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Force-induced melting of DNA--evidence for peeling and internal melting from force spectra on short synthetic duplex sequences.

ABSTRACT: Overstretching of DNA occurs at about 60-70 pN when a torsionally unconstrained double-stranded DNA molecule is stretched by its ends. During the transition, the contour length increases by up to 70% without complete strand dissociation. Three mechanisms are thought to be involved: force-induced melting into single-stranded DNA where either one or both strands carry the tension, or a B-to-S transition into a longer, still base-paired conformation. We stretch sequence-designed oligonucleotides in an effort to isolate the three processes, focusing on force-induced melting. By introducing site-specific inter-strand cross-links in one or both ends of a 64 bp AT-rich duplex we could repeatedly follow the two melting processes at 5 mM and 1 M monovalent salt. We find that when one end is sealed the AT-rich sequence undergoes peeling exhibiting hysteresis at low and high salt. When both ends are sealed the AT sequence instead undergoes internal melting. Thirdly, the peeling melting is studied in a composite oligonucleotide where the same AT-rich sequence is concatenated to a GC-rich sequence known to undergo a B-to-S transition rather than melting. The construct then first melts in the AT-rich part followed at higher forces by a B-to-S transition in the GC-part, indicating that DNA overstretching modes are additive.

SUBMITTER: Bosaeus N

PROVIDER: S-EPMC4081069 | biostudies-literature | 2014 Jul

REPOSITORIES: biostudies-literature

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Force-induced melting of DNA--evidence for peeling and internal melting from force spectra on short synthetic duplex sequences.

Bosaeus Niklas N El-Sagheer Afaf H AH Brown Tom T Åkerman Björn B Nordén Bengt B

Nucleic acids research 20140516 12

Overstretching of DNA occurs at about 60-70 pN when a torsionally unconstrained double-stranded DNA molecule is stretched by its ends. During the transition, the contour length increases by up to 70% without complete strand dissociation. Three mechanisms are thought to be involved: force-induced melting into single-stranded DNA where either one or both strands carry the tension, or a B-to-S transition into a longer, still base-paired conformation. We stretch sequence-designed oligonucleotides in ...[more]

PMID: 24838568

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Project description:BackgroundInternal limiting membrane (ILM) peeling during primary vitrectomy for rhegmatogenous retinal detachment (RRD) prevents the formation of postoperative macular epiretinal membrane (ERM). However, studies that compared vitrectomy with and without ILM peeling for RRD, have reported controversial outcomes.ObjectiveTo assess the efficacy of ILM peeling versus non-ILM peeling during vitrectomy for RRD by a systematic review and meta-analysis of published studies.MethodsPubMed, Medline, Web of Science, Embase databases, and the Cochrane Library were searched up to April 2018 to identify studies that compared primary vitrectomy with and without ILM peeling for RRD with at least six months follow-up. Primary outcomes were the rate of postoperative ERM formation and mean best corrected visual acuity (BCVA) change after vitrectomy. Rate of recurrence of retinal detachment (RD) was assessed as secondary outcome. Risk ratios (RRs) with 95% confidence intervals (CIs) expressed pooled results for rate of ERM formation and rate of RD recurrence in ILM peeling and non-ILM peeling groups. Pooled results for BCVA change in the two groups were expressed as Weighted Mean Difference (WMD) with 95% CIs.ResultsNine studies, one of which was a randomized controlled trial (RCT), with a total number of 404 eyes in the ILM peeling group and 365 eyes in the non-ILM peeling group, were included. The analysis from pooled data indicated a significant lower rate of postoperative ERM formation in the ILM peeling group compared to the non-ILM peeling group (9 studies, 769 eyes, RR = 0.14; CI: 0.07 to 0.28; P < 0.001). There was no statistical difference in mean BCVA change (9 studies, 769 eyes, WMD = 0.02; CI: -0.11 to 0.16; P = 0.75). Rate of recurrence of RD was lower in the ILM peeling group (6 studies, 603 eyes, RR = 0.32; CI = 0.17 to 0.61; P< 0.001).ConclusionILM peeling during vitrectomy for RRD prevents the formation of macular epiretinal membrane postoperatively and reduces the incidence of RD recurrence, but better visual outcome was not found compared to non-ILM peeling vitrectomy.

Project description:BackgroundThe epiretinal membrane (ERM) is a degenerative condition associated with age, which can cause loss of vision and/or metamorphopsia. The treatment of symptomatic ERM involves surgical removal including a vitrectomy followed by peeling of the ERM using a microforceps. As the internal limiting membrane (ILM) is adherent to the ERM, it is sometimes removed with it (spontaneous peeling). If ILM remains in place, it can be removed to reduce ERM recurrence. However, it is important to clarify the safety of ILM peeling, while it increases surgical risks and cause histological disorganization of the retina that can lead to microscotomas, may be responsible for definitive visual discomfort.MethodsPEELING is a prospective, randomized, controlled, single-blind, and multicentered trial with two parallel arms. This study investigates the benefit/risk ratio of active ILM peeling among individuals undergoing ERM surgery without spontaneous ILM peeling. Randomization is done in the operating room after ERM removal if ILM remains in place. After randomization, the two groups-"active peeling of the ILM" and "no peeling of the ILM"-are compared during a total of three follow-up visits scheduled at month 1, month 6, and month 12. Primary endpoint is the difference in microscotomas before surgery and 6 months after surgery. Patients with spontaneous peeling are not randomized and are included in the ancillary study with the same follow-up visits and the same examinations as the principal study. Relevant inclusion criteria involve individuals aged > 18 years living with idiopathic symptomatic ERM, including pseudophakic patients with transparent posterior capsule or open capsule or lensed patients with age-related cataracts. The calculated sample size corresponds to 53 randomized eyes (one eye/patient) per arm that means 106 randomized eyes (106 randomized patients) in total and a maximum of 222 included patients (116 spontaneous peeling).DiscussionILM peeling is often practiced in ERM surgery to reduce ERM recurrence. It does not impair postoperative visual acuity, but it increases the surgical risks and causes anatomical damages. If active ILM peeling is significantly associated with more microscotomas, it may contraindicate the ILM peeling during primitive idiopathic ERM surgery.Trial registrationClinicalTrials.gov, NCT02146144. Registered on 22 May 2014. Recruitment is still ongoing.

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Force-induced melting of DNA--evidence for peeling and internal melting from force spectra on short synthetic duplex sequences.

Publications

Force-induced melting of DNA--evidence for peeling and internal melting from force spectra on short synthetic duplex sequences.

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