AF ablation candidates were enrolled in the present study. LAA SEC was categorized into nondense SEC and dense SEC based on transesophageal echocardiography. Serum immunoglobulin G antibody titers of P. gingivalis fimA subtypes (types I-IV) were measured with an enzyme-linked immunosorbent assay. The levels of antibody titers were categorized into high (> mean + 3 standard deviation) and low values. A total of 513 (90%) patients were included in the nondense SEC group, and 56 (10%) were included in the dense SEC group. Multivariate regression analysis revealed that the high-value serum antibody titers of P. gingivalis types II and IV were independently associated with dense SEC [type II: adjusted odds ratio (OR) 2.220; 95% confidence interval (CI) 1.062-4.643; P = 0.02; and type IV: adjusted OR 3.169; 95% CI 1.058-6.657; P = 0.002]. The results revealed that P. gingivalis types II and IV are related to LAA SEC severity among AF patients who receive appropriate anticoagulation therapy., (© 2021. Springer Japan KK, part of Springer Nature.)

Colibacillosis is one of an economically significant disease in the poultry industry, especially for meat breed chickens. Recently it has become a serious problem for layer especially when the birds start laying and also at the later stage of laying. In Japan, the productivity of field laying hens improved when the Δcrp avian colibacillosis live vaccine ("Gall N tect CBL") was used. The survival rate and egg laying rate increased during almost all of the laying period when compared with the control group. The improvement in productivity was clearly demonstrated by comparing the number of eggs laid per day. The use of an avian colibacillosis live vaccine proved to be cost-effective in laying hens.

Base stacking is important for the base pair interaction of a DNA duplex, DNA replication by polymerases, and single-stranded nucleotide overhangs. To study the mechanisms responsible for DNA stacking interactions, we measured the thermal stability of DNA duplexes containing a non-natural nucleotide tethered to a simple aromatic hydrocarbon group devoid of dipole moments and hydrogen bonding sites. The duplexes containing tetrahydrofuran were paired with a deoxyadenosine derivative (A/T base pair analog) or a deoxycytidine derivative (C/G base pair analog) and showed a lower stability than Watson-Crick base pairing, partly due to the loss of interbase hydrogen bonds. Conversely, non-natural nucleotides present at a dangling end yielded an interaction energy as high as that observed with base pairing. Importantly, the non-natural nucleotides yielded an interaction energy with a linear correlation similar to that of the analogous Watson-Crick base pairs both in the middle and at the end of a DNA duplex, although a different stacking mechanism between the middle and the end was suggested. Moreover, a positive cooperativity was observed in dangling end stacking of the nucleotide base moiety and aromatic hydrocarbon group. These observations are useful to understand nucleic acid interactions and to design new non-natural nucleotides.

A base flipping conformation is found in many biological processes, including DNA repair and DNA and RNA modification processes. To investigate the dynamics and energetics of this unusual conformation in a double helix, base flipping induced by the base pair analogues of deoxyadenosine and deoxycytidine derivatives tethering a phenyl or naphthyl group was investigated. DNA strands bearing the base pair analogues stabilized the base flipping conformation of a complementary RNA, resulting in a site-specific hydrolysis by specific base catalysis. Measurements of the hydrolysis rate and the thermal stability of DNA/RNA duplexes suggested an unconstrained flexibility of the flipped-out ribonucleotide. As established in the base flipping by DNA repair and DNA and RNA modification enzymes, the results suggested that base flipping occurred in competition with base pair formation. In addition, the deoxycytidine derivatives discriminated G from I (inosine), with respect to the base pair interaction energy, as observed for a damaged base or a weakened base pair search by DNA repair proteins. The base pair mimic nucleosides would be useful for investigating the base flipping conformation under the equilibrium with base pairing.

We previously reported that the deoxyadenosine derivative tethering the phenyl group at the N6 position of deoxyadenosine, A(phe) stacked efficiently with the adjacent nucleotide bases at a DNA duplex terminus and in the middle of a DNA duplex. In contrast with the observations for A(phe), this study revealed that the phenyl group of the deoxycytidine derivative, C(phe) located outside the helix and allowed the base pair formation with guanine in a DNA duplex, although its phenyl group could stack with the adjacent DNA bases as efficient as A(phe). Klenow fragment of DNA polymerase I and T7 DNA polymerase selectively incorporated dTTP and dGTP opposite A(phe) and C(phe) in the template DNA, respectively, implying that the conformation of A(phe) differs between in the DNA polymerase and in solution.

On the basis of non-covalent bond interactions in nucleic acids, we synthesized the deoxyadenosine derivatives tethering a phenyl group (X) and a naphthyl group (Z) by an amide linker, which mimic a Watson-Crick base pair. Circular dichroism spectra indicated that the duplexes containing X and Z formed a similar conformation regardless of the opposite nucleotide species (A, G, C, T and an abasic site analogue F), which was not observed for the natural duplexes. The values among the natural duplexes containing the A/A, A/G, A/C, A/T and A/F pairs differed by 5.2 kcal mol(-1) while that among the duplexes containing X or Z in place of the adenine differed by only 1.9 or 2.8 kcal mol(-1), respectively. Fluorescence quenching experiments confirmed that 2-amino purine opposite X adopted an unstacked conformation. The structural and thermodynamic analyses suggest that the aromatic hydrocarbon group of X and Z intercalates into a double helix, resulting in the opposite nucleotide base flipping into an unstacked position regardless of the nucleotide species. This observation implies that modifications at the aromatic hydrocarbon group and the amide linker may expand the application of the base pair-mimic nucleosides for molecular biology and biotechnology.

We have synthesized the deoxyadenosine derivative tethering a phenyl group (X), which mimics the Watson-Crick A/T base pair. The RNA/DNA hybrid duplexes containing X in the middle of the DNA sequence showed a similar thermal stability regardless of the ribonucleotide species (A, G, C, or U) opposite to X, probably because of the phenyl group stacking inside of the duplex accompanied by the opposite ribonucleotide base flipped in an extrahelical position. The RNA strand hybridized with the DNA strand bearing X was cleaved on the 3'-side of the ribonucleotide opposite to X in the presence of MgCl2, and the RNA sequence to be cleaved was not restricted. The site-specific RNA hydrolysis suggests that the DNA strand bearing X has the advantage of the site-selective base flipping in the target sequence and the development of a "universal deoxyribozyme" to exclusively cleave a target RNA sequence.

On the basis of the non-covalent bond interactions in nucleic acids, we have synthesized a novel adenosine derivative tethering a phenyl group. Structure and thermal stability of the DNA duplexes bearing the adenosine derivative in the middle of a strand were investigated by CD spectra and the UV melting curves. We found that the conformation and the interactions of the duplexes were similar regardless of the nucleotide facing with the adenosine derivative in a duplex. This observation suggests the base pair-mimic geometry of the adenosine derivative accompanied with a conformational change of the nucleotide in the complementary strand.

Novel deoxyadenosine derivatives tethering a phenyl or naphthyl group by means of an amido linker have been synthesized, and these derivatives, stacking on the 5' end of a DNA duplex, provide free energy contributions equal to or greater than that of the Watson-Crick A/T base pair.

We synthesized novel adenosine derivatives tethering an aromatic hydrocarbon group by an amido linker. The single adenosine derivatives at 5' dangling end stabilized the DNA duplex of 5'-ATGCGCAT-3' more or equally than Watson-Crick base pair. When the number of the dangling residues increased from one to three, the duplex stability became larger by 1.8-3.6 kcal/mol. When the adenosine derivative was opposite to an abasic site in a DNA duplex, the destabilization by the abasic site was significantly reduced. These observations suggest that the adenosine derivatives developed in this study can stack with a DNA base pair by forming a base pair-mimic geometry.